Genes doi: 10.3390/genes17080961

Authors: Şebnem Yıldırımcan Kadıçeşme

Background/Objectives: Epoxide hydrolase 2 (EPHX2), which encodes soluble epoxide hydrolase (sEH), is involved in arachidonic acid metabolism and has been associated with inflammation, lipid metabolism, and tumor biology. However, its prognostic significance and biological associations in lung adenocarcinoma (LUAD) remain unclear. This study aimed to investigate the expression profile, prognostic value, and molecular pathways of EPHX2 in LUAD using bioinformatics analyses. Methods: EPHX2 expression was evaluated using TNMplot, GEPIA2, and GEO datasets, while protein expression was assessed using the Human Protein Atlas and CPTAC/UALCAN platforms. Prognostic analyses were performed using Kaplan–Meier Plotter, GEPIA2, and Human Protein Atlas datasets. Co-expression and gene set enrichment analyses were conducted using LinkedOmics, and functional enrichment analyses were performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome databases. Correlation and protein–protein interaction (PPI) analyses were evaluated using GEPIA2 and STRING. Results: EPHX2 expression was significantly reduced in LUAD tissues compared with normal lung tissues across datasets, and these findings were supported at the protein level. High EPHX2 expression was associated with better overall survival and retained independent prognostic significance in multivariate Cox analysis. Functional enrichment analyses demonstrated associations with lipid metabolism, arachidonic acid metabolism, cytochrome P450-related pathways, and oxidative processes. Correlation analyses suggested potential associations between EPHX2 and angiogenesis, extracellular matrix remodeling, and hypoxia-related pathways. Conclusions: Bioinformatics analyses suggest that EPHX2 may participate in metabolic and tumor progression-related regulatory networks and may serve as a prognostic biomarker in LUAD.

Genes doi: 10.3390/genes17080960

Authors: Lovyanne Vergel de Dios Catherine Wu Salique H. Shaham Manish K. Tripathi

Background: Lung adenocarcinoma (LUAD) is the most prevalent histologic subtype of non-small cell lung cancer (NSCLC) and exhibits considerable molecular heterogeneity. Among the most clinically significant driver alterations are mutations in EGFR and KRAS, both of which influence treatment selection and oncologic outcomes. The prevalence of these mutations varies by race, yet racial minority populations remain underrepresented in genomic studies. EGFR alterations are more frequently observed in Asian patients, while KRAS mutations predominate in non-Asian cohorts. This study aimed to characterize race-associated differences in driver mutation prevalence among Asian, Black, and White patients with LUAD. Methods: A retrospective secondary cohort analysis was performed using publicly available clinicogenomic data from the Lung Adenocarcinoma Met Organotropism cohort, accessed via cBioPortal, comprising 2653 tumor samples. Patients were stratified by self-reported race into Asian, Black, and White cohorts; cases with missing race data were denoted as either other or unknown. Mutation frequencies for EGFR, KRAS, and TP53 were extracted from OncoPrint cohort study views and compared descriptively across groups. Results: Distinct race-associated differences in driver mutation prevalence were observed. Asian patients exhibited the highest frequency of EGFR alterations (64%), compared with Black (41%) and White (28%) cohorts. In contrast, KRAS mutations were least prevalent in Asian patients (10%) and more frequent in White (33%) and Black (23%) cohorts, indicating an inverse distribution between Asian and non-Asian populations. TP53 mutation prevalence was similar in Asian (52%) and White (53%) cohorts but was notably higher in Black patients (65%). Conclusions: Asian patients with LUAD exhibit a distinct molecular profile characterized by EGFR predominance, with direct implications for eligibility for EGFR-targeted tyrosine kinase inhibitor therapy. Black patients may also benefit from EGFR-based targeted therapies, but lack of large genomic data on Black populations warrants further investigation. White cohorts display a KRAS-dominant mutation pattern, suggesting divergent tumorigenic pathways and the potential need for alternative therapeutic strategies. The elevated TP53 frequency in Black patients remains to be further characterized. These findings support integrating race-associated genomic profiling into precision oncology frameworks to improve treatment selection and reduce disparities in outcomes.

Genes doi: 10.3390/genes17080959

Authors: Hoai Thu Thi Nguyen Thanh-Van Ta Thuy Thi Le Quyen-Diep Nguyen Van Cao Chan Dinh Khac Nguyen Tuan Nguyen Duc Ngoc-Lan Thi Nguyen

Background/Objectives: Host genetic variation contributes to the heterogeneous clinical outcomes of coronavirus disease 2019 (COVID-19), yet evidence from Southeast Asian populations remains limited. Methods: We investigated host genetic factors associated with COVID-19 severity in Vietnamese patients infected with the SARS-CoV-2 Delta variant using whole-exome sequencing. A total of 48 unvaccinated patients were enrolled. During sample-level quality control, one sample was excluded because the genetically inferred sex was discordant with the information recorded in the clinical medical record, leaving 47 samples (23 severe/critical and 24 mild/asymptomatic) for downstream genetic analyses. Gene-based association analysis was performed using MAGMA, followed by functional enrichment and interaction network analyses with Metascape and GeneMANIA. Results: Population structure analysis showed that the study participants clustered closely with the East Asian (EAS) reference population. No individual variant reached the prespecified multiple-testing-adjusted threshold, and no gene-level association survived Benjamini–Hochberg correction. Using a nominal MAGMA gene-based p < 0.01 threshold solely for exploratory prioritization, 44 genes were selected for downstream functional analyses. Functional enrichment highlighted RNA processing and mRNA maturation, together with mitochondrial, metabolic, immune-regulatory, and cellular homeostasis pathways. Network topology analysis further identified several highly connected genes, including CPSF4, MRPS34, ATP5MF, BUD31, SNRPD3, and HDAC1. Conclusions: These hypothesis-generating findings are consistent with a potentially polygenic contribution to severe COVID-19 and provide an exploratory systems-level framework for understanding host genetic susceptibility in the Vietnamese population, while identifying biologically plausible candidate genes and pathways for future validation.

Genes doi: 10.3390/genes17080958

Authors: Tara E. Samson Donato DeIngeniis Maki S. Koyama Roberto Bailey Claire J. Brabander Ariadna Cilleros Portet Corina Lesseur Ahmed Duke Shereen Yoko Nomura

Background/Objectives: Prenatal substance exposure (PSE) to alcohol, cannabis, and other psychoactive drugs affects over 500,000 pregnancies annually in the US and is consistently associated with adverse birth and childhood outcomes, but the underlying biological mechanisms are not well-understood. Given the dopaminergic system’s role in substance use and child development, this study aimed to examine and connect the effects of PSE on dopaminergic placental gene expression at birth and on striatal brain volumes in middle childhood. We hypothesized that PSE would lead to reduced dopamine receptor D1 (DRD1) gene expression and smaller striatal gray-matter volumes (GMVs) and that placental DRD1 gene expression would be positively associated with striatal GMV. Methods: PSE, placental gene expression, and T1-weighted MRI data were drawn from a pilot study (n = 34) within the longitudinal cohort Stress in Pregnancy study. PSE was defined by any amount of alcohol, tobacco, or cannabis use during pregnancy. Results: Unexpectedly, children with PSE had a trend toward increased placental DRD1 gene expression (β = 0.497, p = 0.056) and significantly larger GMV in the right putamen (β = 0.374, p = 0.018) and nucleus accumbens (NAc) (β = 0.389, p = 0.029) than unexposed children. Independent of PSE, higher placental DRD1 gene expression at birth was also associated with larger right NAc GMV (β = 0.617, p = 0.015) in middle childhood. Conclusions: These findings contrast prior cross-sectional work linking high-dosage PSE to smaller striatal volumes and inconsistent patterns of dopaminergic gene expression, suggesting potential compensatory placental mechanisms reflected in biological outcomes across child development.

Genes doi: 10.3390/genes17080957

Authors: Qi Cheng Yanli Wang Deqiang Wang Guoxing Wu Biyun Liu Qien Yuan Fen Zhu

Objectives: Heart failure (HF) arises from multiple interrelated pathological processes. Among these, lysosomal impairment and loss of autophagic homeostasis are increasingly recognized as important contributors to myocardial damage and ventricular remodeling. This study sought to identify lysophagy-associated signature genes in HF and to define their biological roles, cellular origins, and potential diagnostic relevance. Methods: Bulk myocardial transcriptome datasets, including GSE16499, GSE57338, and GSE76701, were integrated with the human cardiac single-cell dataset GSE145154. Differential expression analysis was first performed to identify lysophagy-related differentially expressed genes (DEGs). Candidate hub genes were then screened using support vector machine-recursive feature elimination (SVM-RFE) and least absolute shrinkage and selection operator (LASSO) regression. Functional enrichment analysis, Gene Set Enrichment Analysis (GSEA), immune infiltration assessment, single-cell transcriptomic mapping, and regulatory network analysis were subsequently conducted. The expression profiles of the selected genes were validated in a murine HF model, and VAMP8 overexpression assays were performed in H9c2 cells. Results: Five hub genes, namely VAMP8, STX2, MCOLN1, DERL1, and PTP4A2, were consistently and markedly decreased in failing myocardial tissue. These genes were mainly linked to SNARE-dependent vesicle trafficking and lysophagy regulation. A diagnostic model incorporating these hub genes demonstrated good discriminatory performance in both the training dataset and a small independent validation cohort, supporting further evaluation of their potential diagnostic value. Single-cell analysis further indicated that these genes were primarily enriched in cardiac FOLR2+ tissue-resident macrophages (TRMs). Pseudotime and cell–cell communication analyses associated this module with FOLR2+ TRM cell states and predicted interactions with cardiac stromal cells. In the HF mouse model, the mRNA levels of all five hub genes were decreased, with concurrent reductions in VAMP8, MCOLN1 and DERL1 protein expression. In Ang II/LLOMe-induced H9c2 cells, VAMP8 overexpression was associated with reduced cardiomyocyte injury, attenuation of changes in the abundance of lysosome- and autophagy-related proteins, and fewer ultrastructural abnormalities, suggesting a potential cardioprotective effect. Conclusions: VAMP8, STX2, MCOLN1, DERL1, and PTP4A2 were identified as candidate molecular markers of HF that reflect alterations in a lysophagy- and vesicular-transport-related program associated with FOLR2+ tissue-resident macrophages. These findings provide new insights into immune-microenvironment remodeling in HF and suggest potential directions for mechanistic and therapeutic investigations.

Genes doi: 10.3390/genes17080956

Authors: Kairat Kazbekov Yerbol Zhapparov Nasrulla Shanazarov Valery Benberin Sergey Zinchenko Ainagul Kazbekova

Background/Objectives: GWASs have identified more than 250 prostate cancer (PCa) predisposition loci, predominantly in European and partly Asian cohorts. The Kazakh population is markedly under-represented in international genetic studies, limiting existing risk models. This study aimed to analyze the distribution of 102 PCa-associated single-nucleotide polymorphism (SNP) genotypes and alleles and to identify reliable population-specific associations with PCa risk in Kazakh men. Methods: This retrospective case–control study included 941 Kazakh men (476 with histologically confirmed PCa and 465 cancer-free controls). Genomic DNA extracted from peripheral blood was genotyped with TaqMan® OpenArray® technology on a QuantStudio 12K Flex system. Associations were assessed by Pearson’s χ2 test and logistic regression, with genotypic and allelic odds ratios (OR) and 95% confidence intervals (CI). Two-step multiple-testing correction (Bonferroni and Benjamini–Hochberg false-discovery rate, FDR) was applied. Predictive models were built using classification and regression trees (CART) and stepwise logistic regression. Results: Of 102 SNPs, 39 showed nominally significant genotypic differences; 12 remained significant after Bonferroni correction and 2 after FDR (14 in total). Several of the corrected loci were significant at both the genotypic and allelic level. Allelic ORs ranged from 0.37 (protective rs10187424 T allele) to 4.81 (rs1545985). A parsimonious seven-SNP autosomal logistic-regression model achieved an apparent AuROC of 0.84 (10-fold cross-validated 0.82); adding age as a covariate raised discrimination to 0.87. Ten of the fourteen significant loci remained significant after age adjustment, and six of these formed a core signal robust to both age imbalance and genotyping-quality concerns. Conclusions: This first large-scale SNP-association study in Kazakh men shows allele-frequency profiles resembling East Asian rather than European populations, confirming the need for population-specific genetic risk-assessment tools. The seven-SNP model showed high discriminatory power in the training set and requires external validation before clinical application.

Genes doi: 10.3390/genes17080955

Authors: Rosalba Fumo Katia Scala Sara Gaeta Angela D’Ardia Teresa Infante Giuseppe Ciancia Alessandro Caputo Alessandra Rosati Bianca Serio Antonio D’Antonio Pio Zeppa Massimiliano Chetta

Background/Objectives: Fluorescence in situ hybridization (FISH) is an established component of the diagnostic and prognostic workup of hematologic malignancies. However, most evidence supporting FISH interpretation originates from treatment-naïve diagnostic cohorts, providing limited insight into how cytogenetic findings evolve during longitudinal disease monitoring and therapeutic exposure. We retrospectively analyzed 1357 consecutive FISH assays performed in 1092 patients with hematologic malignancies between 2019 and 2023. Methods: Multivariable logistic regression identified predictors of aberration detection, while longitudinal analyses explored temporal changes in cytogenetic profiles among serially monitored patients. Observed abnormality rates were compared with published diagnostic benchmarks. Results: The cohort had a median age of 68 years and was predominantly composed of patients with myelodysplastic/myeloproliferative neoplasms (27.2%), multiple myeloma (26.9%), and chronic lymphocytic leukemia (21.6%). Overall, 29.2% of informative assays revealed cytogenetic abnormalities. Clinical indication was the strongest predictor of aberration detection. Compared with diagnostic samples, follow-up specimens showed significantly lower odds of abnormal findings (adjusted OR 0.48, 95% CI 0.36–0.64; p < 0.001), whereas relapse samples demonstrated higher odds (adjusted OR 1.82, 95% CI 1.28–2.59; p = 0.001). Increasing age was independently associated with abnormal FISH results (adjusted OR per decade 1.24, 95% CI 1.12–1.38; p < 0.001). Several canonical abnormalities occurred less frequently than expected from historical diagnostic series, including BCR::ABL1 within the chronic myeloid leukemia testing pathway and del(13q14) in both chronic lymphocytic leukemia and multiple myeloma. In contrast, del(17p), involving the TP53 locus, remained consistently represented across disease categories and was enriched in chronic lymphocytic leukemia relative to published diagnostic cohorts. Conclusions: Longitudinal assessment revealed increasing cytogenetic heterogeneity over time, with common lesions progressively declining and rare or complex abnormalities expanding from 16.3% to 36.7% of the observed cytogenetic landscape. The cytogenetic patterns detected by FISH in contemporary hematology practice are strongly associated with clinical context, disease stage, and treatment history; however, the cross-sectional and retrospective design precludes inference of causal influence. The divergence between real-world positivity rates and historical diagnostic benchmarks highlights the need for context-specific interpretation of cytogenetic findings. The persistence of TP53 loss across disease boundaries and the progressive diversification of aberrations over time underscore the dynamic nature of clonal evolution in hematologic malignancies.

Genes doi: 10.3390/genes17080954

Authors: Giorgia Benedetta Dutti Katia Mangialardi Simona Rasola Ludovico Sebastio Francesco Tarantini Cosimo Cumbo Luisa Anelli Antonella Zagaria Nicoletta Coccaro Angela Minervini Giuseppina Tota Immacolata Redavid Maria Rosa Conserva Pellegrino Musto Francesco Albano

Acute myeloid leukemia (AML) persistence is sustained by leukemic stem cells (LSCs) that survive metabolic deprivation, oxidative stress, hypoxia, proteotoxic burden, and therapeutic pressure. The integrated stress response (ISR) has emerged as a central adaptive network in this process. Through phosphorylation of a subunit of eukaryotic initiation factor 2 (eIF2α) and selective translation of activating transcription factor 4 (ATF4), the ISR coordinates stress-responsive transcriptional programs that may either preserve cellular fitness or promote apoptotic commitment, depending on the intensity, duration, and biological context of activation. In AML, ATF4 occupies a critical position at the interface between stemness, metabolic adaptation, redox control, ferroptosis resistance, and treatment response. In primitive leukemic compartments, ISR–ATF4 signaling appears to support stress tolerance, amino acid metabolism, serine biosynthesis, autophagy, and leukemic persistence. At the same time, pharmacologic or sustained ISR activation may lower the apoptotic threshold by inducing pro-apoptotic mediators such as CHOP, PUMA, and NOXA, thereby modulating MCL-1 dependency and enhancing sensitivity to venetoclax-based strategies. Conversely, adaptive ISR signaling may promote resistance through mechanisms such as ATP-binding cassette subfamily B member 1 (ABCB1) enhancer activation and mitochondrial stress tolerance. This duality creates a therapeutic paradox: ISR–ATF4 signaling may need to be inhibited in adaptive, resistance-promoting states but amplified in apoptosis-permissive contexts. This review discusses the biological and therapeutic relevance of ISR–ATF4 dysregulation in AML and highlights the need for biomarkers capable of distinguishing adaptive ATF4 dependency from inducible apoptotic vulnerability.

Genes doi: 10.3390/genes17080953

Authors: Xiaoru Dai Peng Sun Minyun Jiang Lizhuang Xie Hengdong Zhang Baoli Zhu Boshen Wang

Background: Noise-induced hearing loss (NIHL) is a pervasive occupational health challenge, yet the individual susceptibility mechanisms remain unclear. Ferroptosis, an iron-dependent form of programmed cell death, has been implicated in cochlear hair cell damage. This study aims to elucidate the regulatory role of the transcription factor FOXA2 and the deacetylase SIRT1 in ferroptosis and to investigate the association between SIRT1 genetic polymorphisms and NIHL susceptibility in occupational populations. Methods: We employed a multi-level study design combining epidemiological investigation, animal models, and cellular experiments. First, a case–control study was conducted involving 1314 noise-exposed workers (639 cases vs. 675 controls) from a chemical fiber enterprise in Jiangsu Province to analyze the association between SIRT1 single nucleotide polymorphisms (SNPs) and NIHL risk. Second, a C57BL/6J mouse model exposed to 120 dB white noise was established to assess cochlear morphology and protein expression. Third, in HEI-OC1 cochlear hair cells, we performed siRNA-mediated knockdown of Foxa2 and dual-luciferase reporter assays to verify the transcriptional regulation of SIRT1 and its downstream effects on the ferroptosis pathway. Results: Population analysis revealed that the SIRT1 rs12778366 C allele was significantly associated with increased NIHL risk (OR = 1.386, 95% CI: 1.084–1.772, p = 0.009), and this association remained significant after adjustment (p = 0.041). Stratified analysis further revealed a significant gene–environment interaction in workers with >15 years of noise exposure (OR = 2.126, 95% CI: 1.401–3.226, p < 0.001). In vivo, noise exposure led to significant downregulation of Sirt1 and Foxa2 in cochlear tissues, accompanied by elevated ferroptosis markers (Fe2+, MDA) and depleted antioxidant defenses (GSH, xCT, and GPX4). Mechanistically, we demonstrate that FOXA2 transcriptionally activates SIRT1 by binding to its promoter. Knockdown of FOXA2 in vitro suppressed SIRT1 expression, suppressed xCT, a key component of the System Xc−/GPX4 antioxidant axis, and promoted ferroptosis-related cellular changes. Conclusions: This study identifies a novel protective axis where FOXA2 prevents noise-induced ferroptosis in cochlear hair cells by transcriptionally upregulating SIRT1 and maintaining xCT-mediated antioxidant defense. Furthermore, the SIRT1 rs12778366 polymorphism is identified as a candidate variant warranting further investigation in independent cohorts before clinical translation.

Genes doi: 10.3390/genes17080951

Authors: James C. Barton J. Clayborn Barton Ronald T. Acton

Background: HFE (homeostatic iron regulator) p.S65C (rs1800730) is associated with European ancestry, although there is no comprehensive geographic study of p.S65C in Europe. Methods: We tabulated published p.S65C genotypes in European population/control cohorts, depicted allele frequency ranges in a map, and computed correlations of p.S65C allele frequencies with latitudes and longitudes of cohort recruitment sites. Results: We identified 44 cohorts from 24 of the 44 countries of Europe. These 24 countries comprise ~62.9% of Europe’s population. There were 233,528 subjects, including 38 HFE p.S65C homozygotes (~1 in 6145 subjects) and 4347 p.S65C heterozygotes (~1 in 54 subjects). Genotypes in 42 cohorts (95.5%) were consistent with Hardy–Weinberg equilibrium. The median allele frequency was 0.0129 (range 0–0.0350). p.S65C was not reported in Bulgaria, although the allele frequency in non-Bulgarian cohorts did not differ significantly (0/200 vs. 4423/462,432, respectively; p = 0.2728). Allele frequency ranges (means) were 0–0.0100 (0.0087), 0.0101–0.0200 (0.0146), and ≥0.0201 (0.0253) in 7, 14, and 3 respective aggregate country cohorts (p < 0.0001, all mean comparisons). The seven countries with low-range frequencies extend from north to south (Estonia to Italy). The three countries with high-range frequencies are east of ~14.1° E (western-most border of Poland). Correlations of allele frequencies with latitudes and longitudes in 44 cohorts were not significant (p = 0.1745 and 0.6031, respectively). Conclusions: We conclude that the median HFE p.S65C allele frequency in Europe is 0.0129, allele frequencies differ between some countries, and there is no linear north-to-south or west-to-east allele frequency gradient.

Genes doi: 10.3390/genes17080952

Authors: Yannis L. Loukas Katherine Anagnostopoulou Georgia Thodi Maria Spanou Christos Gavalas Elina Molou Stefania Antonopoulou Antigoni Poulopoulou Yannis Dotsikas Maria Alvanou Konstantinos Tegopoulos Roser Pons Konstantinos Tziouvas Georgios Vartzelis Eleni Skouteli Eirini Loukatou Antonia Charitou Konstantinos Douros Soultana Siahanidou Melpomene Giorgi Artemis Stephanede Maria Angeli Maria Nikolaidou Eleftheria Kokkinou Ioanna Kouri Vasiliki Koute Eleni Frysira Argirios Dinopoulos

Background/Objectives: Genomic sequencing can shorten the diagnostic pathway for selected symptomatic neonates and young infants, but evidence from such cohorts should not be extrapolated to population newborn screening. This study describes molecular findings and potential clinical implications in 25 unrelated patients younger than 6 months at referral with heterogeneous, predominantly neurological phenotypes and no established molecular diagnosis. Methods: The first 17 patients underwent whole-exome sequencing (WES), and the subsequent 8 underwent whole-genome sequencing (WGS) under sequential laboratory protocols; allocation was not randomized, and the study was not designed to compare platforms. Results: Pathogenic or likely pathogenic findings providing a definitive or likely molecular diagnosis were identified in 7/25 patients (28.0%; 95% confidence interval [CI], 14.3–47.6), including sequence variants, one 20q13.33 deletion, and mosaic trisomy 9. An additional RANBP2 variant was interpreted as a susceptibility-associated finding in a patient with infection-related encephalitis, yielding clinically relevant findings in 8/25 patients (32.0%; 95% CI, 17.2–51.6). Three definitive diagnoses involved disorders with established disease-specific management considerations; however, patient-level treatment changes, turnaround times, and outcomes were not systematically assessed. Conclusions: These findings support the diagnostic value of genomic testing in selected symptomatic neonates and young infants, while the small, heterogeneous cohort, sequential non-equivalent workflows, and incomplete outcome data preclude conclusions about comparative WES/WGS performance or population newborn screening.

Genes doi: 10.3390/genes17080950

Authors: Yaping Shen Rongrong Pan Chen Liu Jing Zheng Xin Yang

Background: Pathogenic variants in ZNF292 cause intellectual disability type 64 (MIM#619188), characterized by intellectual impairment ranging from mild to severe, speech delay, and autism spectrum disorder. However, reports of ZNF292-related neurodevelopmental disorders remain scarce, and most published studies are based on multi-center cohorts. Methods: We performed whole-exome sequencing in eight unrelated individuals presenting with unexplained neurodevelopmental disorders, including global developmental delay and/or intellectual disability. Detailed clinical characterization, neuroimaging, and developmental assessments were conducted. Results: Seven de novo variants in ZNF292 were identified, including two nonsense and five frameshift variants, namely, c.4189C>T (p.Arg1397Ter), c.6343C>T (p.Arg2115Ter), c.1533del (p.Ile511Metfs*11), c.3094dup (p.Ser1032Phefs*18), c.3997_3998del (p.Thr1333Glnfs*8), c.6028_6031del (p.Ala2010Ter) and c.6160_6161del (p.Glu2054Lysfs*14). Among these, c.1533del (p.Ile511Metfs11), c.3094dup (p.Ser1032Phefs18) and c.3997_3998del (p.Thr1333Glnfs*8) are reported here for the first time. All variants were classified as pathogenic. All individuals exhibited global developmental delay, intellectual disability, and short stature. The majority presented with language impairment, motor delays, autism spectrum features, and dysmorphic facial features, while brain magnetic resonance imaging revealed nonspecific abnormalities such as ventriculomegaly. Conclusions: This study contributes additional cases to the expanding phenotypic and mutational spectrum of ZNF292-related neurodevelopmental disorder. Growth retardation was observed in all eight individuals, but given the limitations of a single-center referral cohort, this observation should be interpreted with caution and requires validation in larger studies.

Genes doi: 10.3390/genes17080949

Authors: Guang Zeng Jing Yin Jianrong Huang Xianyi Wang Songxian Yan

Background: The genus Anomala is exceptionally species-rich and includes many species recognized as major agricultural and forest pests. Nevertheless, the taxonomic status of certain species remains contentious, and the phylogenetic relationships within the genus are still poorly resolved and in need of further investigation. Objectives: To better elucidate the evolutionary relationships among these insects, we assembled the complete mitochondrial genomes (mitogenomes) of four Anomala species—A. aulax, Anomala sp., A. vitalisi, and A. xantholoma. Multiple molecular datasets were integrated to reconstruct the phylogenetic framework of Scarabaeidae. Methods: Wild adult specimens of four Anomala species were collected. After total DNA extraction, complete mitogenomes were assembled and annotated for comparative analysis of core genomic traits. Multiple datasets were applied to construct phylogenetic trees via maximum likelihood and Bayesian inference, so as to evaluate the evolutionary characteristics of each taxon. Results: Our analyses reveal that the mitogenomes of Anomala species exhibit a conserved architecture, characterized by similarities in genome size, AT nucleotide bias, and gene order, suggesting a high degree of evolutionary stability within the genus. The resulting phylogenetic trees robustly support the monophyly of the following families: Passalidae, Lucanidae, Geotrupidae, Trogidae, Hybosoridae, and Glaphyridae. Additionally, the phylogenetic findings revealed the paraphyly of both Scarabaeidae and Anomala, and further suggested that Melolonthinae is likely a paraphyletic group. Conclusions: This study enriches the currently available mitogenomic data and provides a preliminary foundation for understanding the phylogeny, resource conservation, and genetic diversity of Anomala.

Genes doi: 10.3390/genes17080948

Authors: Jingjing Jiang Xianhua Mao Weiqian Lou Weiwei Lou Ziqiang Li Xinrong Zhang Qing Xie Rongtao Lai

Background/Objectives: At-risk metabolic dysfunction-associated steatohepatitis (MASH) is associated with increased risks of cirrhosis, hepatocellular carcinoma, and liver-related mortality. Because impaired efferocytosis contributes to persistent hepatic inflammation and fibrotic remodeling in MASH, we investigated whether efferocytosis-associated molecular signatures could identify at-risk MASH. Methods: Bulk RNA-sequencing datasets from Gene Expression Omnibus (GSE135251 and GSE174478) were analyzed to identify differentially expressed efferocytosis-related genes and characterize associated pathways and immune infiltration patterns. Machine learning-based feature selection was used to identify hub genes, which were incorporated into a transcriptomic nomogram. Experimental validation involved reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blotting of liver tissues from a Western diet-induced murine metabolic dysfunction-associated steatotic liver disease (MASLD) model. Plasma proteomic data were analyzed to explore the discriminatory performance of hub gene products. Results: A total of 17 efferocytosis-related genes (ERGs) associated with at-risk MASH were identified and enriched in pathways related to efferocytosis, inflammation, and immune regulation. Five hub genes, CD24, CHI3L1, TREM2, PTGS2, and LGR6, were shared by all three feature-selection approaches and significantly upregulated in at-risk MASH. A transcriptomic nomogram yielded area under the curve (AUC) values of 0.866 and 0.805 in the training and external cohorts, respectively. In the murine MASLD model, all five hub genes showed increased mRNA and protein expression in advanced disease. Exploratory plasma proteomic analysis identified elevated circulating TREM2 and CHI3L1 levels in at-risk MASH, and a simplified plasma-based model achieved an AUC of 0.736. Conclusions: This study identified a five-gene efferocytosis-associated signature and developed models for identifying at-risk MASH, suggesting that these genes warrant further evaluation as candidate biomarkers.

Genes doi: 10.3390/genes17080946

Authors: Xiaotong Zhao Hua Chang Quanpeng Zhang Zhuoyu Zhao Sihui He Zongyan Lu Xun Xiang

Background/Objectives: Bovine heat-stress RNA-seq studies differ in tissue, age, physiological state, and exposure design. We asked which responses recur across these contexts and which depend on the evidence base. Methods: We reprocessed 107 libraries from five in vivo Bos taurus studies and synthesized within-study heat-minus-control log2 fold changes using restricted maximum-likelihood random-effects models with modified Knapp–Hartung inference. Eight tissue- and age-aware scenarios tested the cross-context estimate. A six-component heat-stress transcriptomic stability index (HSTSI) was benchmarked against five simpler rankings, and an independent mammary single-nucleus dataset provided cell-resolved comparison. Results: Of 266 FDR-significant pathways, 259 retained direction across all five study deletions and 21 remained significant in every deletion. Translation, ribosome, protein folding, endoplasmic-reticulum processing, proteasome, and heat-response programs formed the most recurrent axis. Four principal sensitivity scenarios retained 0.920–0.932 gene-direction agreement and 0.957–0.981 effect-rank correlation with the five-study analysis. In the single-nucleus dataset, leading-edge genes from the principal proteostasis programs showed 89.4–100% pooled-nucleus direction agreement and 94.7–100% agreement among published cluster-level differentially expressed genes. HSTSI had the highest mean top-200 held-out direction agreement (0.583 versus 0.516–0.562), with variation among folds. None of 16,756 genes met a modified Knapp–Hartung FDR below 0.10. IL1R2 and SDCBP2 were externally concordant, whereas GZMK and CD8A were context-dependent. Conclusions: A coordinated proteostasis program was the most transferable heat-stress signal. Energy remodeling, immune-associated bulk signals, and individual genes showed greater context dependence and define priorities for tissue-matched follow-up.

Genes doi: 10.3390/genes17080947

Authors: Xiaohui Pan Qiufei Wu Lixia Zhou

Biotic stresses (pest feeding, pathogenic fungal/bacterial/viral infection) and diverse abiotic stresses (extreme temperature, drought, waterlogging, saline–alkali soil, heavy metal pollution, nutrient deficiency, UV-B, ozone) severely restrict crop growth and global agricultural yield. Lipids act as core membrane structural constituents and vital secondary signaling messengers, executing multi-layered adaptive balancing functions during cell-type interactive stress acclimation, rather than uniform whole-plant lipid responses. They sustain membrane structural integrity across distinct cell populations, serve as synthetic precursors of bioactive signaling molecules, and trigger cascaded transcriptional and metabolic reprogramming upon environmental stimuli to rebalance physiological status among different cell types. This review systematically summarizes cell-type interactive lipid-mediated plant defense and acclimation balance mechanisms across biotic and abiotic stress contexts. We elaborate the biological functions of fatty acids, phospholipids, galactolipids, sphingolipids and their derivatives (jasmonate, salicylic acid, phosphatidic acid, oxylipin) in stress signal transduction and antioxidant defense and strictly distinguish two categories of lipid changes under all stress types: active adaptive lipid remodeling and passive stress-induced lipid oxidative damage. Key contents include stress-triggered cell-type-specific membrane lipid remodeling, the hierarchical transcriptional regulatory network mediated by WRI1, LEC1, PHR, MADS and other transcription factors governing oil metabolism, as well as crosstalk between lipid metabolism and compartmentalized reactive oxygen species (reactive oxygen species (ROS)) signaling. We further compare conserved lipid-regulatory modules and species-specific divergent responses across model plants and economic oilseed crops, integrating state-of-the-art targeted/untargeted lipidomics, single-cell spatial lipidomics and multi-omics joint breeding strategies to improve multi-stress tolerance in oilseed crops. By consolidating global research progress up to 2025, including the two latest 2026 cross-species meta-analysis reviews, this review provides systematic theoretical support and operable multi-level technical frameworks for genetic engineering targeting conserved lipid pathways to breed stress-resilient high-oil crop germplasm, and highlights reliable lipid stress biomarker screening as a promising translational research direction.

Genes doi: 10.3390/genes17080945

Authors: Evelyne Minucchi Francesca Dragoni Rosalinda Di Gerlando Gaia Pavanello Matteo Cotta Ramusino Alfredo Costa Stella Gagliardi

Background: Frontotemporal dementia (FTD) is a neurodegenerative disease that shares numerous clinical features with other forms of dementia. In this context, non-coding RNAs, specifically microRNAs (miRNAs), represent a promising tool for differential diagnosis. Since these miRNAs can be isolated from circulating extracellular vesicles (EVs) in peripheral blood, they provide a direct insight into FTD-specific molecular processes. Consequently, while EV-contained miRNAs hold potential as disease-specific biomarkers, investigating their relative target genes can help elucidate their precise functional roles. Aim: This work aimed to identify a specific miRNA signature to better characterize FTD pathology. Methods: Building on a previous Next-Generation Sequencing (NGS) analysis, three candidate miRNAs were selected for validation in both EVs and peripheral blood mononuclear cells (PBMCs) of FTD patients. Subsequently, the predicted target genes of two of these miRNAs were validated in PBMCs to assess their expression levels. Results: Our findings revealed that miR-365a-3p and miR-212 were significantly down-regulated in FTD. Conclusions: Together with their target genes, these miRNAs are involved in cell cycle and apoptotic pathways, suggesting a potential role in the pathological mechanisms of the disease.

Genes doi: 10.3390/genes17080944

Authors: Viktoria M. Petrova Dmitry V. Bulgin Elena Yu. Radomskaya Vsevolod A. Shevelov Darya S. Zhukova Olga. P. Chzhu Andrey D. Manakhov Alexander V. Popov Stanislav A. Rybtsov

Background: One of the key hallmarks of aging is the age-related decline in immune system function, accompanied by a chronic low-grade inflammation, or “inflammaging”. Simultaneously, a reduced capacity of immune cells to recognize and eliminate pathogens, along with immune exhaustion, is also defined as a sign of aging. Cynomolgus macaques (Macaca fascicularis) belong to a group of non-human primates evolutionarily close to humans and are often used for preclinical research. Methods: In this study, we performed mRNA sequencing of bone marrow and peripheral blood samples from young (5 years old) and old (over 19–21 years old) cynomolgus macaques to identify key markers of immunosenescence. Results: Although an increase in p16 expression was detected, we did not observe the increase in the senescence-associated secretory phenotype (SASP) cytokines reported in previous studies. Instead, we observed a transcriptional profile characterized by increased lymphocyte cytotoxic activity combined with a decrease in proinflammatory signaling, reduced markers of myeloid cells, and lowered sensitivity to pathogen-associated patterns. Similar changes were detected in both blood and bone marrow: decreased expression of naive T-cell markers (CCR7, LEF1, SELL, and FOXO1), reduced markers of the myeloid lineage—neutrophils and monocytes (CD177, CD14, CD163, FPR1, FPR2, and CXCR1)—and downregulation of genes belonging to different pattern-recognition receptor families (TLR1, TLR2, TLR4, TLR5, TLR6, TLR8, TLR10, IFIH1, CLEC4E, NOD2, NLRC4, NLRP12, NLRX1, and NAIP). In contrast, the group of old animals showed increased expression of markers associated with terminally differentiated cytotoxic lymphocytes (CD8+ T cells and NK cells): GZMB, PRF1, KLRK1, FASLG, TBX21, CCR5, and GNLY. Conclusions: Our findings offer new perspectives on the molecular mechanisms of age-associated immune dysregulation in non-human primates, serving as a baseline for selecting key candidate genes in subsequent functional investigations.

Genes doi: 10.3390/genes17080943

Authors: Alfredo Pauciullo Davide Nicodemo Neyrouz Letaief Halina Černohorská Svatava Kubičková Miluše Vozdová Pietro Parma Leopoldo Iannuzzi Gianfranco Cosenza

Background/Objectives: The domestic yak (Bos grunniens) is a livestock species of major relevance in high-altitude environments and an important model for studying adaptation and reproductive isolation within Bovini. Despite its close phylogenetic relationship with cattle (Bos taurus), yak × cattle hybrids show a marked sex-biased fertility pattern, with fertile females and generally sterile F1 males, suggesting that subtle chromosomal or genomic differences may underlie post-zygotic reproductive barriers. In this study, we performed a cytogenetic characterization of eight adult yak bulls imported and reared in Central Italy using conventional and molecular cytogenetic approaches. Results: GTG-, RBG-, RBA- and CBA-banding confirmed the yak diploid number as 2n = 60 and the fundamental number as NF = 62, with banding patterns highly comparable to the standardized cattle karyotype. CBA-banding showed an X chromosome lacking evident constitutive heterochromatin and a Y chromosome with distal C-positive blocks. Chromosome instability was low, with 3.75% abnormal metaphases, mainly represented by chromatid and iso-chromatid breaks, while the mean sister chromatid exchange (SCE) rate was 5.19 ± 2.14 per cell. Sequential Ag-NOR/RBA staining localized nucleolar organizer regions (NORs) at the telomeres of autosomes 2, 3, 4, 11 and 25, as in cattle. Zoo-FISH using bovine chromosome paints for X, Y, 5 and 15 showed complete hybridization to the corresponding yak chromosomes, and BAC-FISH mapped the Y-linked ZFY and SRY genes to positions homologous to those reported in cattle. A comparative bioinformatics analysis of available yak genome assemblies confirmed the overall genome-wide correspondence with cattle, while revealing chromosome orientation issues and small local inconsistencies that may be relevant for comparative mapping and probe design. Conclusions: Overall, at the resolution tested, these findings support broad macrostructural conservation of yak and cattle karyotypes and provide cytogenetic reference data for yak populations reared outside of their traditional range. The persistence of F1 male sterility despite this large-scale chromosomal conservation suggests that fine-scale sex chromosome differences, particularly involving pseudoautosomal regions, recombination boundaries, or heterochromatin organization, may deserve targeted investigation.

Genes doi: 10.3390/genes17080942

Authors: Rieke Ollermann Fei Song Marta Owczarek-Lipska Amilcar Perez-Riverol Gregor Dombrowsky Andreas Radeloff John Neidhardt

Background/Objectives: Hearing loss is one of the most prevalent sensory disorders in humans, with genetic factors accounting for approximately 60% of cases. Cochlear implantation is an effective intervention for individuals with severe-to-profound hearing loss. However, substantial variability in postoperative auditory performance persists, complicating the prediction of individual outcomes. This study investigated the genetic findings associated with hearing loss in a cohort of seven affected adults with cochlear implants (CIs). Methods: A total of seven patients with severe-to-profound hearing loss underwent genetic testing. Two of them were part of diagnostic screening, and five of them were part of research genetic analyses. Results: High-throughput genomic DNA sequencing identified twelve variants across multiple genes, including four new sequence variants. Based on ACMG/AMP criteria, integrating computational predictions, population frequency data, ClinVar annotations, and in silico pathogenicity assessments, the identified variants were classified as pathogenic variants, likely pathogenic variants, and variants of uncertain significance (VUS). We detected one pathogenic variant, two likely pathogenic variants and nine variants of uncertain significance (VUS). Novel variants were further analyzed using multiple sequence alignment to assess evolutionary conservation. Conclusions: The identification of four novel variants within the analyzed patients underscores the genetic heterogeneity of hearing loss and the importance of genetic analyses for improving the understanding of its molecular basis. Further functional and clinical studies are required to determine the pathogenicity of these variants and their potential clinical relevance.

Genes doi: 10.3390/genes17080941

Authors: Kağan Gökçe Mehrdad Sheikhvatan

Background/Objectives: N6-methyladenosine (m6A) RNA modification is a major epitranscriptomic regulator of mRNA stability and translation. Genetic variants in the m6A pathway may influence gastric cancer progression, but their prognostic significance after curative gastrectomy remains uncertain. Methods: This retrospective study included 226 patients with gastric adenocarcinoma who underwent curative gastrectomy. Single nucleotide polymorphisms in five m6A-related genes (METTL3, METTL14, FTO, ALKBH5, and YTHDF1) were genotyped. Overall survival (OS) and disease-free survival (DFS) were analyzed using Kaplan–Meier and log-rank tests. Multivariable Cox regression was performed after adjustment for age, sex, tumor stage, lymph node status, and adjuvant therapy. Results: During a median follow-up of 38 months, 78 patients (34.5%) died and 92 (40.7%) experienced recurrence. High-risk m6A genotypes were associated with significantly poorer survival. The 5-year OS was 68.2% in the low-risk group versus 41.5% in the high-risk group (p < 0.001), while 5-year DFS was 61.4% versus 36.8% (p < 0.001). High-risk genotypes independently predicted worse OS (HR 1.87, 95% CI 1.28–2.74; p = 0.001) and DFS (HR 1.94, 95% CI 1.36–2.78; p < 0.001). Patients with the highest genetic risk scores had the poorest outcomes, particularly those with stage III–IV disease. Conclusion: Genetic variants in the m6A RNA modification pathway are independently associated with poorer survival after curative gastrectomy and may serve as prognostic biomarkers for risk stratification and personalized management in gastric cancer.

Genes doi: 10.3390/genes17080940

Authors: Anthony X. J. Wong Zachary Chua Jing Guo Hwee Goon Tay Zhen Xun Wang Mathieu Quinodoz Tien-En Tan Carlo Rivolta Beau J. Fenner

Background: To assess how historical patterns in retinitis pigmentosa (RP) gene inheritance, functional category, and phenotypic onset may inform the remaining unsolved RP discovery space. Methods: We manually reviewed PubMed-indexed primary reports in the RetiGene database, supplemented with PubMed-indexed human studies where necessary to improve extractable phenotype data. Gene-level variables extracted included age of symptom onset, inheritance pattern, functional category and syndromic association. Gene-level associations between earliest year of RP gene discovery and mean age of symptom onset were assessed, alongside temporal analyses for functional category, inheritance, and syndromic patterns. Results: Later year of gene discovery was associated with later mean age of symptom onset, both in the primary analysis restricted to genes with at least 5 extractable onset cases (n = 83, p < 0.001) and in a stricter sensitivity analysis restricted to genes with at least 10 onset cases (n = 66, p = 0.00525). Year of discovery differed significantly across functional categories (p < 0.001). No significant temporal association was observed for AR versus non-AR inheritance or syndromic status. Conclusions: This hypothesis-generating analysis suggests that observed patterns likely reflect a combination of biological detectability, study design, and publication dynamics rather than intrinsic gene–phenotype relationships alone; within this context, future RP-solving efforts may benefit from greater attention to less obvious biological pathways (such as ciliary, transport, and metabolic categories), along with later-presenting or less conspicuous phenotypes.

Genes doi: 10.3390/genes17080939

Authors: Tianyu Sun Feiyao Zhang Chang Liu Junhao Huang

Objective: Genetic factors contribute to physical activity (PA) and sedentary behavior (SB), two complex behavioral traits. They may be associated with musculoskeletal and inflammatory diseases. However, the relationships of domain-specific PA and SB traits with osteoporosis (OS), psoriatic arthritis (PsA), and rheumatoid arthritis (RA) remain unclear. A two-sample Mendelian randomization (MR) analysis assessed potential bidirectional associations between these behavioral traits and the three diseases. Methods: GWAS summary statistics were used to examine five domain-specific PA traits, three SB traits, and OS, RA, and PsA. Primary causal estimates were obtained using the inverse-variance weighted (IVW) method. Complementary analyses used MR-Egger regression, the weighted median method, and the weighted mode method. Sensitivity analyses were performed using Cochran’s Q test, the MR-Egger intercept test, MR-PRESSO, and leave-one-out analysis. Multiple testing was addressed using false discovery rate (FDR) correction. Results: In the forward MR analyses, genetically predicted liability to Light DIY was associated with lower odds of PsA after FDR correction (OR = 0.006, 95% CI = 0.0002–0.236, FDR-adjusted p = 0.018). Genetically predicted longer television viewing was linked to increased odds of PsA (OR = 2.205, 95% CI = 1.089–4.463, FDR-adjusted p = 0.028) and RA (OR = 1.006, 95% CI = 1.002–1.010, FDR-adjusted p = 0.004). Walking for pleasure showed a nominal inverse association with PsA, and computer use showed a nominal inverse association with RA. Neither association remained significant after FDR correction. No evidence of associations with the broad self-reported OS diagnosis was observed. Reverse MR analyses showed lower odds of Walking for pleasure (OR = 0.662, 95% CI = 0.484–0.906, FDR-adjusted p = 0.013) and Other exercises (OR = 0.651, 95% CI = 0.490–0.864, FDR-adjusted p = 0.006) for genetic liability to RA. RA liability was also associated with longer television viewing time (β = 0.708, 95% CI = 0.251–1.165, FDR-adjusted p = 0.006). No reverse associations were observed for PsA. Conclusions: This bidirectional MR study identified several potential genetically predicted associations of domain-specific PA and SB traits with PsA and RA. The findings for television viewing and RA may suggest a potential bidirectional association. However, the results should be considered hypothesis-generating. These findings require independent replication and further validation before causal or clinical conclusions can be drawn.

Genes doi: 10.3390/genes17080938

Authors: Luojin Wu Chenghao Ou Xuan Liu Miaohan Yan Jinghan Guan Xinfeng Wang Liming Mao Qiuyun Xu Zhaoxiu Liu

Background: Ankylosing Spondylitis (AS) and inflammatory bowel disease (IBD) exhibit substantial pathophysiological overlap, including dysregulated innate immunity, barrier dysfunction, and Th17-mediated inflammation. However, whether Na+ overload-related genes (NRGs) exhibit shared transcriptional alterations in IBD and AS remains unclear. This study aimed to characterize the expression patterns of NRGs across IBD and AS and to identify candidate genes associated with both diseases. Methods: Differential expression analysis was performed to identify differentially expressed NRGs (DE-NRGs) in diseased tissues relative to normal tissues. Shared DE-NRGs between IBD and AS were screened and defined as common differentially expressed NRGs (Co-DE-NRGs). We then analyzed the correlations of these Co-DE-NRGs and explored their relationships with immune cell infiltration in target tissues. Four machine learning algorithms were applied to screen key NRGs associated with both IBD and AS. Potential therapeutic agents targeting these core biomarkers were predicted using drug–gene interaction databases, and molecular docking was conducted for further validation. Results: A total of 32 shared Co-DE-NRGs were identified for IBD and AS, with nine key regulatory NRGs recognized: CALR, CD63, CYBA, DYSF, HYOU1, IL1B, JAK1, MMP9, and STAT3. Exploratory MR analysis identified disease-specific associations between genetically predicted expression of NRGs and CD, UC, and AS. Genetically predicted STAT3 expression showed positive associations with CD and UC but an inverse association with AS and therefore did not represent a consistent risk factor across the three diseases. Furthermore, transcriptome-based drug-response analysis identified four candidate agents shared between AS and at least one IBD dataset: ciclosporin, BCL-LZH-4, BRD-K79669418, and CID-5951923. Exploratory molecular docking generated STAT3 binding poses for BCL-LZH-4 and CID-5951923, with DOCK Grid Scores of −35.321896 and −28.361128, respectively. CID-5951923 was selected for representative visualization of its predicted interaction with STAT3. Single-cell RNA-sequencing analysis identified tissue- and cell-type-specific STAT3 mRNA expression patterns in the analyzed IBD colonic and AS peripheral-blood datasets, with monocytes representing a major cell population exhibiting detected STAT3 expression in the AS dataset. Conclusions: These findings identify shared NRG-related transcriptional alterations in IBD and AS, with STAT3 emerging as a candidate gene associated with both diseases. Further experimental studies are required to determine whether these alterations reflect the involvement of NECSO and to evaluate their potential diagnostic or therapeutic relevance.

Genes doi: 10.3390/genes17080937

Authors: Francesco Maria Bogliardi Pino D’Ambrosio Giorgia Quattromini Giordana Di Mario Maria Grazia Pomponi Luca Miele Edoardo Vergani Giuseppe Zampino Antonio Liguori Marcella Zollino Antonino Crinò

Maternal uniparental disomy of chromosome 15 [UPD(15)mat] and imprinting defects account for about 30% of cases of Prader–Willi syndrome (PWS). Mosaic UPD(15)mat is rare and may escape routine testing. We describe a 45-year-old male patient in whom persistent clinical suspicion of PWS was not genetically confirmed by repeated methylation-based analyses. Clinical manifestations included neonatal hypotonia with low birth weight, early hyperphagia, severe obesity, short stature, growth hormone deficiency, type 2 diabetes mellitus, dyslipidemia, and MASLD/MASH with compensated cirrhosis. He presented with very mild neurodevelopmental impairment. Following the detection of proteinuria and microalbuminuria from age 22 years, focal segmental glomerulosclerosis was diagnosed upon renal biopsy. A family history of cerebrovascular events was recorded. Combined SNP-array and MS-MLPA analyses across tissues established a diagnosis of PWS due to mosaic UPD(15)mat. The mosaic fraction, estimated by SNP-array, was approximately 10% in peripheral blood and 40% in buccal cells; MS-MLPA detected abnormal methylation only in buccal cells, explaining the previous negative blood-based results. Exome sequencing identified the paternally inherited pathogenic NOTCH3 variant NM_000435.2:c.3016C>T, p.(Arg1006Cys). Subsequent brain MRI showed chronic vascular-type leukoencephalopathy consistent with CADASIL, despite the absence of overt ischemic events in the proband. Collectively, these investigations established a dual molecular diagnosis of PWS due to mosaic UPD(15)mat and NOTCH3-related CADASIL. This report highlights the pivotal role of clinical genetics in assessing the precise diagnosis in rare diseases. With respect to PWS, it demonstrates that mosaicism can lead to a missed diagnosis when the genetic investigation is limited to peripheral blood. In addition, following the diagnosis of CADASIL, and based on the available evidence linking NOTCH3 to renal physiology and disease, we discuss whether NOTCH3-related renal microangiopathy may have contributed to the renal phenotype. However, given the patient’s multiple renal risk factors, FSGS was considered most likely multifactorial, and a causal association with CADASIL cannot be established from this single case.

Genes doi: 10.3390/genes17080936

Authors: Fawang Liu Lei Pan

Background/Objectives: This study aims to reveal the physiological and molecular regulatory mechanisms of the genuine medicinal herb I. suzhouensis K. F. Zhai, Z. B. Han & S. B. Zhou (Wangzaozi) of Anhui province in response to drought stress, and clarify the regulatory patterns of drought adversity on the accumulation of its medicinal active ingredients. Methods: Mild natural drought treatment was applied to I. suzhouensis. Combined with Illumina high-throughput transcriptome sequencing and HPLC-MS/MS targeted metabolomics detection, this study jointly deciphered the dynamic changes in gene expression and metabolite accumulation of I. suzhouensis under drought. Key drought-responsive metabolic pathways, core regulatory genes and marker metabolites were screened. Results: A total of 56,823 high-quality unigenes were obtained via transcriptome sequencing, among which 23,580 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that DEGs were predominantly enriched in pathways, including plant hormone signal transduction, phenylpropanoid biosynthesis, flavonoid biosynthesis and photosynthesis. A total of 4171 metabolites were qualitatively and quantitatively characterized via metabolomics, and 1632 differentially expressed metabolites (DEMs) were screened, mainly enriched in phenylpropanoid biosynthesis, tyrosine metabolism, flavone and flavonol biosynthesis pathways. Physiological measurements of antioxidant indices demonstrated that the activities of SOD and POD increased by approximately 2-fold, while PAL activity rose by 1.55-fold, and chlorophyll content decreased significantly. Multi-omics joint analysis indicated that mild drought stress modulates the expression of genes involved in phenylpropanoid, flavonoid and diterpenoid biosynthetic pathways, alters antioxidant enzyme activities, and coordinately regulates the formation of drought tolerance and the accumulation of bioactive compounds in I. suzhouensis. Conclusions: This study systematically elucidates the drought response mechanism of I. suzhouensis cultivated in northern Anhui province. It provides theoretical evidence and candidate core responsive gene resources for standardized cultivation of I. suzhouensis and precise regulation of medicinal quality in drought-prone production areas.

Genes doi: 10.3390/genes17080934

Authors: Mei Zhang Siyang Duan Ji Zhang Riwen Fei Xiuting Zhao Changbo Ji Li Liu

Background: Flower color is a primary determinant of ornamental value in flowering plants. Although the biosynthetic pathways of major petal pigments have been extensively documented, the systems-level mechanisms coordinating color diversification across multiple cultivars of Kalanchoe blossfeldiana remain less understood. This study aimed to establish a comparative metabolomic and transcriptomic framework to elucidate these mechanisms. Methods: Petal tissues were collected from five cultivars with white, yellow, orange, red, and purple–red flowers at the full-bloom stage. Metabolomics was performed for flavonoids and carotenoids using UPLC-MS/MS, and transcriptome sequencing was conducted via Illumina NovaSeq 6000. Integrative analysis of metabolome and transcriptome data, together with weighted gene co-expression network analysis, was employed to identify key metabolites, differentially expressed genes, and associated regulatory networks. Quantitative PCR was used to validate the expression patterns of key structural genes. Results: Petal color variation was shaped by coordinated flux partitioning between flavonoid and carotenoid networks rather than by isolated activation of single pathways. A metabolic relay pattern was observed in the phenylpropanoid–flavonoid axis, wherein shared upstream activation fed divergent downstream branches that directed accumulation toward distinct anthocyanin or flavonol profiles. Notably, yellow pigmentation relied more heavily on flavonoid flux than on carotenoid accumulation, and orange coloration arose from the synergistic co-accumulation of multiple pigment classes. Transcriptional module analysis identified gene networks associated with specific color phenotypes. Conclusions: These findings provide a systems-level understanding of pathway crosstalk in flower color formation and offer candidate targets for molecular breeding in K. blossfeldiana and related ornamental plants.

Genes doi: 10.3390/genes17080935

Authors: Daniel R. Martin Georgina K. Stebbings Shane M. Heffernan Robert M. Erskine Mark Antrobus Jon Brazier Sarah Lockey Alex L. Jackson Stephen Day Liam Kilduff Mark Bennett Stuart M. Raleigh Tom Cullen Malcolm Collins Yannis Pitsiladis Peter Callus Adam J. Herbert Alun G. Williams

Background/Objectives: Adenosine monophosphate deaminase deficiency has been implicated in impaired exercise capacity. We examined whether the AMPD1 C34T (rs17602729) genotype was associated with athlete status and performance in distance runners (DRs) and rugby union (RU) athletes. Methods: Participants included 621 elite male RU athletes, 666 elite/sub-elite male and female DRs, and 1029 male and female non-athletes (NA), all of European ancestry. Genotyping was performed using real-time PCR with TaqMan reagents. Genotype and allele frequencies were compared using χ2 tests, while performance data were analysed using Kruskal–Wallis H, Mann–Whitney U, one-way ANOVA, and t-tests, with Benjamini–Hochberg correction applied for multiple comparisons. Results: Genotype and allele frequencies did not differ between athletes and NA or between athlete groups. In all DRs, run times did not differ between genotypes, although participants with the CT genotype in the elite and elite male subgroups were up to 5% faster than CC and TT homozygotes. In RU, participants with the CC genotype played 13% longer per appearance than those with the CT genotype, while forwards and front five participants with the CC genotype played 13% and 26% longer per appearance than T-allele carriers, respectively. Front five T-allele carriers made 75% more clean breaks than the front five with the CC genotype despite playing for a shorter time, although this finding should be interpreted cautiously. Conclusions: In summary, while the AMPD1 C34T genotype was not associated with athlete status, the CC genotype was associated with greater RU playing time per appearance in forwards, and the CT genotype was associated with superior performance in elite DRs.

Genes doi: 10.3390/genes17080933

Authors: Mitică Ciorpac Vasile Alexe Alexandru-Cătălin Doroșencu Lucian-Eugen Bolboacă Janos Botond Kiss Dumitru Murariu Marian Tudor Mihai Marinov

Background/Objectives: The White-tailed Sea-eagle, Haliaeetus albicilla, experienced severe population declines throughout Europe during the nineteenth and twentieth centuries, followed by a remarkable recovery in recent decades. Although the genetic structure of northern and central European populations has been extensively investigated, the phylogeographic history and contribution of the lower Danube population to the mitochondrial genetic diversity of the species remain poorly understood. Methods: We analyzed mitochondrial control region (MT-CR HVR1) sequences from White-tailed Sea-eagles breeding in the Danube Delta Biosphere Reserve (DDBR) and integrated these data with previously published sequences covering the species’ distribution across Europe and Asia; a total of 480 samples were examined. Results: The analysis revealed 47 haplotypes, including 11 haplotypes unique to the DDBR population. Phylogeographic analyses support the Scandinavian Peninsula as the ancestral source area of the species, followed by an early colonization of Central Europe and subsequent expansion into the Balkan Peninsula through the Danube corridor. The Romanian population exhibited the highest haplotype diversity among the investigated regions (Hd = 0.9367) and was characterized by numerous private haplotypes and a predominance of haplogroup C (approximately 76% of individuals), which was rare or absent in most northern and central European populations. Demographic analyses revealed significant evidence of recent population expansion following historical bottlenecks (Fu’s Fs = −5.736, p = 0.006), whereas gene-flow estimates indicated only moderate connectivity with neighbouring Balkan and Central European populations. Conclusions: The high frequency of private haplotypes, the absence of significant isolation-by-distance patterns, and the distinct distribution of mitochondrial haplogroups, characterized by the predominance of haplogroup C, suggest that the current DDBR population may have originated primarily through local demographic recovery rather than recent large-scale recolonization. Our results indicate that the lower Danube region represents an important reservoir of genetic diversity and support the hypothesis that the Danube Delta may have acted as a potential secondary refugium and center of diversification for H. a. in southeastern Europe.

Genes doi: 10.3390/genes17080932

Authors: Andrey Timofeev Alexander Bratchikov Alexander Anufriev

Background/Objectives: The hierarchical organization of topological associating domains (TADs) is a fundamental feature of three-dimensional genome architecture, yet its systematic characterization remains challenging due to the scale-dependent nature of conventional detection methods. Here, we applied hyperbolic embedding into a Poincaré disc to analyze TAD hierarchies from Hi-C data. Methods: Genomic loci were projected onto the disc such that the radial coordinate encodes hierarchical depth: subTADs localize near the center, while metaTADs shift toward the periphery. The method was validated on ten cell lines, including the isogenic MCF10A/MCF7 pair, and does not require manual parameter tuning across resolutions. Results: In the MCF10A/MCF7 isogenic system, neoplastic transformation was associated with a redistribution of the hierarchy: the number of small TADs (levels 1–3) decreased by 6.7%, whereas large TADs (levels 4–6) increased by 4.7%, with the largest domains (level 6) showing a 33.9% increase. Comparison with standard approaches—Insulation Score (IS) and Directionality Index (DI)—yielded an average Jaccard index of 0.568 and F1 score of 0.718 against DI. Conclusions: Unlike IS and DI, which operate at fixed scales, the proposed approach recovers the full TAD hierarchy from a single embedding, enabling cross-resolution and cross-cell-line comparisons without parameter reoptimization. These results demonstrate that the Poincaré disc method provides a robust, interpretable, and scale-invariant framework for detecting hierarchical chromatin rearrangements associated with cancer.

Genes doi: 10.3390/genes17080931

Authors: Josep De Alcaraz-Fossoul Samantha J. Sawyer

Background/Objectives: Latent fingerprints (LFs) have been a cornerstone of forensic identification through conventional friction ridge pattern analysis; however, the microbial communities they harbor remain a largely untapped source of information. Estimation of the time-since-deposition (TsDp) of LFs is still an unresolved challenge in forensic science, as existing 2D and 3D imaging methodologies provide limited temporal resolution. This study investigated whether temporal shifts in LF-associated microbiota could potentially complement dating approaches via genetic analyses. Methods: LFs were collected from two healthy donors from both hands, pre- and post-hand washing, across three time points spanning 192 h (8 days) under monitored, but uncontrolled, indoor conditions. LF friction ridges were optically examined via 2D and 3D imaging, while microbial communities were characterized by 16S rRNA gene sequencing targeting the V3-V4 region. Microbial profiles were analyzed to distinguish temporally stable core microbiota from transient taxa (alpha and beta diversity) and to statistically identify microbial panels associated with donor, handedness, hand-washing status, and/or temporal succession. Results: A stable core microbiota, dominated by Actinobacteria and Bacilli, persisted across donors, handedness, hand-washing status, and time points. Transient low-abundance taxa, including Nitriliruptoria and Phycisphaerae, exhibited temporal fluctuations influenced by donor characteristics, hand-washing status, and post-deposition interval. Upon excluding time-invariant stable taxa, donor-specific biological profiles comprising 32 and 28 class-rank taxa were selected for each donor, revealing individualized patterns of microbial dynamics. Conclusions: LF-associated microbiomes contain both stable and temporally dynamic taxa, with the potential to provide personalized biological information for TsDp estimation. These preliminary findings contribute to the molecular toolkit of forensic microbiomics by laying the foundation for prospective multimodal models integrating LF microbial and topographical data to improve the temporal interpretation of crime evidence touched by bare hands. Further validation with broader donor cohorts and environmental conditions are essential before operational forensic implementation.

Genes doi: 10.3390/genes17080930

Authors: Xuebing Zhu Xiaozhu Guo Lihui Wang Shipeng Yang Xuemei Sun

Background: Clematis tangutica (Maxim.) Korsh. is a Tibetan medicinal plant, but its chloroplast genome and plastid gene evolution remain unexplored. Here, we assembled the complete chloroplast genome of C. tangutica and investigated the adaptive evolution of the ycf2 gene. Methods: Chloroplast DNA was extracted from fresh leaves and sequenced on the Illumina HiSeq PE150 platform. We then performed comprehensive genomic analyses, including genome structure characterization, repeat and SSR identification, comparative genomics, and positive selection analysis of the ycf2 gene. Results: The genome is 159,584 bp with a typical quadripartite structure, containing 134 genes and 23 SSRs. Comparative analyses revealed that ycf2 is the most variable gene among the 13 divergent loci identified. Positive selection analysis detected 12 significant sites in ycf2, all clustered in the middle region of the protein. Conclusions: This study provides the first complete chloroplast genome resource for C. tangutica, offers new insights into the adaptive evolution of ycf2 in Ranunculaceae, and yields molecular markers applicable to population genetics, phylogenetic studies, and conservation planning for this species of medicinal importance.

Genes doi: 10.3390/genes17080929

Authors: Lajos Molnár Viktor Stéger Petra Zenke

Background/Objectives: African swine fever (ASF) has caused substantial wild boar (Sus scrofa) mortality across Europe and prompted intensive density-reduction measures, yet its long-term effects on population genetics remain poorly understood. To our knowledge, this is the first study to compare genetic diversity, population structure, demographic signatures, and wildlife forensic identification parameters in the same wild boar population before ASF emergence and after several years of ASF-related management. Methods: Wild boar samples collected before ASF emergence in Hungary (n = 67) were compared with samples collected after several years of ASF-related management from the same geographic area (n = 65). All 132 individuals were genotyped at 13 tetrameric microsatellite loci. Diversity was assessed using allelic richness, allele number, and heterozygosity; differentiation using F-statistics, analysis of molecular variance, and discriminant analysis of principal components; demographic history using a two-phase mutation model; and forensic performance using probability of identity and probability of identity among siblings. Results: The post-ASF population showed lower genetic diversity and significant temporal differentiation. Paired Wilcoxon tests indicated a significant reduction in the number of alleles, whereas changes in heterozygosity were not significant. Bottleneck analyses provided no robust evidence of a recent genetic bottleneck. Forensic discrimination power declined modestly while remaining sufficient for individual identification. Conclusions: Because no contemporaneous unaffected reference population was available, these changes cannot be attributed specifically to ASF or management rather than to genetic drift or natural turnover, although they are consistent with sustained demographic disturbance. Nevertheless, this study provides the first temporal genetic comparison of a European wild boar population before ASF emergence and after several years of ASF-related management and demonstrates that a routinely used STR marker panel remains suitable for wildlife forensic individual identification despite these genetic changes.

Genes doi: 10.3390/genes17080928

Authors: Xin Yang Rongrong Pan Fan Yu Huidan Wu Neil Manish Shah Hong Li

Background: CLTC-related neurodevelopmental disorder is a rare condition primarily characterized by global developmental delay (GDD) and intellectual disability (ID). To date, approximately 41 cases involving CLTC gene alterations have been reported. We present the first individual with a complete deletion of the CLTC gene. Methods: The proband is a male from a non-consanguineous family, presenting with congenital nystagmus, hypotonia, GDD, and autism spectrum disorder (ASD). Chromosomal microarray analysis and trio exome sequencing were performed. A systematic review of previously reported CLTC variant cases was conducted to delineate the phenotypic spectrum. Results: A de novo 363-kb heterozygous deletion at 17q23.1 spanning the entire CLTC gene was identified. The systematic review confirmed GDD/ID as core features and revealed various ocular abnormalities in a subset of cases. These findings indicate that the clinical phenotype extends beyond neurodevelopment, with multi-system involvement. Conclusions: The phenotypic heterogeneity of CLTC-related disorders underscores the need for comprehensive physical examination to identify extra-neurological manifestations. Accurate diagnosis relies on integrating detailed clinical phenotyping with comprehensive genomic testing. Early, precise diagnosis facilitates multidisciplinary management, informed genetic counseling, and the establishment of long-term surveillance protocols.

Genes doi: 10.3390/genes17080927

Authors: Jorge Carretero-García David Varillas-Delgado

Background/Objectives: The physiological adaptations required to sustain elite football performance are influenced by both genetic background and dynamic biochemical responses, although their interaction across a full competitive season remains insufficiently characterized. This study aimed to examine the association between polygenic profiles and longitudinal biochemical adaptations in professional football players. Methods: Forty male professional football players competing in the Spanish league were monitored across two consecutive seasons. Blood samples were collected at six time points representing different phases of the competitive cycle. Biomarkers related to muscle metabolism, iron status, and hepatic function were analyzed. Polygenic profiles were calculated using Total Genotype Scores (TGS) for muscle performance, hepatic resilience, and metabolic efficiency. Associations were initially explored using Pearson correlations and subsequently evaluated using linear mixed-effects models accounting for repeated measurements within subjects. Results: Exploratory correlation analyses identified several associations between polygenic profiles and biochemical markers. Muscle performance TGS was inversely associated with serum iron (r = −0.36, p = 0.017) and positively associated with CK (r = 0.32, p = 0.041), Hb (r = 0.29, p = 0.046), and Hct (r = 0.33, p = 0.024). Hepatic resilience TGS showed inverse associations with ALT (r = −0.39, p = 0.012), urea (r = −0.51, p = 0.011), and BUN (r = −0.51, p = 0.011). Metabolic efficiency TGS was negatively associated with AST (r = −0.43, p = 0.044), ALT (r = −0.33, p = 0.025), and GGT across multiple time points (p = 0.001–0.013). However, although several nominal associations emerged in linear mixed-effects models accounting for repeated measurements, none remained statistically significant after false discovery rate correction. These findings should therefore be interpreted as exploratory and hypothesis-generating. Conclusions: Polygenic profiles may be associated with inter-individual variability in biochemical adaptations throughout a competitive season. These findings suggest the integration of genomic and biochemical data in precision athlete monitoring, while highlighting causal relationships and predictive applications require further investigation.

Genes doi: 10.3390/genes17080926

Authors: Xiaozhen Zhu Qifeng Lu Changqiu Liu Xinghua Hu Jiatong Ye Tao Deng Yunbo Duan Yufeng Wang

Background: Siraitia grosvenorii (monk fruit) is a dioecious medicinal crop native to southern China, yet its terpene synthase (TPS) gene family and the molecular basis of floral sexual dimorphism remain unexplored. Methods: Genome-wide identification of the TPS gene family was performed using HMMER and BLAST-based approaches. Phylogenetic classification, gene structure and conserved motif characterization, and comparative synteny analyses were conducted. Transcriptome data from leaves and fruits at different developmental stages were analyzed for tissue-specific expression profiling. Promoter cis-element analysis, protein–protein interaction network prediction, and molecular docking were performed to characterize the fruit-specific candidate SgTPS49. Results: A total of 58 SgTPS genes were identified and classified into six subfamilies, with TPS-a and TPS-b comprising 72.4% of the family. Approximately 88% of SgTPS genes arose from lineage-specific tandem duplication. Female flowers exhibited monoterpene-dominant scents and smaller corollas, whereas male flowers displayed a mid-morning sesquiterpene burst and greater morphological variation. SgTPS49 was specifically upregulated at 20 days post-pollination and possessed a unique promoter architecture devoid of classical hormone-responsive elements. Molecular docking supported its annotation as a putative monoterpene synthase with favorable GPP binding. Conclusions: This study provides the first comprehensive genomic resource for the SgTPS family in S. grosvenorii, reveals significant sexual dimorphism in floral traits, and identifies SgTPS49 as a key candidate for future functional validation.

Genes doi: 10.3390/genes17080925

Authors: Andrey Vl. Timofeev Alexander Bratchikov Alexander Anufriev

Background: DNA methylation is a key epigenetic mechanism whose dynamics are closely linked to ageing. Modern epigenetic clocks predict biological age based on the average methylation level. The concept of “epigenetic rejuvenation” posits that at early stages of development, the biological age of the embryo may decrease, reaching a minimum (“ground zero”) at the gastrulation stage. However, standard averaging methods may not account for important rearrangements in the internal structure of methylation. Objective: To apply the apparatus of information theory and topological data science to the analysis of scNMT-seq data and to test whether DNA methylation entropy decreases from stage E4.5 to E6.5, which would correspond to an approach towards the biological zero state. Methods: Publicly available scNMT-seq data (GSE121690) were analyzed. Five entropy measures were calculated for each cell (Shannon, Renyi, Tsallis, LZ-complexity, local gradient entropy (entropy of variations in the smoothed histogram of the methylation distribution), and persistent entropy (PE)—a topological complexity measure). For the five-dimensional entropy feature space, a Rips complex was constructed, and persistence diagrams H_0 and H_1 were computed. Results: All five entropy measures decreased significantly, with LZ complexity showing the largest relative reduction (−28.4%) and the strongest independent signal (partial r = −0.181). Among all the complexity measures studied, LZ complexity exhibited the largest relative reduction, underscoring its heightened sensitivity to the progressive ordering of the epigenetic landscape. Notably, the ternary encoding of LZ complexity showed strong correlation with Shannon entropy (r = 0.71), indicating that algorithmic complexity, when accounting for partial methylation states, aligns closely with statistical entropy while retaining sensitivity to spatial order. The consistency of results across binary and ternary encodings confirms the robustness of LZ complexity as a structural biomarker. Persistent entropy confirmed the general dynamics (decrease from 15.91 to 14.89, p = 0.01). Topological analysis of the multidimensional space revealed a qualitative reorganization: at stage E6.5, stable cyclic structures (H1) emerge, while at E4.5 the space is dominated by a single large-scale cycle. Null model validation confirmed that the observed H1-cycles are genuine topological features rather than random fluctuations. Comprehensive topological characterization showed that normalized persistent entropy increases from 0.846 to 0.882 (p < 0.001), while maximum persistence decreases from 0.446 to 0.218 (p < 0.001), reflecting a transition from a homogeneous state to structured diversification—multiple, evenly distributed cycles corresponding to distinct cell lineages. Consistent with this, regional disorder (RE/RD) at the single-cell level decreases from E4.5 to E6.5 (RE: −25.5%, RD: −27.4%, p < 10−13), while global entropy also decreases, together painting a picture of epigenetic rejuvenation as ordered consolidation at the whole-genome scale. An SVM model trained on 15 entropy and structural features achieved stage classification with an accuracy of 93.4% and AUC of 0.981, confirming the diagnostic potential of the approach. Conclusions: The decrease in DNA methylation entropy from E4.5 to E6.5 corresponds to an approach to “ground zero”—the point of minimum biological age in embryogenesis—and supports the hypothesis of a link between decreasing entropy and epigenetic rejuvenation. The addition of topological analysis reveals the hidden organization of epigenetic diversity, showing that ordering does not lead to homogenization but is accompanied by the formation of distinguishable cell lineages.

Genes doi: 10.3390/genes17080924

Authors: Rudy Sleigh Stella K. Kantartzi

Background: Nitrogen (N) availability is an important factor affecting soybean growth, photosynthetic capacity, and seed development. Identification of genomic regions associated with N-responsive traits may enable the development of cultivars with enhanced performance under reduced fertilizer inputs. Methods: A soybean diversity panel consisting of 193 accessions was evaluated under N-deficient (N−) and N-sufficient (N+) conditions during the 2024 and 2025 growing seasons. Best linear unbiased predictors were estimated for SPAD area under the curve (SPAD AUC) and 1000-seed weight (SW) under N− and N+ conditions and used for genome-wide association analysis with 37,429 single-nucleotide polymorphism (SNP) markers. Results: Six loci associated with SPAD AUC under N−, four with SW under N−, and 10 with SW under N+ exceeded the Bonferroni-corrected significance threshold, whereas no significant loci were detected for SPAD AUC under N+. Candidate genes near significant loci encoded proteins including receptor-like kinases, WRKY transcription factors, peroxidases, and protein kinases, which are involved in signal transduction, transcriptional regulation, oxidative stress responses, carbohydrate metabolism, and developmental processes. Allelic effect analyses revealed significant phenotypic differences between favorable and unfavorable alleles at representative loci, supporting the biological relevance of the identified associations. Conclusions: These findings provide insight into the genetic architecture of chlorophyll accumulation and seed weight under contrasting N environments and identify candidate loci that may facilitate the improvement of nitrogen-use efficiency and agronomic performance in soybean.

Genes doi: 10.3390/genes17080923

Authors: Emily Payne Sara M. Sarasua Curtis Rogers Rebekah Martin Katy Phelan Laura Beamer Luigi Boccuto

Objectives and Background: Individuals with Phelan–McDermid Syndrome (PMS) present with a variety of symptoms, including a breadth of behavioral issues. Clinically assessing behavior in PMS remains challenging due to the overabundance of behavioral assessments and the lack of tools validated explicitly for use in individuals with intellectual disability (ID) and neurodevelopmental disorders. This review sought to suggest which assessment tools would best clinically assess behavior in individuals with PMS. Methods: Validated behavioral assessment tools were identified using a systematic search of the literature, and relevant data for each assessment were extracted. The consensus guidelines for PMS were reviewed. Results: This review identified 131 validated assessment tools that were categorized by the intended age group and into specific behavioral domains: Autism spectrum disorder (ASD) screening, adaptive behavior, restricted and repetitive behaviors, challenging/disruptive behaviors, mental health screening, and other miscellaneous behaviors such as avoidance and impulsivity. Discussion: Based on the 2023 consensus guidelines, suggestions were given on which tools would be best for assessing various symptoms and behaviors in PMS. Choosing the best assessment tools to appraise behavior and related symptoms in individuals with PMS will aid clinicians in decision-making and lead to more personalized treatment plans.

Genes doi: 10.3390/genes17080921

Authors: Pengcheng Chen Yindan Lin Jingjia Li Yiwei Gu Xueyun Zhang

Background: Cellular senescence exerts a complex influence on BRCA progression and TME remodeling. However, the specific roles of ASIGs in regulating the TME and determining patient outcomes remain unclear. Methods: Using TCGA (training), METABRIC (validation), and single-cell RNA-seq datasets, we systematically characterized ASIGs in BRCA. Prognostic ASIGs were identified to define molecular subtypes and construct a 17-gene LASSO-Cox risk model, which was integrated with clinical factors to develop a prognostic nomogram. Microenvironmental features and cell–cell communication networks were deconstructed using computational deconvolution and single-cell algorithms (SCISSOR and CellChat). Results: We established a robust 17-gene ASIG-based prognostic signature that effectively stratified BRCA patients into high- and low-risk groups and served as an independent prognostic predictor (HR = 3.94, p < 0.001). The nomogram accurately predicted 1-, 3-, and 5-year overall survival. Notably, the two risk groups exhibited strikingly distinct TME landscapes. The low-risk group was characterized by a coordinated, B cell-centric immune network, whereas the high-risk group displayed T cell exhaustion and immunosuppressive myeloid infiltration. Conclusions: The ASIG-based prognostic risk model is independent of traditional clinicopathological factors, providing a robust tool for patient risk stratification and offering biological insights into senescence-driven microenvironmental remodeling.

Genes doi: 10.3390/genes17080922

Authors: Chung-Ying Lee Hsu-Jui Pan Yu-Cheng Lee Hieu Duc Nguyen Yi-Chun Ni Ke Xin Yee Man Thi Nguyen Yung-Fu Wu Kuen-Haur Lee

Background/Objectives: Early-onset colorectal cancer (EOCRC), defined as colorectal cancer diagnosed before 50 years of age, is increasing worldwide and may exhibit molecular features distinct from late-onset colorectal cancer (LOCRC). This study aimed to identify EOCRC-associated genes and evaluate the functional relevance of the leading candidate. Methods: Public transcriptomic datasets were used for age-stratified candidate-gene discovery and validation. Overall survival analysis prioritized candidates, followed by loss-of-function studies and pathway-focused analyses in colorectal cancer cell lines. Results: CEMIP, NKD2, and FOXQ1 were elevated in the EOCRC groups in the discovery and integrated validation analyses. Among them, only CEMIP was significantly associated with poorer overall survival. HCT116 and HT29 cells showed relatively high endogenous CEMIP expression, and CEMIP knockdown reduced relative viable cell biomass and migration in wound-healing and Transwell assays. CEMIP-associated transcripts were enriched in several pathways, including Hedgehog, Wnt/β-catenin, and TGF-β signaling. In TCGA colon adenocarcinoma samples, CEMIP correlated most strongly with PTCH1; however, the correlations with other Hedgehog components were weak or absent. CEMIP silencing decreased PTCH1 and GLI1 transcripts while increasing SMO, suggesting a coordinated but non-linear relationship. Conclusions: CEMIP is an EOCRC-associated candidate biomarker and a functional contributor to colorectal cancer cell viability and migration. Its relationship with PTCH1-related Hedgehog signaling is exploratory and warrants direct mechanistic validation.

Genes doi: 10.3390/genes17080920

Authors: Phonemany Thammachak Ton Huu Duc Nguyen Rinrapat Nitipatpornpanya Anh Huynh Luu Edem Uduak Linus Thitipong Panthum Kednapat Sriphairoj Sittichai Hatachote Satid Chatchaiphan Chaiwut Grudpan Jarungjit Grudpan Suphada Kiriratnikom Jiraboon Prasanpan Orathai Sawatdichaikul Worapong Singchat Kornsorn Srikulnath

Background/Objectives: Clariid catfishes are a cornerstone of Southeast Asian aquaculture, where intensive breeding and interspecific hybridization have significantly decreased genetic diversity. To address the limited understanding of growth-governing molecular determinants, we characterized the genomic architecture and evolutionary dynamics of the myogenic factor 5 (Myf5) gene, a master regulator of myogenesis, in 511 individuals from 17 catfish populations in Thailand. Methods: A total of 511 individuals representing 17 catfish populations were analyzed. A 334-bp fragment of exon 1 of the Myf5 gene was sequenced using Illumina short-read technology. Genetic diversity indices were calculated to evaluate sequence variation, population structure, and selective constraints acting on the locus. Results: Sequence analysis of a 334-bp segment of exon 1 using Illumina short-read technology identified 17 haplotypes and 92 variable sites, which revealed moderate allelic richness despite low overall nucleotide diversity (π ≈ 0.008). Evolutionary analyses indicated that the Myf5 locus is governed by stringent purifying selection (ω = 0.063), wherein site-specific constraints preserve the stability of the α-helix folding architecture, which is essential for myogenic regulation. Population genetic analyses revealed substantial differentiation among taxa (56% among-population variation), while Bayesian clustering successfully resolved a hierarchical structure (K = 2) that distinguished Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus. These findings demonstrate that species-specific Myf5 haplotypes serve as diagnostic markers for identifying parental species and assisting in the identification of F1 hybrid stocks. Conclusions: Overall, this study provides the molecular markers for species identification, broodstock authentication, hybrid detection, and sustainable genetic management of Thai Clariid resources, which are critical for balancing production efficiency with the conservation of native biodiversity in Southeast Asia.

Genes doi: 10.3390/genes17080919

Authors: Carlos Casanova Claudia Valencia-Peña Wilmar Saldarriaga-Gil Edgar Lozano-Cruz Andrés Castillo

Background/Objectives: Primary open-angle glaucoma (POAG) is a complex multifactorial optic neuropathy involving genetic, vascular, oxidative, inflammatory, and neurodegenerative mechanisms. Despite advances in genome-wide studies, the contribution of genetic variants remains incompletely characterized in underrepresented Latin American populations. This study aimed to characterize the genetic landscape of POAG in a Colombian cohort by identifying previously reported glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers and integrating these findings into biologically relevant pathways. Methods: An exploratory descriptive study was conducted in 21 Colombian patients with confirmed POAG. Whole-exome sequencing (WES) was performed at an average sequencing depth of approximately 100×. Variants were quality-filtered, functionally annotated, and prioritized within 446 POAG-associated genes retrieved from DisGeNET. Previously reported glaucoma-associated variants and rare candidate variants were identified, while pharmacogenomic variants related to latanoprost and timolol response were evaluated using ClinPGx/PharmGKB. Identified genes were classified according to major biological pathways relevant to glaucoma pathophysiology. Results: Of the 446 POAG-associated genes, 381 were detected in the patients’ exomes. A total of 10,220 molecular variants were identified, of which 1,187 synonymous variants were excluded, leaving 9,033 variants for downstream analysis. Among these, 955 were non-synonymous SNVs, including 26 variants previously reported in association with glaucoma and 929 potentially novel coding variants. Previously reported variants included loci in SIX6, LOXL1, CYP1B1, NOS3, and SOD2. Two rare candidate variants (minor allele frequency <1%) were identified in FMNL2 and C3. Pharmacogenomic variants in PTGS1, ADRB1, and ABCC4 with potential implications for response to latanoprost or timolol were also detected. Functional integration highlighted pathways involving oxidative stress, extracellular matrix remodeling, vascular regulation, neurodegeneration, and inflammation. Conclusions: This exploratory analysis identifies known glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers in Colombian patients with POAG. The findings support a multifactorial biological framework involving interconnected oxidative, structural, vascular, neurodegenerative, and inflammatory pathways. The FMNL2 and C3 variants represent candidates for further investigation, while the identified pharmacogenomic variants highlight the potential relevance of genomic profiling for personalized glaucoma management. Larger ancestry-informed case–control studies are required to validate these observations and determine their clinical significance.

Genes doi: 10.3390/genes17080918

Authors: Job Pakisi Vicente Martín-Sánchez Cruz S. Sebastião Sergio Rodríguez Núñez Celina Capingala-Pakisi Victor Moreno Enrique Bayón-Darkistade

Background/Objectives: Non-communicable diseases (NCDs) are a leading cause of death globally, particularly in low- and middle-income countries undergoing rapid epidemiological transition. Apolipoprotein E (APOE) polymorphisms have been implicated in modulating risk for cardiovascular and neurodegenerative diseases. This study characterizes the distribution of APOE alleles and genotypes in an Angolan population sample and explores associations with demographic variables. Methods: A cross-sectional study was conducted in Huambo Province, Angola, with 200 unrelated adults aged 40–70 years. Genotyping for ε2, ε3, and ε4 was performed via real-time PCR. Allelic and genotypic frequencies were calculated and tested for Hardy–Weinberg equilibrium. Associations with sex, age (≤54 vs. >54 years), and urban vs. rural residence were analyzed. Results: ε3 was the most frequent allele (63%), followed by ε4 (24.8%) and ε2 (12.2%). The ε3 homozygous genotype was prevalent (44%), with ε3/ε4 (19%) and ε2/ε3 (18%) also common. Significant Hardy–Weinberg disequilibrium was observed due to excess ε4 homozygotes and deficit of certain heterozygotes; possible contributing factors, including population structuring, convenience sampling, and technical aspects of genotyping, are discussed. ε4 prevalence was higher in urban residents and older individuals, while ε3 and ε2 were more common in rural areas and younger participants. Conclusions: Our results reveal notable genetic heterogeneity and highlight the epidemiological and evolutionary importance of ε4 in Angola. The findings underscore the need for integrating population genomics into public health strategies targeting NCD prevention, especially in rapidly urbanizing African contexts.

Genes doi: 10.3390/genes17080917

Authors: Kaichen Tang Shiqi Fan Rui Zhang Miao Sun Dong-Lai Ma Xue Zhang

Background: DNA Ligase 4 (LIG4) catalyzes the final ligation step during V(D)J recombination. Biallelic pathogenic variants in LIG4 cause severe combined immunodeficiency (SCID), a life-threatening immunodeficiency characterized by the lack of mature T and B cells. Case Presentation: An 18-year-old male exhibited widespread verrucous and keratotic cutaneous lesions across the face, neck, and extremities. The proband manifested early-onset short stature, chronic malnutrition, recurrent pulmonary infections with bronchiectasis, chronic diarrhea, and bilateral tenosynovitis. Immunophenotyping revealed persistent panhypogammaglobulinemia, absent B cells, reduced T and natural killer (NK) cells, and nearly undetectable naïve T cells. Both α-HPV and β-HPV were detected in the cutaneous lesions. Compound heterozygous LIG4 variants (hg19, NM206937.2, c.833G > T; p.Arg278Leu inherited from the mother; c.833G > A; p.Arg278 His inherited from the father) were identified. Conclusions: This study reports a proband with LIG4 syndrome presenting with rare phenotypes of multiple viral warts and combined lymphopenia of T, B, and NK cells. This proband harbors compound heterozygous variants at the same codon (c.833G), which not only confirm the clinical diagnosis but also enrich the known phenotypic spectrum of LIG4 syndrome.

Genes doi: 10.3390/genes17080916

Authors: Van Huynh Guliang Wang Karen M. Vasquez

Background/Objectives: Cisplatin is used in the treatment of ovarian cancer; however, the development of resistance, often due to the efficient repair of cisplatin-induced DNA damage, remains a major barrier to effective therapy. Among these lesions, DNA interstrand crosslinks (ICLs) are particularly cytotoxic because they prevent DNA replication and transcription. HMGB2, a member of the high-mobility group box (HMGB) protein family, can bind DNA lesions and has been implicated in genome maintenance and DNA repair. This study investigated whether HMGB2 contributes to the processing of cisplatin-induced DNA damage and modulates cisplatin sensitivity in human ovarian cancer cells. Methods: HMGB2 expression was suppressed by siRNA in cisplatin-sensitive A2780 and cisplatin-resistant CP70 human ovarian cancer cells. Cellular responses to cisplatin were assessed using clonogenic survival assays, cell cycle analysis, Western blotting, slot blot analysis, and modified alkaline comet assays. Results: HMGB2 depletion reduced clonogenic survival in cisplatin-resistant CP70 cells and increased the sub-G1 population, indicating enhanced apoptotic DNA fragmentation following cisplatin treatment in both cell lines. Depletion of HMGB2 resulted in increased persistence of cisplatin–DNA adducts and impaired ICL processing, as demonstrated by persistent DNA damage over time and reduced ICL unhooking efficiency. DNA damage response signaling following cisplatin treatment was also altered by HMGB2 depletion in both cell lines, whereas the expression levels of key DNA repair proteins were unchanged. Conclusions: Our findings demonstrate that HMGB2 is involved in the cellular response to cisplatin treatment by promoting the efficient processing of cisplatin DNA adducts, particularly ICLs, thereby modulating cisplatin sensitivity in human ovarian cancer cells. These findings suggest that targeting HMGB2 may serve as a potential therapeutic strategy for overcoming cisplatin resistance in ovarian cancer.

Genes doi: 10.3390/genes17080915

Authors: Christina D. Sotiropoulou Christos K. Kontos Giannis Vatsellas Vasiliki Pappa Andreas Scorilas Sotirios G. Papageorgiou

Background: Circular RNAs (circRNAs) constitute an emerging research field, as these RNA molecules play a crucial role in cellular functions and the progression of various human pathologies. Little is known about alternative circularization leading to the formation of distinct circRNAs from the same primary transcript, the role of circRNAs with slightly different back-splice junctions (BSJs) resulting in very similar circRNA sequences—called circRNA isoforms—and the extent to which the same primary transcripts produce alternative circRNAs. In this study, we discovered alternative circRNAs produced by two apoptosis-related genes, BAX and BCL2L12, expressed in established human cell lines originating from myelodysplastic syndrome (MDS) and different types of acute myeloid leukemia (AML). Methods: After total RNA extraction from one MDS cell line and five AML cell lines, first-strand cDNA synthesis, and multiple nested PCRs with distinct sets of divergent primers (10 and 16 primer pairs for BAX and BCL2L12 circRNAs, respectively) annealing in each exon of BAX and BCL2L12 genes, amplicon libraries were prepared and sequenced by both nanopore sequencing and NGS. Detailed bioinformatic analysis was then performed, based on existing bioinformatic tools and our own algorithms. Results: Our approach led to the identification of 72 BAX circRNAs and 52 BCL2L12 circRNAs with distinct expression patterns in MDS and AML cell lines. Most of these circRNAs—either merely exonic or exonic–intronic—were detected for the very first time. Furthermore, several BAX circRNA isoforms were detected in a unique cell line. Moreover, the back-splice sites joined together to form the BSJ of each circRNA were non-canonical, in many cases. The identified circRNAs are predicted to sponge distinct sets of miRNAs, some of which are known to regulate the activity of pivotal pathways. Conclusions: Overall, our findings support the notion that alternative splicing and back-splicing lead to the production of tens of distinct circRNAs from the same human gene.

Genes doi: 10.3390/genes17080914

Authors: Qiangping Ma Jianqing Liang Jintian Li Juan Li

Objectives: Lung adenocarcinoma (LUAD) is molecularly heterogeneous, and the prognostic relevance of fatty acid metabolism (FAM) remains incompletely defined. We aimed to develop a concise FAM-associated prognostic signature and examine its associations with the immune microenvironment and candidate therapeutic vulnerabilities. Methods: TCGA-LUAD transcriptomic and survival data were integrated with MSigDB FAM gene sets. Univariate Cox and elastic-net Cox regression were used to derive a risk score. The locked formula was evaluated in a Japanese cohort (GSE31210) and a U.S. cohort (GSE72094). Immune-infiltration algorithms as well as TIDE, GDSC2, and CPTAC data were used for exploratory immune, drug sensitivity, and protein-level analyses. Results: The six-gene signature comprised CYP4B1, ACOXL, DPEP2, HPGDS, CA4, and ALOX15. High-risk patients had shorter overall survival in the TCGA and both external cohorts (GSE31210, log-rank p = 0.0039; GSE72094, p < 0.0001). The risk score remained independently prognostic after adjustment for age, sex, and clinical stage. High-risk tumours showed lower immune and stromal signals, greater immune exclusion, and a lower TIDE-predicted ICB response proportion. GDSC2 analyses and expression comparisons identified associations with predicted drug sensitivity and lipogenic target expression. Five detectable signature proteins were less abundant in tumours in CPTAC data. Conclusions: This signature stratified patients by prognosis in two geographically distinct external cohorts and generated testable metabolic and immune hypotheses. Prospective validation, assay standardisation, and functional studies are required before clinical use.

Genes doi: 10.3390/genes17080909

Authors: Jinghao Jin Zhaoyi Yi Hongyun Wang Lei Gong Yazhuo Zhang Weiyan Xie

Background/Objectives: Pituitary neuroendocrine tumors (PitNETs) frequently exhibit invasive behaviors that complicate clinical treatment. While cyclin-dependent kinase 5 (CDK5) and lymphokine-activated killer T-cell-originated protein kinase (PBK, also known as PDZ-binding kinase) are implicated in tumor progression, their reciprocal regulatory mechanism remains unclear. This study aims to elucidate the CDK5-PBK interaction in PitNETs and identify potential therapeutic agents targeting this pathway. Methods: We utilized proximity labeling and phospho-specific assays to characterize the CDK5 and PBK interaction in PitNET cell lines. Immunohistochemical analysis was performed on patient tumor tissues to evaluate clinical relevance. Artificial intelligence (AI)-based virtual screening was employed to discover dual-target inhibitors. The therapeutic efficacy of the identified compound, proguanil hydrochloride, was subsequently evaluated using in vitro functional assays, alongside in vivo xenograft animal models. Results: We identified a mutual phosphorylation loop between CDK5 (at S159) and PBK (at T9) that activates insulin signaling, thereby promoting cellular proliferation and invasion in PitNETs. Patient tumor analysis revealed that the co-expression of phosphorylated CDK5 (S159) and PBK (T9) significantly correlates with tumor invasiveness (p < 0.001). Through AI screening, proguanil hydrochloride was identified as a candidate dual-target inhibitor. In vitro assays confirmed that it effectively reduces tumor cell growth, while in vivo xenograft studies validated its capacity to inhibit tumor progression. Conclusions: The CDK5-PBK mutual phosphorylation axis serves as a key driver of invasiveness in PitNETs. Proguanil hydrochloride represents a promising candidate dual-target therapeutic agent capable of disrupting this pathway to suppress tumor growth.

Genes doi: 10.3390/genes17080913

Authors: Gulnur Zhunussova Nazgul Omarbayeva Aigul Zhunussova Diana Abdullayeva Liliya Skvortsova Nursultan Nurdinov Ainash Oshibayeva

Background: Germline PALB2 variants are associated with hereditary breast cancer risk, but their clinical impact in Central Asian populations remains largely uncharacterized. This case study aims to evaluate the clinical significance of PALB2 variants in two Kazakh women with early-onset breast cancer. Methods: Molecular genetic testing identified germline PALB2 pathogenic variants (NM_024675.4:c.18_22delGAAGC and NM_024675.4:c.1034T>G) in two Kazakh women with early-onset invasive ductal carcinoma. Clinical courses, treatment responses, and outcomes were followed. Results: Neither patient had a reported family history of breast or other malignancies. Patient 1, a 26-year-old pregnant woman, was diagnosed with stage IIIB luminal B, HER2-negative invasive ductal carcinoma and received neoadjuvant chemotherapy, radical surgery, radiotherapy, endocrine therapy, and subsequent treatment for metastatic disease. Despite an initial response, she developed extensive skeletal metastases and died from metastatic breast cancer. Patient 2, a 33-year-old woman, presented with de novo stage IV luminal B, HER2-negative invasive ductal carcinoma with hepatic metastases. Following multimodal treatment, including chemotherapy, surgery, radiotherapy, endocrine suppression, and systemic therapy for disease progression, she experienced further metastatic spread and ultimately died from breast cancer-related complications. Conclusions: Both patients exhibited aggressive clinical courses characterized by early disease onset, metastatic progression, and poor outcomes despite comprehensive treatment. These cases highlight the potential clinical significance of germline PALB2 variants in apparently sporadic breast cancer and underscore the importance of genetic testing, risk assessment, and genetic counselling in young breast cancer patients, particularly in underrepresented.

Genes doi: 10.3390/genes17080912

Authors: Federica Nozza Beatrice Bravi Lidia Fortaner-Uyà Alessia Giovanelli Marco Paolini Cristina Lorenzi Sara Spadini Greta D’Orsi Cristina Colombo Sara Poletti Francesco Benedetti

Background. Bipolar disorder (BD) is characterized by circadian rhythm disruptions, contributing to mood instability and recurrence. These rhythms are regulated by clock genes in the suprachiasmatic nucleus, including the CLOCK 3111T/C (rs1801260) polymorphism that has been linked to delayed sleep phase, insomnia, and altered circadian expression. Both circadian disruption and adverse childhood experiences (ACEs) correlate with white matter (WM) abnormalities. We hypothesized that rs1801260 moderates ACE effects on WM microstructure in BD. Methods. We enrolled 137 BD patients in depressive episodes. Participants underwent 3T MRI, rs1801260 genotyping and completed the Childhood Trauma Questionnaire. Moderation (PROCESS) tested genotype–ACE interactions on whole-brain fractional anisotropy (FA), axial diffusivity (AD), mean diffusivity (MD), and radial diffusivity (RD) values; voxel-wise TBSS (FSL Randomize) localized effects, with sex-stratified and GLZ analyses for genotype–sex interactions. Results. Significant rs1801260 × ACE interactions emerged for FA and RD across physical abuse, physical neglect, and emotional neglect. Higher ACEs were associated with lower FA/higher RD only in CLOCK rs1801260*C carriers, mainly females. TBSS showed physical abuse × rs1801260 interaction in the corpus callosum, internal capsule and corona radiata. A GLZ model with separate slopes confirmed physical abuse × sex × rs1801260 interactions on FA/RD, with effects specific to female CLOCK rs1801260*C carriers but genotype-independent in males. Conclusions. rs1801260 moderates the impact of early-life stress on WM integrity in BD, particularly in emotion-regulation tracts, with CLOCK rs1801260*C carriers showing greater vulnerability. Effects are genotype-specific in females but genotype-independent in males, possibly reflecting sex-dimorphic neurodevelopment driven by estrogen–androgen modulation of clock genes, HPA axis, and myelination.

Genes doi: 10.3390/genes17080911

Authors: Maria Giusy Bruno Giacomo Menichetti Angela Valentino Aqsa Javaid Francesca Belpinati Alessandra Ruggiero Maria Teresa Valenti Giovanna Paolone Fabio Cavaliere Elisabetta Trabetti Maria Grazia Romanelli Cristina Bombieri

Genetic mutations, altered RNA regulation, and protein aggregation are the main hallmarks of Parkinson’s disease (PD), a neurodegenerative disorder. Investigation into the molecular basis of the disease revealed that post-transcriptional regulation, specifically RNA processing, contributes to neuronal vulnerability in PD. Alterations in alternative splicing affecting genes involved in neuronal function and cellular homeostasis have been reported in PD, including SNCA, LRRK2, MAPT, PRKN, and BIN1. These alterations impact central neuronal pathways, including cytoskeletal maintenance, mitochondrial function, synaptic activity, oxidative stress, and intracellular trafficking. This review aims to provide an overview of alternative splicing in key PD gene transcripts, with a focus on their roles in pathogenesis and disease progression. Emerging data suggest that dysregulation of RNA binding proteins (RBPs) may influence RNA processing in PD. We will examine current evidence on the RNA regulatory networks in PD, highlighting the role of transcript isoforms and RBPs in neuronal dysfunction. Finally, we will discuss emerging experimental models such as 3D-brain organoids that offer new opportunities to investigate splicing regulation.

Genes doi: 10.3390/genes17080910

Authors: Danielle Devine Aaron Tien Haoting He Tracy Baust Rod Ghassemzadeh Jiuann-Huey Ivy Lin

Introduction: Congenital heart defects (CHD) occur in 1% of live births, with an estimated at least 33% of affected infants having genetic defects. It has become standard to screen children with CHD for genetic findings that could aid clinical decision-making, yet modern testing yields large volumes of information without understanding clinical utility. Genome-wide studies have identified associations between large copy number variants and neurocognitive outcomes in patients with CHD. Still, little research exists on the prognostic power of screening tests such as microarrays. The goal of this study was to determine if abnormal microarray results in infants with CHD were associated with worse clinical outcomes in the cardiac intensive care unit (CICU). Method: This was a single-center retrospective cohort study. The Society of Thoracic Surgery (STS) and Pediatric Cardiac Critical Care (PCICU) registries (PC4) were queried for all surgical admissions of neonates and infants between 1 January 2014 and 31 December 2019. Patient demographics, surgical details, and post-operative outcomes were collected for surgical admissions related to the patient’s index operation. A chart review was performed to ascertain microarray results, further genetic testing, and longitudinal outcomes. Patients without microarray results or long-term institutional follow-up were excluded. Wilcoxon rank-sum and chi-square tests were used to compare outcomes defined and collected in the PC4 registry between patients with normal and abnormal microarray results. Subgroup analysis was then performed using the same outcome measures to compare normal and abnormal microarray groups in children who required cardiac surgeries within 30 days of life and in children who presented with ventricular septal defect (VSD), atrioventricular septal defect (AVSD), aortic stenosis (AS), or Tetralogy of Fallot (TOF). Results: Of the 412 infants with surgical admissions to the CICU between 2014 and 2019, 43 infants had no longitudinal follow-up, and 65 infants had no microarray results. Three hundred and four infants were included in this study, of which 196 children had normal microarrays and 108 infants had abnormal microarrays. Both groups had similar distributions of gestational age and birth weight, but fundamental diagnoses and primary procedures differed significantly between groups (p < 0.005). STS score, deep hypothermic circulatory arrest (DHCA) time, and bypass time were each significantly lower in children with abnormal microarrays than in those with normal microarrays across the study. The patients with abnormal microarrays had a higher incidence of gastrostomy (G)-tube placement during their lifetime than infants with normal microarrays. On subgroup analysis, despite the differences in fundamental diagnoses and the fact that primary procedures differed significantly between normal and abnormal microarray groups that required cardiac surgery within 30 days of life, there were no detectable differences in the surgical and PCICU outcomes. DHCA time was once again significantly lower in the abnormal microarray subgroup in the second subgroup analysis. Conclusions: Our data indicate that microarray results have limited value in predicting immediate post-operative outcomes, but children with copy number variants should be included in future CHD research.

Genes doi: 10.3390/genes17080908

Authors: Tianyuan Nie Jiaman Li Siqi Ye Lin Wang Ruining Wang Xuyong Zhao Huawei Li Keshan Zhang Yaqiong Ye Mengmeng Zhao

Background/Objectives: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains the predominant genotype circulating in China and continues to evolve through mutation and recombination. Although NSP1 is recognized as a multifunctional nonstructural protein involved in immune regulation, its genetic variation among PRRSV-2 strains circulating in China has not been comprehensively characterized. Methods: In this study, 425 complete NSP1 sequences, primarily representing PRRSV-2 strains circulating in China, were analyzed, and 48 representative strains were selected for pairwise percent-identity visualization. Results: Pairwise nucleotide identity among the 48 representative strains was found to range from 80.1% to 100.0%, with the lowest value detected between AHBZ and SD-R, whereas pairwise amino-acid identity ranged from 79.6% to 100.0%, with the lowest value detected between AHBZ and HNhx. Among the 425 aligned amino-acid sequences, 290 variable sites and 93 completely conserved sites were identified. The broad-lineage distribution was composed of Lineage 1 (n = 79), Lineage 3 (n = 4), Lineage 5 (n = 21), and Lineage 8 (n = 321). A global FEL dN/dS of approximately 0.2979 was estimated from 379 non-recombinant unique haplotypes, and seven high-confidence candidate positively selected sites—42, 239, 255, 302, 367, 370, and 378—were supported by MEME, FEL, and FUBAR. A descriptive lineage-biased pattern concentrated in Lineage 5 was observed for NSP1β Val19Ile, corresponding to full-length NSP1 V199I. Eight candidate recombination events were identified using RDP4, and six representative events were further examined using SimPlot. Conclusions: Overall, NSP1 was found to be under predominant purifying selection while retaining localized variability, lineage-biased residue patterns, and candidate recombination signals that should be interpreted cautiously and validated experimentally.

Genes doi: 10.3390/genes17080907

Authors: Timur Nasrytdinov Dilyara Kaidarova Venera Israilova Saken Khaidarov Bayan Nurgaliyeva Slu Izmailova Gulmira Rapilbekova Marat Rabandiyarov Bibigul Abdygalyk Askar Aidarov Daulet Aidarov Aray Aidarova

Background/Objectives: Colorectal cancer (CRC) is molecularly heterogeneous, and the KRAS (Kirsten rat sarcoma viral oncogene homolog) genotype both governs eligibility for anti-EGFR (epidermal growth factor receptor) therapy and carries prognostic weight. Central Asian data are scarce: no Kazakhstani series has described the KRAS variant spectrum, linked it to survival, or reported mutation detection rates across specimen types and PCR platforms. Methods: We studied 332 patients with morphologically confirmed stage II–IV colorectal adenocarcinoma. KRAS status was determined in formalin-fixed paraffin-embedded (FFPE) tumor tissue by allele-specific real-time PCR (RT-PCR) covering six selected codon 12 and 13 variants. Overall survival (OS) was estimated by the Kaplan–Meier method for the whole cohort and with stage stratification. Separately, mutation detection rates were recorded in three non-overlapping groups of different patients: plasma RT-PCR on the Idylla platform (n = 30), plasma nanoplate digital PCR (dPCR) on QIAcuity One (n = 120), and a routine tissue RT-PCR series (546 evaluable of 550). Because these groups differed in patients, specimen type, and mutation panel, this comparison describes observed detection rates only and supports no inference about analytical sensitivity, specificity, or concordance. Results: KRAS was mutated in 149/332 tumors (44.9%); codon 12 supplied 80.5% of variants, led by G12D (32.2%), G12V (24.8%) and G13D (19.5%). Median OS did not differ between mutant and wild-type tumors (39.0 vs. 36.6 months; p = 0.40). Variant-level differences were directionally consistent, but none was significant, and all were exploratory and unadjusted for multiplicity. Observed detection rates were 40.3% for tissue RT-PCR (220/546), 13.3% for plasma RT-PCR (4/30; continuity-corrected p = 0.006 vs. tissue), and 50.8% for plasma dPCR (61/120; continuity-corrected p = 0.044, Pearson p = 0.034 vs. tissue). BRAF V600E was detected by plasma dPCR in 11/120 cases (9.1%). Conclusions: This first Kazakhstani series places KRAS frequency within the internationally reported range and shows that variant-level reporting reveals prognostic structure that a binary call conceals. The higher detection rate seen with plasma dPCR is hypothesis-generating, not evidence of platform superiority, and motivates a prospective paired-sample study with harmonized mutation panels.

Genes doi: 10.3390/genes17080906

Authors: Huda Ahmed Fairooz Rania Abdelhedi Sarab Hussain Khalil Najla Kharrat Mounira Hmani

Background/Objectives: β-thalassemia major is a common inherited hemoglobin disorder caused by Hemoglobin Subunit Beta (HBB) mutations and often complicated by iron overload and oxidative stress. This study characterized the clinical, hematological, biochemical, and molecular profile of β-thalassemia major in Al-Diwaniyah, Iraq, focusing on HBB mutations and CAT promoter polymorphisms as oxidative modifiers. Methods: A retrospective case–control study included 100 transfusion-dependent patients and 50 healthy controls. Sociodemographic data, complete blood count, ferritin, lipid profile, catalase (CAT), and malondialdehyde (MDA) were assessed. HBB mutations, namely IVSI-1 (G>A), IVSI-6 (T>C), and CD39 (C>T), and CAT polymorphisms, namely rs1001179 (C>T) and rs7943316 (A>T), were genotyped. Results: Patients had high rates of family history (80%), consanguinity (80%), rural residence (74%), low education (60.6%), and poor socioeconomic status (71.4%). Compared with controls, they showed lower RBC, HGB, HCT, HDL, LDL, and CAT but higher ferritin, triglycerides, and MDA (all p < 0.001). Overall, 69% of patients carried at least one studied HBB mutations, while 31% remained uncharacterized. Mutant allele frequencies were 29% for IVSI-1 (A) and 25.5% each for IVSI-6 (C) and CD39 (T). The CAT polymorphism rs1001179 (C>T) was associated with disease risk (CT: 33% vs. 14%; OR = 3.25, p = 0.019), whereas rs7943316 (A>T) was not. IVS-I-1 (G>A)/CD39 (C>T) β0 mutations were associated with lower CAT activity (β = −0.205; p = 0.046). Conclusions: β-thalassemia in Al-Diwaniyah, Iraq, shows substantial clinical, genetic, and oxidative heterogeneity. Integrated HBB–CAT analysis may improve molecular diagnosis, risk stratification, and preventive strategies in high-consanguinity populations.

Genes doi: 10.3390/genes17080904

Authors: Hui Chen Sunlei Ding Haiyan Bi Qimike Shan Xiaolei Shi Bingbing Lei Zhigang Liu Yangyang Yang Rui Tian Yongliang Yan

Background: Soybean is an important crop with multiple uses for oil, food, and feed, providing 50% of the vegetable protein and 20% of the edible oil in the world. The WD40 family genes play crucial regulatory roles in growth, development, secondary metabolism, and stress responses. However, the definition of WD40 family genes in soybean remained unclear, which limited their application potential in genetic improvement. Methods: To identify soybean WD40 family members and screen candidate genes for breeding improvement, this study performed genome-wide identification of the soybean WD40 gene family via bioinformatic approaches based on the latest Williams 82 reference genome (Wm82.a6.v1). Meanwhile, the function of the family gene GmWD40-257 regulating seed quality was analyzed. Results: The results showed that a total of 458 GmWD40 genes were identified, which were distributed on the 20 chromosomes. Subcellular localization showed that most members were mainly concentrated in the nucleus, chloroplast, and cytoplasm. Phylogenetic tree analysis divided the 458 GmWD40 genes into eight groups. Synteny analysis identified 160 syntenic genes between soybean and Arabidopsis thaliana. Conserved motif analysis identified ten core motifs. The promoter regions of GmWD40 contained 19 types of cis-acting elements. Functional analysis revealed that the nonsense mutation of GmWD40-257 significantly reduced the content of oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while significantly increasing the contents of protein, γ-tocopherol and δ-tocopherol. Conclusions: A total of 458 members of the WD40 gene family were identified in soybean. Among these, GmWD40-257 was found to positively regulate the contents of soybean oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while negatively regulating the contents of soybean protein, γ-tocopherol and δ-tocopherol.

Genes doi: 10.3390/genes17080905

Authors: Viktoria M. Petrova Evgeniia V. Simoroz Natalia A. Dudko Jelena Vasilevska

Non-human primates (NHPs) serve as indispensable models for aging research due to their evolutionary proximity to humans, conserved epigenetic mechanisms, and lifespans amenable to longitudinal investigation. This review synthesizes age-related epigenetic modifications in NHPs, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA regulation, and evaluates their alignment with human epigenetic markers. Epigenetic clocks developed on human data demonstrate robust predictive capacity in NHPs, and numerous age-associated methylation patterns are evolutionarily conserved. However, most epigenetic changes exhibit pronounced tissue specificity, with only a limited number of markers showing cross-tissue and cross-species consistency. Critical modulating factors such as sexual dimorphism, social hierarchy, environmental stressors, and early-life adversity significantly influence epigenetic aging trajectories. Current research remains restricted to a narrow subset of NHP taxa, predominantly macaques and baboons; expanding to include great apes would deepen our understanding of primate epigenetic aging. Advancing the field requires integrating multi-tissue, multi-species, and multi-omics approaches, including single-cell resolution analyses, to distinguish conserved mechanisms from lineage-specific adaptations. Such an integrative framework is essential for translating epigenetic discoveries into clinical interventions. By leveraging the unique advantages of NHPs, controlled interventional studies, longitudinal multi-tissue sampling, and causal mechanistic dissection, researchers can bridge basic discovery and therapeutic development. This approach promises to refine our understanding of aging biology and guide the rational design of next-generation therapeutics, from epigenetic modulators to lifestyle interventions, ultimately paving the way for personalized strategies that extend both lifespan and healthspan.

Genes doi: 10.3390/genes17080903

Authors: Ummahan Öz

Background/Objectives: Citrus sinensis, Olea europaea var. sylvestris, Populus nigra, Prunus dulcis, and Punica granatum are economically and medicinally important perennial plant species. Carotenoid cleavage oxygenase (CCO) genes encode key enzymes involved in carotenoid degradation and play essential roles in plant growth, development, and responses to environmental stresses. In this study, a comprehensive genome-wide comparative analysis of the CCO gene family was conducted in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum to investigate their structural diversity, evolutionary relationships, and potential biological functions. Methods: Chromosomal distribution, phylogenetic relationships, gene structure, conserved protein motifs, homology modeling, subcellular localization, cis-regulatory elements, and miRNA interactions were analyzed. Results: A total of 12, 23, 22, 11, and 17 CCO genes were identified in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum, respectively. Most CCO proteins were acidic, and genes were concentrated on specific chromosomes. Phylogenetic analysis grouped CCO genes into three main clades. Gene structure analysis revealed intronless and intron-containing genes of varying lengths. Some CCO proteins possessed all conserved motifs, while others lacked certain motifs or had multiple copies. β-sheets were the predominant secondary structural elements, and CCO proteins were predicted to be localized in chloroplasts, mitochondria, peroxisomes, the cytoplasm, and the nucleus. Stress-related cis-elements and miRNAs were identified. Conclusions: These findings provide valuable insights into the diversity and evolutionary characteristics of the CCO gene family and suggest that CCO genes may contribute to plant stress responses and metabolic processes. Overall, this study provides a comprehensive comparative analysis of the CCO gene family in these five perennial plant species and offers a valuable genomic resource for future functional characterization, comparative genomic studies, and molecular breeding applications.

Genes doi: 10.3390/genes17080902

Authors: Melloni N. Cook Kristin M. Hamre

This Special Issue of Genes, entitled “Genetics of Neuropsychiatric Disorders,” collects articles advancing our understanding of these disorders and their genetic bases [...]

Genes doi: 10.3390/genes17080901

Authors: Limei Li Jie Peng Gang Chen

Background: Peanut (Arachis hypogaea) is a globally important legume crop with high nutritional and economic value. In the plant, the highly conserved 14-3-3 proteins participate in various biological functions. This study investigated the characterization and evolution of the 14-3-3 gene family in peanut and explores its potential roles in stress resistance. Methods: The 14-3-3 gene families in cultivated peanut and its ancestral species Arachis duranensis and Arachis ipaensis were identified and characterized via a genome-wide approach. We subsequently analyzed their structural features, conserved motifs, genomic distribution, phylogeny and promoter cis-acting elements. Results: A total of 22, 10, and 12 14-3-3 genes (also called general regulatory factors, GRFs) were identified in A. hypogaea, A. duranensis, and A. ipaensis, respectively. Cultivated peanut exhibits extensive genomic synteny with its progenitors, and segmental duplication appears to be a key mechanism underlying the expansion of this gene family. Moreover, according to cis-acting element prediction, these genes may contribute to stress tolerance under diverse environmental conditions. Conclusion: This comprehensive analysis enhances our understanding of the 14-3-3 (GRF) gene family in peanut and provides a valuable basis for further functional research on these genes.

Genes doi: 10.3390/genes17080900

Authors: Ha Duc Chu Trung Quoc Nguyen Loc Van Nguyen Nguyen Nguyen Chuong Quyen Thi Ha Nguyen Thi Phuong Thao Touhidur Rahman Anik Saad Sulieman Weiqiang Li Lam-Son Phan Tran

Background: Rice breeding requires faster development of high-yielding, climate-resilient, resource-efficient, and high-quality cultivars for production systems exposed to environmental variability and increasing input constraints. Genomic selection offers an opportunity to predict breeding value before extensive field evaluation, although its effectiveness depends on the integration of genomic, phenotypic, and environmental information. Methods: This narrative review critically examines recent advances in genomic selection for rice and its integration with high-throughput genotyping, high-throughput phenotyping, machine learning, multi-environment prediction, and speed breeding. Results: Genome-wide marker data can support early ranking of breeding materials for grain yield, grain quality, disease resistance, drought tolerance, salinity tolerance, and nutrient-use efficiency. Prediction performance is influenced by trait architecture, marker density, training-population size, genetic relatedness between training and candidate populations, phenotypic data quality, and genotype-by-environment interaction. Red-green-blue, multispectral, hyperspectral, thermal, and light detection and ranging platforms can generate temporal traits associated with plant architecture, biomass, water status, nutrient status, and stress responses, which may improve prediction under suitable population and validation designs. Speed-breeding systems shorten generation intervals and facilitate rapid advancement, recurrent selection, and recycling of superior parental lines. Conclusions: Integrated breeding pipelines that combine genomic prediction, high-throughput phenotyping, environmental data, and speed breeding can improve selection efficiency and shorten rice improvement cycles. Wider adoption will require affordable technology platforms, standardized data systems, multi-environment validation, breeder capacity development, and collaborative data-sharing frameworks for smart and greener agriculture.

Genes doi: 10.3390/genes17080899

Authors: Kaixiang Lin Zijiao Song Qiutang Huang Ali Hasnain Tao Tang Wei Xu Priscilla Amponsah Chunqing Zhao

Background/Objectives: Glutamate-gated chloride channels (GluCls) are essential inhibitory neurotransmitter receptors in insects and key targets of several insecticides. In Spodoptera frugiperda (FAW), mutually exclusive alternative splicing (MEAS) of exon 3 in SfGluCl produces three splice variants (SfGluCl 3A, SfGluCl 3B and SfGluCl 3C), yet the cis-regulatory elements involved in this splicing event remain unknown. This study aimed to identify candidate cis-regulatory regions associated with exon 3 MEAS and characterize their effects on exon 3 selection in a Sf9 cell-based minigene system. Methods: Semi-quantitative RT-PCR was used to assess the expression levels of three splice variants of exon 3 in SfGluCl across developmental stages. Comparative sequence analysis, combined with intron-deletion and exon-exchange assays, were performed to identify candidate cis-regulatory regions. A total of 27 constructs (23 intron-deletion and 4 exon-exchange constructs) were generated and analyzed using a minigene splicing assay in Sf9 cells. Results: Three splice variants were consistently detected across all developmental stages. In the Sf9 cell-based minigene system, two candidate cis-regulatory regions affecting SfGluCl 3B inclusion were identified: a 20 bp intronic region spanning nucleotides +13 to +32 downstream of the 5′ splice junction in the intron between exons 3B and 3C, corresponding to the region deleted in ExonB-C (Exon 3B-exon 3C)-Intdel52, and an 11 bp region within exon 3B containing six nucleotide substitutions in Ex3B (Exchanged exon 3B)-SubA2. Deleting the ExonB-C-Intdel52 or modifying the Ex3B-SubA2 significantly increased the SfGluCl 3B inclusion. Conclusions: These candidate intronic and exonic regions can influence exon 3B inclusion in the Sf9 cell-based minigene system. Although their functional effects and in vivo relevance remain to be validated in further study, our findings still provide a basis for future studies of GluCl splice variant regulation, receptor biology, and insecticide response in insects.

Genes doi: 10.3390/genes17080898

Authors: Shuaibin Lian Huajin Feng Haojie Hou Liang Zhang Youchao Tu Ke Gong Wei Zhang

Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding.

Genes doi: 10.3390/genes17080897

Authors: Kursat Ozdilli Yeliz Ogret Suleyman Rustu Oguz Cigdem Kekik Cinar Fatma Oguz

Background/Objectives: Aging is characterized by genomic instability, reduced biological diversity, and clonal dominance across multiple biological systems. While short tandem repeats (STRs) are traditionally considered neutral genetic markers, emerging evidence raises the possibility that variation in these regions may be examined in relation to broader genomic processes associated with aging. Methods: STR profiles from 400 individuals were analyzed, including 275 young participants aged 21–43 years and 125 elderly participants aged ≥65 years. Genetic diversity was assessed using parameters such as expected heterozygosity (He), individual heterozygosity ratio, and allelic dominance. Additionally, STR loci were mapped to the hg38 reference genome (±100 kb), and nearby genes were annotated with KEGG pathway information to provide exploratory biological context for the investigated loci. Results: No statistically significant differences were observed in heterozygosity or allelic dominance between the young and elderly groups. However, a slight trend toward decreased heterozygosity and increased allelic dominance was noted in the elderly population. Genomic mapping indicated that some STR loci are located in proximity to genes annotated in aging-related pathways; however, this finding is based on genomic proximity and should be interpreted as exploratory. Conclusions: The primary analyses did not demonstrate statistically significant differences in STR-based genetic diversity between the young and elderly groups. The observed trends and genomic proximity findings should therefore be considered exploratory and hypothesis-generating. Validation in larger, independent prospective cohorts and integration with functional genomic data are required before any biological significance can be inferred.

Genes doi: 10.3390/genes17080896

Authors: Dmitry Adamov Georgy Ponomarev Larissa Damba Elena Balanovska

Background/Objectives: Due to advances in paleogenetic research, a substantial amount of data has been accumulated on the Y-chromosome of the ancient Scytho-Siberian population that inhabited South Siberia and the adjacent territories of modern Mongolia and North-West China. It became possible to compare the Y-chromosomes of ancient men and modern Tuvans of various clans. Methods: We analyzed Y-SNPs and Y-STRs of ancient and modern samples. Results: During Tuvan ethnogenesis, the total frequency of the haplogroups Q and R1a dropped from 85% in Scytho-Siberian populations to 35% in modern Tuvans. Today, the gene pool of Tuvans is dominated by haplogroups N-P43, N-M178 and O-M175, which remain undetected in the samples from the Scytho-Siberian period. An analysis of the Y-STR phylogenetic networks that integrated data on Y-STR haplotypes and Y-SNPs of the Q and R1a haplogroup branches of both ancient and modern specimens provides findings that should be interpreted as broad phylogenetic affinities consistent with the paternal lineage continuity of haplogroups Q-YP1102 and R1a-Y39884. At the same time, the TMRCA estimate for the Y-STR cluster of the dominant branch of haplogroup Q in modern Tuvans, Q-YP1102-YP1691, is only 670 ± 130 YBP. Clusters of Y-STR haplotypes of the R1a-Y39884, R1a-YP1506, and R1a-YP1543 branches in modern Tuvans are also young and date back to between 1200 and 400 YBP. The Scytho-Siberian haplogroups R1a-YP1272, Q-BZ180, and N-Y147969 were not found in our sample set of modern Tuvans (n = 633). Conclusions: Haplogroups Q-YP1102 and R1a-Y39884 originated in Siberia and their branches are typical for the modern indigenous populations of South and West Siberia. Q-YP1102 marks the Yeniseian substrate and R1a-Y39884 was common in the ancient Siberian Andronovo culture. Overall, the gene pool of the Tuvan population was shaped (at least since the Scytho-Siberian period) by close interactions with the gene pools of Siberia and West Mongolia. However, the resolution of Y-SNP and Y-STR genotyping, as well as the limited sample size of ancient samples and their location in a limited area of the Eerbek River valley, do not allow us to conclude about the direct inheritance of modern Tuvan lineages from the ancient Scytho-Siberian population.

Genes doi: 10.3390/genes17080895

Authors: Louíse B. Faverzani Andreia K. Zwirtes Dinah P. A. Rodrigues Thais F. Machado Daniele A. Oliveira Luiza C. Silveira Nathalia P. Seixas Evandro N. Silva Danielly B. S. Silva Ricardo Z. Vaz Thaise P. Melo

Background: The major histocompatibility complex (MHC) is a well-known gene complex that plays a fundamental role in immune recognition; however, its influence on reproductive processes in cattle is not yet fully established, particularly regarding how it modulates the female response to the embryo. Therefore, this study aimed to investigate the relationship between MHC genes and reproductive processes in cattle and to identify potential molecular targets involved in these mechanisms. Methods: Data from four studies identified through a systematic review were integrated. MHC genes associated with reproduction were identified, neighboring genomic regions were explored to detect candidate genes and transcription factors, and biological process networks were constructed using differentially expressed genes associated with cattle. Results: The integrated analysis led to the identification of six MHC genes associated with reproduction, along with 54 candidate genes from genome-wide association studies and 46 from transcriptomic studies located in neighboring regions. Among these, BoLA-DQB and BoLA-DQA5 stood out in all analyses, while the transcription factors FOXA1, FOXO3, ELF5, and STAT3 appeared across the different datasets. These genes and factors may represent potential targets for future functional validations and could be explored using genome editing technologies to better understand their roles in reproductive processes. The identified biological pathways were related to embryonic development and reproductive organ formation, providing a preliminary foundation for future investigations. Conclusions: This work integrates currently available evidence and highlights potential molecular targets that can be explored in cattle breeding and reproductive biology, associating MHC genes with these roles and advancing innovative perspectives in the field of molecular genetics.

Genes doi: 10.3390/genes17080894

Authors: Vasiliki Kefala Efthymios Oikonomou Eleni Sfyri Vasiliki-Sofia Grech Niki Tertipi Eleni Andreou Efstathios Rallis

Background: Parkinson’s disease (PD) is a progressive neurodegenerative disorder with a well- documented prodromal phase during which non-motor symptoms appear years before motor onset. Seborrheic dermatitis (SD) is a chronic inflammatory skin disease that is significantly more prevalent in PD patients than in the general population. The biological mechanisms underlying this association have not been integrated into a single framework. Objectives: This narrative review aims to synthesise the available evidence on the molecular, genetic, and pathophysiological mechanisms linking SD and PD. Methods: A literature search was conducted across PubMed/MEDLINE, Scopus and ScienceDirect, supplemented by manual searches in OMIM and GeneCards. Results: Four major biological links between SD and PD have been proposed. First, alpha-synuclein deposits are detectable in cutaneous nerve fibres and autonomic fibres innervating sebaceous glands in PD patients and their pattern has been associated with disease subtype and progression. Second, dysfunction in ceramide and sphingolipid metabolism, associated with variants in GBA1, LRRK2, and ZNF750, has been linked to impaired lysosomal function and skin barrier integrity in both brain and skin tissue. Third, Malassezia, a commonly associated organism and possible trigger in susceptible hosts, produces metabolites that activate neuroinflammatory pathways relevant to PD and PD patients show altered Malassezia species composition on their skin. Fourth, NLRP3 inflammasome activation, which can be triggered by ceramide accumulation and fungal metabolites, has been proposed as a shared inflammatory mechanism that may operate in both keratinocytes and dopaminergic neurons. Conclusions: SD and PD appear to share overlapping genetic, lipidomic, microbial, and neuroinflammatory features. These associations are consistent with, but do not yet prove, a common pathological basis rather than a coincidental one. SD may therefore represent a potential prodromal feature or risk marker of PD. Future research should examine whether targeted intervention in high-risk SD patients can delay or modify PD onset.

Genes doi: 10.3390/genes17080893

Authors: Mingxuan Yao Yuhao Chu Xiaokang Dai

The HAK/KUP/KT family represents a major group of plant potassium transporters involved in K+ uptake, ion homeostasis and stress responses. However, the accession-level diversity of HAK/KUP/KT genes in Brassica napus remains insufficiently characterized. In this study, we performed a pan-family analysis of HAK/KUP/KT genes across eight B. napus accessions. A total of 269 annotated HAK/KUP/KT family members were identified and classified into core, soft-core, dispensable and private orthogroups based on their representation across the analyzed genome annotations. Phylogenetic analysis grouped these proteins into four major clades together with reference HAK/KUP/KT members from Arabidopsis thaliana and rice. Ka/Ks analysis indicated that HAK/KUP/KT orthogroups were predominantly under purifying selection, while accession-variable orthogroups showed greater variation in sequence conservation. Gene structure, conserved domain, motif and predicted promoter cis-element analyses revealed conserved transporter-related protein features together with orthogroup-level structural and sequence variation. Expression profiling using the ZS11 BnIR dataset further revealed tissue-, hormone- and stress-responsive expression patterns among ZS11 HAK/KUP/KT genes. By integrating expression features, predicted promoter information, evolutionary characteristics, published salt GWAS context and BnVIR haplotype–phenotype information, BnaA08T0085800ZS was prioritized as a candidate locus located near salt-associated variation. This study provides a pan-genome perspective on HAK/KUP/KT family diversity in B. napus and establishes a framework for prioritizing candidate genes for future functional investigation.

Genes doi: 10.3390/genes17080892

Authors: Beloslava Malakova Simeon Karpuzov Dobromir Tsolyov Georgi Petkov Milen Zamfirov

Background: Variant-based pathogenicity predictors such as REVEL evaluate missense variants in isolation, discarding the gene-length and allele-frequency context needed to compare collections of genes. Methods: We introduce a composite gene-level metric integrating Hardy–Weinberg heterozygosity, coding-sequence length, and REVEL scores. The metric returns a single value per gene expressing variant burden per unit of coding sequence within a given cohort, so that the ratio between a case and a control cohort quantifies gene-level enrichment. It was evaluated on 55 high-confidence autism genes, defined as the intersection of three large-scale ASD sequencing studies, against the 1000 Genomes reference. Results: It identifies elevated pathogenic burden in 48 of 55 genes, removes gene-length and variant-count confounds, and substantially outperforms naive gene-level aggregation of REVEL scores. Bootstrap resampling and a label-permutation control confirm the enrichment is stable and not an artefact of the scoring construction. Conclusions: The metric allows genes to be ranked within a set and aggregate burden to be compared across gene sets. We present it as a complementary gene-level layer for case–control and gene-set comparisons, with a nonlinear successor outlined as future work.

Genes doi: 10.3390/genes17080891

Authors: Dabao Yin Xue Li Li Zhou Zhongchun Xiao

Background: Imidacloprid, a widely used neonicotinoid insecticide, is routinely applied to control pests in Astragalus membranaceus var. mongholicus, a crucial medicinal herb producing Astragali Radix. However, the early short-term transcriptional and metabolic responses of its seedlings under imidacloprid gradient stress remain poorly characterized. Methods: In this study, 80-day seedlings were subjected to three foliar spray treatments: blank control (CK), the recommended imidacloprid concentration (2000-fold dilution, 475 mg·L−1), and an excessively high concentration (500-fold dilution, 1900 mg·L−1). Leaf samples were harvested 24 h post-treatment for untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) metabolomics (6 biological replicates) and RNA-seq transcriptome sequencing (3 biological replicates). Results: The low- and high-dose treatments induced 1076 and 860 differential metabolites and 6818 and 7283 differentially expressed genes, respectively. Flavonoids, saponins, terpenoids, amino acid metabolites, and energy-related pathways were prominently affected. KEGG enrichment indicated activation of flavone/flavonol biosynthesis, phenylpropanoid metabolism, amino acid metabolism, MAPK signaling, cutin/suberin/wax biosynthesis, and ABC transporter pathways, whereas high-dose exposure was associated with stronger changes in genes related to DNA replication and cell wall remodeling. Integrated network analysis highlighted CHS, PAL, MYC2, KCS, and ABCG40 as candidate regulators linking stress signaling, secondary metabolism, and metabolite transport. Conclusions: Seedlings of A. membranaceus var. mongholicus exhibit dose-dependent acute responses to imidacloprid. Moderate pesticide exposure primarily activates defensive secondary metabolism, whereas excessive dosage triggers genome-wide transcriptional reprogramming. This work identifies key metabolic pathways and hub genes, offering candidate molecular markers for investigating pesticide stress adaptation in medicinal Astragalus and guiding standardized pesticide application in cultivation.

Genes doi: 10.3390/genes17080890

Authors: Jiahao Cao Yufei Cheng Yichuan Liang Ao Li Mingming Yang Xiaotong Guo Linlin Dong

Background: This study aimed to investigate the molecular mechanisms underlying the response of Codonopsis pilosula roots to Fusarium oxysporum infection, which causes root rot and significant economic losses, and to provide a theoretical basis for breeding resistant varieties and developing effective control strategies. Methods: Root samples of C. pilosula were inoculated with F. oxysporum and harvested across five distinct intervals (0, 6, 24, 72, and 120 h after inoculation). Transcriptome sequencing was performed on 15 samples, generating 171.65 GB of clean data. De novo assembly was used to construct unigenes, followed by functional annotation and differential expression analysis. In addition, CpMAPK9 was transiently overexpressed in C. pilosula leaves to evaluate its role in jasmonic acid (JA) biosynthesis and disease resistance. Results: A total of 94,896 unigenes were obtained. Functional analysis showed that genes involved in hormone signal transduction, the MAPK signaling pathway, and plant–pathogen interactions were consistently activated in response to infection. Among the MAPK gene family, CpMAPK9 showed significant expression changes. Transient overexpression of CpMAPK9 significantly increased JA accumulation, indicating that CpMAPK9 positively regulates JA biosynthesis and may enhance resistance to root rot. Conclusions: In conclusion, our findings indicate that CpMAPK9 actively modulates JA-mediated defense pathways in C. pilosula during F. oxysporum invasion. Our findings shed light on the intricate molecular networks that drive disease defense, offering valuable theoretical insights to guide subsequent crop improvement initiatives.

Genes doi: 10.3390/genes17080889

Authors: Priyanka Banerjee Rachel Phillips Anna G. Holliman Soren P. Rodning Wellison J. S. Diniz Paul W. Dyce

Background/Objectives: Reproductive inefficiency remains a major contributor to heifer culling and reduced herd longevity in beef systems. This study examined the molecular basis of fertility by analyzing granulosa cells and follicular fluid from Angus–Simmental crossbred heifers classified as fertile or subfertile. Methods: Granulosa cells and follicular fluid were collected for RNA sequencing and metabolomic analysis. Differential expression, network, and gene–metabolite integration analyses identified genes, metabolites, and pathways associated with fertility differences between groups. Results: We identified 90 differentially expressed genes from the granulosa cells, including CXCL12 and HOXD family members, CALCRL, DNER, GADD45G, immune-related genes, and nine metabolites differentially abundant in follicular fluid, including parabanic acid, pimelic acid, α-tocopherol, glycine, and arachidonic acid. Network analysis revealed extensive rewiring in the network from the subfertile heifers for both genes and metabolites as compared to the fertile heifers. The gene–metabolite integration revealed a high degree of connectivity between arachidonic acid and α-tocopherol, correlating with immune and signaling genes, and between CXCL12 and carbohydrate intermediates. Pathway over-representation analysis highlighted carbohydrate and purine metabolism in fertile heifers, and aminoacyl-tRNA biosynthesis, alanine/aspartate/glutamate metabolism, and Hippo signaling in the subfertile heifers. ABC transporters, ferroptosis, mineral absorption, and glyoxylate/dicarboxylate metabolism were common pathways identified in both groups. Integrative granulosa-follicular fluid analysis revealed coordinated gene–metabolite rewiring in subfertility, including functional candidates (CXCL12, CALCRL, DNER; α-tocopherol, arachidonic acid, fucose, parabanic acid) and fertility-associated pathways. Conclusions: These signatures provide novel targets and pathways underlying beef heifer fertility.

Genes doi: 10.3390/genes17080888

Authors: Katarzyna Piórkowska Ewa Ocłoń Ksenia Wróblewska Karolina Zygmunt Piotr Pawlicki Laura Pardyak

Background: The long non-coding RNA MALAT1 is known to regulate various cellular processes; however, its role in porcine adipose tissue remains largely unexplored. Methods: In this study, we examined MALAT1 in pigs differing in fat-deposition traits by combining promoter sequencing, in silico analysis of transcription factor binding site analysis, expression profiling, and in vitro adipogenesis assays. Results: We identified three novel polymorphisms in the MALAT1 promoter regions. Several SNPs were predicted to alter binding sites for transcription factors related to metabolism and immunity, such as NFAT5, NFATC1, and BCL6B. One variant, rs329590882, differed significantly in frequency between breeds and may influence MALAT1 regulation. During adipocyte differentiation, expression of the MALAT1 isoform ENSSSCT00000080860 increased as adipogenesis progressed. Notably, this isoform was more highly expressed in lean-type Pietrain pigs than in the fatty Złotnicka Spotted (ZS) breed, suggesting that its function may not be directly related to fat accumulation. Additionally, we identified novel exon–exon junctions in MALAT1, including a junction associated with the ENSSSCT00000077869 isoform. Conclusions: These findings provide new insights into the potential role of MALAT1 in porcine adipose tissue development and immunometabolic regulation and highlight the need for improved annotation of porcine lncRNAs.

Genes doi: 10.3390/genes17080887

Authors: Shan Ji Tongzeng Li

Background/Objectives: Infection susceptibility and systemic infection severity arise from distinct tissue barriers and host-response compartments, but plasma-protein genetic studies often treat infection as a broad phenotype. We aimed to define a site-resolved host plasma-protein architecture of infection susceptibility across urinary, lower-respiratory, systemic, and skin/soft-tissue infection outcomes. Methods: We performed proteome-wide two-sample cis-protein quantitative trait locus (cis-pQTL) Mendelian randomization (MR) using UK Biobank Pharma Proteomics Project (UKB-PPP) instruments and registry-derived FinnGen R13 infection endpoints. Prioritized protein–outcome pairs underwent regional colocalization, prior-sensitivity analysis, Steiger-like directionality sensitivity, Finnish and broader European reference-panel linkage disequilibrium (LD) assessment, candidate-level deCODE pQTL-source follow-up where feasible, and druggability and safety-domain annotation. Results: Across 18,766 harmonized tests, evidence was strongly site-resolved. PSCA emerged as the principal novel cystitis-specific candidate (OR 0.977, 95% CI 0.967–0.987), with strong colocalization and high Finnish reference-panel linkage disequilibrium between the MR instrument and the top colocalization single-nucleotide polymorphism (SNP) (r2 = 0.980). UMOD anchored urinary host-defense coherence. APOE showed strong evidence for the registry-derived implicit sepsis endpoint but was interpreted as a pleiotropy-prone broad host-response or severity-associated locus. TNFSF8 retained a robust pneumonia MR signal, but colocalization was moderate (PP.H4 = 0.544) and became weak under stringent priors (PP.H4 = 0.107), despite high-LD deCODE proxy-instrument follow-up. Skin/soft-tissue infection lacked a convergent lead. Conclusions: This study supports a site-resolved architecture of genetically anchored plasma-protein candidates for infection susceptibility. PSCA and UMOD define complementary urinary signals, whereas APOE and TNFSF8 require cautious interpretation as broad host-response and lower-respiratory follow-up hypotheses rather than established therapeutic targets.

Genes doi: 10.3390/genes17080886

Authors: Xinrui Peng Wangxin Ding Xin Kang Yuhao Yan Yanjing Chen Yan Zhang

Background: Beijing’s 2024 school physical education reforms have substantially increased activity demands on children, yet population-level genotype data for Chinese schoolchildren remain scarce. Objectives: To characterize ACTN3 R577X, MTHFR C677T, MTHFR A1298C, and MTRR A66G polymorphisms in 564 Beijing schoolchildren; test Hardy-Weinberg equilibrium (HWE); compare allele frequencies with East Asian reference populations; and perform multi-locus cumulative allele analysis across all four loci. Methods: Cross-sectional study of 564 primary and secondary school students (265 males, 299 females) in Beijing. Genotyping was performed by PCR and Sanger sequencing using saliva-derived DNA; the overall call rate was 100% (564/564). HWE was assessed using the exact test of Wigginton et al. Allele frequencies were compared with 1000 Genomes CHB (n=103) and gnomAD EAS (n≈2604) using chi-squared or Fisher’s exact tests. Cumulative variant allele counts (0–8) were computed across all four loci. Linkage disequilibrium (LD) and haplotype frequencies were estimated using the EM algorithm. Results: All four loci were in HWE (all p>0.05). Genotype frequencies were: ACTN3 R577X—RR 31.56%, RX 49.11%, XX 19.33%; MTHFR C677T—CC 18.62%, CT 46.99%, TT 34.40%; MTHFR A1298C—AA 71.81%, AC 26.42%, CC 1.77%; MTRR A66G—AA 56.21%, AG 35.82%, GG 7.98%. No significant sex differences were observed at any locus (all p>0.05). Allele frequencies were consistent with East Asian reference populations. Across all four loci, 87.23% of students carried ≥2 variant alleles; 29.26% carried ≥4. LD between MTHFR C677T and A1298C was moderate to strong (|D′|=0.97, r2=0.23). The double-mutant T-C haplotype was rare (frequency =0.002). Conclusions: This study provides genotype frequency data for exercise- and folate metabolism-related polymorphisms in a sample of Beijing schoolchildren. These descriptive frequency data establish a baseline for future genotype–phenotype association studies; however, the sample is limited to two schools in two districts of Beijing and does not represent the broader Chinese pediatric population. Studies incorporating fitness, biochemical, and dietary data are required before such genetic profiles can inform educational or clinical recommendations. Given the purely descriptive, cross-sectional nature of the study and the absence of phenotypic data, these genotype frequency data do not, on their own, provide a basis for individualized physical education programming or nutritional recommendations.

Genes doi: 10.3390/genes17080885

Authors: David Bienjonetti-Boudreau Camille Tremblay-Laganiere Efthymia Gkogkou Annick Martinez Cecilia Gonzalez Corcia

Long QT Syndrome type 2 (LQT2) and Brugada syndrome are inherited cardiac channelopathies that predispose affected individuals to ventricular arrhythmias and sudden cardiac death. We report the case of a 15-year-old male carrying two pathogenic variants: one in SCN5A and one in KCNH2, genes classically associated with Brugada syndrome and LQT2, respectively. The patient presented with an atypical phenotype characterized predominantly by atrial arrhythmias, atrioventricular (AV) conduction abnormalities, and wide complex tachycardia and sinus node disease without the characteristic electrocardiographic features of either syndrome. The phenotype was most likely driven predominantly by the SCN5A variant. Given his unpredictable episodes of high-grade conduction block and potential risk of ventricular arrhythmias, a transvenous implantable cardioverter-defibrillator (ICD) was implanted. Family screening revealed segregation of SCN5A and KCNH2 variants in different relatives, each with mild or absent phenotype. This case highlights the complexity of genotype–phenotype correlations in inherited arrhythmia syndromes and the importance of individualized genetics-informed management.

Genes doi: 10.3390/genes17080884

Authors: Likuan Liu Yifan Wang Haoyu Liu Tianyu Zhao Jianfen Ma Haotian Wang Kaidi Su Jinping Li

Background: Myricaria squamosa Desv., a perennial shrub of the Tamaricaceae family, holds significant ecological, medicinal and economic values on the Qinghai–Tibet Plateau. Methods: This study performed chloroplast whole-genome sequencing of M. squamosa and analyzed its genomic characteristics, codon usage bias, and phylogenetic relationships. Results: The M. squamosa chloroplast genome spans 154,689 bp, with a GC content of 36.3%. A total of 129 functional genes were annotated, including 84 protein-coding genes, 37 transport RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Structural analysis revealed that contraction and expansion of the inverted repeat (IR) boundaries in Tamaricaceae species primarily involve the rps19 and ycf1 genes. We identified 214 simple sequence repeat (SSR) loci. Comparative genomic analysis indicated higher variability in the large single-copy (LSC) and small single-copy (SSC) regions compared to the IR regions, and greater divergence in intergenic spacers than in protein-coding regions. All protein-coding sequences contain a total of 26,045 codons, with leucine (2750) being the most frequent, and a pronounced preference for adenine/thymine (A/T) endings. Phylogenetic reconstruction revealed that M. squamosa is most closely related to Myricaria laxiflora. Conclusions: This study provides valuable insights into the chloroplast genomic structure, codon usage patterns, and SSR distribution of M. squamosa, contributing to genomic evolution studies and taxonomic revision within the Tamaricaceae family.

Genes doi: 10.3390/genes17080883

Authors: Mingyuan Yuan Fei Zhou

Artemisinin, a sesquiterpene lactone produced by Artemisia annua, is synthesized and stored predominantly in glandular secretory trichomes (GSTs). Despite substantial advances in elucidating its biosynthetic pathway and transcriptional regulation, a key challenge remains: how developmental processes, hormone signaling, and metabolic pathways are coordinately integrated to overcome the trade-off between trichome density, metabolic flux, and vegetative biomass, which ultimately limits whole-plant yield. Recent studies have identified basic helix–loop–helix (bHLH) transcription factors (TFs) as central integrative hubs in this network. AabHLH113 functions as a convergence node linking jasmonic acid (JA) and abscisic acid (ABA) signaling to activate core biosynthetic genes. AaMYC3 bridges development and metabolism by promoting GST initiation via AaHD1 while enhancing pathway flux and cooperating with other bHLH factors to amplify amorpha-4,11-diene synthase (ADS) and artemisinic aldehyde delta-11(13) reductase (DBR2) expression. Extending this regulation to the whole-plant level, AaSPATULA coordinates GST formation with photosynthetic capacity, carbon assimilation, and biomass accumulation. Here, we propose a unified framework in which bHLH TFs integrate hormone signaling, trichome development, metabolic flux, and carbon allocation into a coherent regulatory system. We further discuss implications for next-generation metabolic engineering and highlight future directions, including multi-omics-guided, multi-target editing of regulatory hubs. This developmental–metabolic integration framework provides a conceptual basis for optimizing artemisinin production and improving high-value metabolite biosynthesis in other trichome-bearing plants.

Genes doi: 10.3390/genes17080882

Authors: Carlotta Pia Cristalli Maria Alessandra Schiavo Miryam Rosa Stella Foti Sara Calabrese Federica Isidori Alice Margutti Pierluigi Laricchiuta Giulia Governatori Francesco Lai Vera Uliana Federico Barocelli Elia De Maria Alessandro Fucili Biagio Sassone Giulia Parmeggiani Enrica Perugini Camilla Lucca Francesca Cappuccini Laura Pezzoli Maria Iascone Maria Piane Giovanni Vitale Claudio Graziano Rita Selvatici Alessandra Ferlini Maddalena Graziosi Elena Biagini Daniela Turchetti Francesca Gualandi Cesare Rossi

Background: Founder mutations in MYBPC3 may contribute substantially to the genetic burden of hypertrophic cardiomyopathy (HCM) and provide important insights into genotype–phenotype correlations and population-specific disease mechanisms. In this study, we investigated two recurrent canonical splice-site variants, MYBPC3 c.1458-1G>A and c.3331-1G>A, identified in patients with HCM from the Emilia-Romagna region of Northern Italy. Methods: Ninety-one unrelated patients with HCM carrying either MYBPC3c.1458-1G>A or c.3331-1G>A were analyzed. Haplotype reconstruction was performed to assess a possible founder effect and estimate the approximate age of the shared ancestral allele. Functional characterization was carried out by RNA sequencing of myocardial tissue to evaluate the impact of the variants on splicing. Clinical and phenotypic data were compared with those of carriers of other truncating MYBPC3 variants or pathogenic variants in other sarcomeric genes. Results: Both variants, classified as pathogenic according to ACMG criteria, shared a conserved variant-specific core haplotype. Founder age was estimated at approximately 10.5 generations (~262 years), consistent with a regional founder effect. RNA sequencing demonstrated aberrant splicing for both variants, resulting in premature termination codons and presumably subsequent nonsense-mediated mRNA decay. Clinically, carriers showed delayed disease onset, with a mean onset in the fifth decade of life, and a comparatively milder phenotype, including a lower incidence of sudden cardiac death, than patients carrying other truncating MYBPC3 variants or pathogenic variants in other sarcomeric genes. Both variants exhibited partial penetrance (approximately 63–67%) and age-dependent variable expressivity. Conclusions:MYBPC3 c.1458-1G>A and c.3331-1G>A represent novel founder alleles associated with HCM in Northern Italy. Identification of these locally prevalent variants improves molecular diagnosis, family screening, and supports the development of variant-targeted therapeutic approaches.

Genes doi: 10.3390/genes17080881

Authors: Francesco Sessa Martina Francaviglia Emina Dervišević Pietro Zuccarello Mario Chisari Serena Matera Grazia Giulia Panté Monica Salerno Massimiliano Esposito

Background/Objectives: DNA-based identification of degraded human remains represents a major challenge in forensic science, particularly in cases involving burned, fragmented, or commingled bodies. Advances in forensic genetics have expanded the analytical capabilities for such samples; however, the effectiveness of different approaches and their integration within Disaster Victim Identification (DVI) workflows remain heterogeneous. This systematic review aims to critically evaluate current evidence on DNA-based identification of degraded remains, focusing on methodological strategies, emerging genomic technologies, and DVI applications, while integrating laboratory evidence and operational forensic practice into a structured analytical framework. Methods: A systematic literature search was conducted in Scopus and Web of Science from database inception to 5 June 2026, following PRISMA 2020 guidelines. Eligible studies included original research addressing DNA analysis of degraded, thermally altered, or highly compromised human remains in forensic or DVI contexts. After a multistep screening process involving title/abstract and full-text evaluation, 37 studies were included. Data were extracted and organized into three thematic categories: (i) core DNA analysis, (ii) advanced molecular technologies, and (iii) DVI case applications. Results: The findings demonstrate that DNA recovery from degraded remains is influenced by thermal exposure, tissue type, and sampling strategy. Teeth and dense cortical bone consistently provide higher DNA yield. While autosomal STR profiling remains the primary analytical approach, its limitations in highly degraded samples are mitigated through the complementary use of mitochondrial DNA (mtDNA), Y-chromosome STRs (Y-STRs), and SNP markers, together with advanced sequencing technologies such as massively parallel sequencing (MPS). Emerging technologies, including rapid DNA systems and predictive models based on macroscopic indicators, significantly enhance efficiency and success rates. DVI studies report identification rates exceeding 90–95% when multidisciplinary and structured workflows are applied. The evidence further supports a flexible triage-based analytical strategy, in which marker selection is guided by tissue preservation and degradation level. Conclusions: DNA-based identification of degraded human remains has evolved into an adaptive, multi-level forensic process. Successful outcomes rely on the integration of optimized sampling, hierarchical genetic analysis, and coordinated DVI strategies. The findings support a triage-based framework that links tissue selection, degradation assessment, and analytical methodology to maximize identification success. Future developments should focus on predictive models, advanced genomic tools, and standardized workflows to further improve identification in challenging forensic scenarios.

Genes doi: 10.3390/genes17080880

Authors: Zhiguo Hu Yuyuan Wu Jiahui Liu Xusheng Guo Baohua Duan

Background: The oriental river prawn (Macrobrachium nipponense) is an economically important aquaculture species in China. Methods: In this study, the genetic diversity and population structure of 12 populations were investigated using ten microsatellite markers. Among them, the Xiaolong Mountain (XLS) population is a cultured stock, while the Songjiachang Reservoir (SJC) population originates from the Yangtze River as an outgroup. Results: A total of 213 alleles were detected across 342 individuals, with an average of 21.3 alleles per locus. The observed heterozygosity (Ho) ranged from 0.362 to 0.902 (mean = 0.724), and the expected heterozygosity (He) ranged from 0.581 to 0.925 (mean = 0.805). Shannon’s diversity index (I) ranged from 1.224 to 2.810 (mean = 2.130). The polymorphism information content (PIC) varied from 0.532 to 0.920 (mean = 0.787), indicating high informativeness of the markers. Population structure analysis revealed a weak genetic subdivision with a subtle clustering signal (K = 2), but evaluation of LnP(K) indicated that K = 1 could not be confidently rejected. Pairwise Fst values ranged from 0.008 to 0.058, with high gene flow (Nm = 4.060–31.000), denoting low-to-moderate genetic differentiation. AMOVA showed that 98% of genetic variation resided within populations, with only 2% among populations (overall Fst = 0.020, p < 0.01). Nei’s genetic distances ranged from 0.094 to 0.277. Conclusions: Overall, the 12 populations of M. nipponense exhibited high genetic diversity, low-to-moderate genetic differentiation, and a weak population structure with most variation residing within populations. These findings provide valuable molecular markers for selective breeding and offer theoretical guidance for the conservation and sustainable utilization of M. nipponense germplasm resources, although the inferred population structure should be interpreted with caution given the weak differentiation signal.

Genes doi: 10.3390/genes17080879

Authors: Jinglan Liu

Chromosomes form the foundation of both the structure and function of the human genome [...]

Genes doi: 10.3390/genes17080878

Authors: Wei Xu Xuanyu Zhang Biyi Zhao Xiaoyun Li Ronghua Zhang

Background: The directional relationship between epigenetic age acceleration (EAA) and musculoskeletal disease remains unresolved. This study integrated bidirectional Mendelian randomization (MR) with multi-layer genomic evidence to evaluate directionality, shared genetic architecture, and robustness to instrument definition. Methods: Four EAA clocks (IEAA, PhenoAA, HannumAA, and GrimAA) and ten musculoskeletal phenotypes were analyzed in a 10 × 4 bidirectional two-sample MR design. EAA instruments underwent GRCh37 functional annotation, genome-wide-significant external-association screening for the index variants and European linkage-disequilibrium proxies, pair-specific Steiger filtering, and conservative Set A/B/C sensitivity analyses. The juvenile-arthritis reverse models underwent instrument-flow reconstruction, strength assessment, liability-scale directionality testing, and minimum-detectable-effect analysis. Additional analyses comprised LD score regression (LDSC), PLACO+ cross-trait locus mapping, Bayesian colocalization, multivariable MR (MVMR) with exact-SNP matched univariable comparators, and integrated evidence synthesis. Results: Forward MR yielded two nominal HannumAA associations. The inverse HannumAA–spondyloarthritis estimate remained directionally consistent across the original, Steiger-filtered, and conservative external-association-filtered sets, whereas the HannumAA–pain-in-thoracic-spine estimate lost nominal significance in the conservative set; no forward result survived correction across 40 tests. GrimAA forward estimates were sensitive to use of the fallback instrument threshold. Reverse MR identified ten nominal associations. For juvenile arthritis, three harmonized instruments had F statistics of 51.25–102.35; liability-scale Steiger comparisons supported the tested direction under all 16 outcome-by-prevalence combinations, although the 788-case discovery GWAS and possible winner’s curse remained important limitations. LDSC identified FDR-significant positive genetic correlations of GrimAA with hip osteoarthritis (r_g = 0.267, p = 8.49 × 10−5, q = 0.0019) and knee osteoarthritis (r_g = 0.269, p = 9.52 × 10−5, q = 0.0019). PLACO+ identified 738 genome-wide-significant cross-trait variants and 65 independent loci; six of 37 evaluable loci showed strong colocalization. Of 96 MVMR models, 43 had primary-exposure conditional F ≥ 10, and 32 also had candidate-trait conditional F ≥ 10. After exact-SNP matching, the 43 primary-strength models were operationally classified as 35 partially attenuated and eight independent-signal models, with no fully attenuated model; no adjusted association survived multiplicity correction. Conclusions: The results support a prioritized genomic map with substantial instrument- and model-specific uncertainty. Disease-to-clock signals were richer than clock-to-disease signals, GrimAA shared polygenic architecture with osteoarthritis, and selected loci showed strong shared-variant evidence, while the MR and MVMR findings remained unsuitable for definitive causal or mediation claims.

Genes doi: 10.3390/genes17080877

Authors: Tayyaba Kazmi Ruqaya Nangrejo Eraj Abbas Nazish Waris Iftikhar Ahmed Siddiqui Rehana Rehman Paul Laurance-Young

Objective: The study was conducted to investigate the frequency of MED12 gene (rs5030619) mutations and to evaluate DNA methylation patterns in uterine leiomyomas among women at a tertiary care hospital in Karachi, Pakistan. Methods: In this cross-sectional study, 200 women with uterine fibroids and 50 controls were recruited from tertiary care hospitals after ethical approval. Baseline data and history were collected. Serum levels of estradiol, progesterone, and FSH were measured. Genomic DNA was extracted from fibroid and myometrial tissues and analyzed using allele-specific PCR for MED12 genotyping. DNA methylation profiling was conducted to evaluate epigenetic modifications. Statistical analyses were performed using the Statistical Package for social sciences (SPSS) version 27.0. Results: The majority of cases were aged 31–50 years, with 41.5% overweight and 24.5% obese. An increased WHR was observed in 65% of cases, compared to only 36% of controls. Serum estradiol, progesterone, and FSH levels were significantly higher in cases across all menstrual phases (p < 0.01). The MED12 A/C genotype was significantly associated with fibroid risk (OR = 11.72, 95% CI: 5.59–24.57, p < 0.001), and the C/C genotype conferred the highest risk (OR = 18.17, 95% CI: 4.00–82.54, p = 0.001). C allele was associated with increased disease susceptibility (OR = 4.65, 95% CI: 2.69–8.03, p < 0.001). Hyper-methylation was the most prevalent finding, observed in 125 cases of leiomyomas (69.4%). Multivariable logistic regression identified age (OR = 1.04, p = 0.012), BMI (OR = 1.09, p = 0.004), multiple fibroids (OR = 2.31, p = 0.005), intramural fibroid location (OR = 1.88, p = 0.041), and positive family history (OR = 2.74, p = 0.003) as significant independent predictors. Conclusions: Uterine leiomyomas may be influenced by a combination of hormonal, metabolic, genetic, and epigenetic factors. Overall findings suggest that MED12 C allele and A/C genotype variation was significantly associated with increased DNA methylation in uterine leiomyomas.

Genes doi: 10.3390/genes17080876

Authors: Audrey J. Majeske Juliet M. Wong Carlos A. Farkas Pool Jose M. Eirin-Lopez Jose V. Lopez Walter Wolfsberger Nikolaos V. Schizas Alondra M. Díaz-Lameiro Stephanie O. Castro-Márquez Kenneth Hilkert Alejandro J. Mercado Capote Taras K. Oleksyk

Background/Objectives: The long-spined sea urchin Diadema antillarum is a keystone herbivore whose grazing maintains Caribbean coral reefs; basin-wide mass mortalities in 1983–1984 and 2022 have made genomic resources a conservation priority, yet no nuclear genome existed for the species. We aimed to generate the first nuclear reference and to resolve the high heterozygosity that complicates genome assembly in broadcast-spawning marine invertebrates. Methods: For the assembly, we combined PacBio HiFi, Oxford Nanopore, and Illumina sequencing. Genome size and heterozygosity were estimated by k-mer profiling. We compared standard and haplotype-aware assembly strategies (hifiasm), evaluated completeness with BUSCO, and annotated repeats using a species-specific RepeatModeler library. Results: k-mer profiling estimated a haploid genome of ~703 Mb with 2.52% heterozygosity. Standard assembly then produced an inflated 1.75 Gb assembly (98.4% BUSCO-complete but 84.4% duplicated), indicating retention of both haplotypes. Haplotype-aware reassembly separated this into a collapsed primary assembly (1.03 Gb) and two phased haplotypes (0.95 and 0.89 Gb), each comparable in size to the chromosome-level congener D. antillarum (886 Mb). BUSCO completeness reached 99.0%, with single-copy orthologs rising to 85–90%, and reference-free consensus quality reached QV 44.5 (Merqury; initial assembly). This genome is repeat-rich (42.84% repetitive; 29.96% unclassified). Conclusions: We provide the collapsed primary assembly together with both phased haplotypes as a haplotype-resolved reference for D. antillarum, establishing a foundation for immunogenomic, comparative, and population-genetic studies and for monitoring and restoration of this ecologically critical species. More broadly, the study shows that haplotype-aware assembly is essential for resolving such highly heterozygous genomes and delivers the genomic foundation needed to guide the conservation of this keystone Caribbean reef species.

Genes doi: 10.3390/genes17080875

Authors: Ebtihal Alharbi Yousef Almehmadi

Background/Objectives: Improved preoperative prediction of nodal metastasis in prostate cancer could refine selection for extended pelvic lymph node dissection, a high-morbidity procedure. Sperm-associated antigen 1 (SPAG1) is a candidate marker of nodal status, but its incremental value beyond clinical staging and the associated transcriptional state remain unevaluated. Methods: In The Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) cohort (497 patients with matched clinical and RNA-sequencing data), we evaluated the association between SPAG1 expression and pathological N stage by logistic regression with 2000-resample bootstrap optimism correction and sensitivity analyses for missing nodal data and batch effects. Hallmark enrichment analysis compared SPAG1 expression extremes (quartile 4 vs. 1) and, separately, N1 versus N0 tumours adjusted for T stage, Gleason grade, and tissue source site; directional concordance was assessed. Results: N1 rates rose across SPAG1 quartiles from 7.6% to 39.0% (per-quartile odds ratio [OR], 1.83; p = 2.55 × 10−5). After adjusting for T stage and Gleason grade, SPAG1 remained an independent predictor (adjusted OR, 2.14; 95% confidence interval [CI], 1.50–3.13; p = 4.8 × 10−5), stable across both sensitivity analyses. Adding SPAG1 improved discrimination (area under the receiver-operating characteristic curve, 0.783 to 0.838; ΔAUC, 0.056; paired DeLong p = 3.03 × 10−5). The SPAG1 transcriptional programme showed cell-cycle, immune–inflammatory, and mTORC1/TGF-β signalling activation with suppressed differentiation and metabolism; all 15 overlapping Hallmark pathways were directionally concordant with the adjusted N1 signature. Conclusions: SPAG1 expression in primary prostate tumours is a candidate predictor of pathological lymph node metastasis with statistically robust incremental discrimination beyond clinical staging. Independent external validation and biopsy-based feasibility studies are required before clinical application.

Genes doi: 10.3390/genes17080874

Authors: Dan Zhao Junzhi Guo Ying Zhang Yuanfeng Lan Tian Zhao Yiliang Xu Qizhou Yang Haihong Ye

Background: Although genetic-environmental interactions are established in autism spectrum disorder (ASD), how environmental toxicants confer susceptibility remains unclear. This study aimed to investigate potential relationship between genetically predicted cerebrospinal fluid (CSF), metabolite levels and ASD liability, and to prioritize regulatory genes, key pathways, and candidate environmental toxicants. Methods: Using two ASD GWAS datasets (exploration data: 18,381 ASD cases/27,969 controls; validation data: 18,235 ASD cases/36,741 controls), we applied multi-omics approaches to prioritize ASD-associated CSF metabolites, regulatory SNPs, and genes. Enrichment analysis and protein–protein interaction (PPI) network analysis were performed on these metabolite-related genes to explore the potential mechanisms linking CSF metabolic disturbances to ASD. Finally, candidate environmental neurotoxicants were screened through protein-chemical interaction analysis, with binding relationships assessed via molecular docking prediction. Results: Two-sample Mendelian randomization (MR) analysis prioritized adenine and proline as candidate CSF metabolites with potential risk associations with ASD. Summary-data-based MR (SMR) prioritized 39 brain-specific quantitative trait loci (QTL) involving 35 candidate regulatory genes, including dual-metabolite modulator GRM8. Functional enrichment analyses suggested potential associations with mitochondrial dysfunction, Hippo signaling pathway, and microtubule dynamics impairment, with protein–protein interaction networks highlighting KATNA1/KATNAL2 as hubs. Protein-chemical interaction screening nominated 14 candidate environmental toxicants, including established chemicals (acetaminophen, valproic acid, estradiol) and novel candidates (SB-431542, K 7174, benzo[a]pyrene), with docking affinity assessed computationally. Conclusions: Our study provides suggestive evidence that elevated adenine and proline may be potential risk factors for ASD and suggests possible involvement of the mitochondrial–Hippo–microtubule pathway. We also propose benzo[a]pyrene as a candidate environmental toxicant that may perturb CSF metabolism. However, given the limited statistical significance, these findings require further validation.

Genes doi: 10.3390/genes17080873

Authors: Yajie Duan Ruihong Zeng Yongsheng Cai Xiaoju Liu Fenglei Sun

Background/Objectives: Tubulins (Tub) are central components of microtubules, but intraspecific variation and developmental expression of the Tub family in Gossypium barbadense remain poorly characterized. This study aimed to characterize the GbTub family using a pan-genome framework and identify candidates associated with fiber development and strength. Methods: A total of 50 GbTub genes were identified in the G. barbadense 3-79 reference genome, and their orthologous presence–absence patterns were subsequently assessed across 12 additional G. barbadense accessions. Phylogenetic, presence–absence variation (PAV), Ka/Ks, structural variation (SV), RNA-seq, RT-qPCR, co-expression, and GO enrichment analyses were integrated. Results: Among the 50 reference-defined GbTub genes, 43 were classified as core genes, 6 as near-core genes, and 1 as an accessory gene, and the encoded proteins were classified into α-, β-, and γ-tubulin clades. All genes showed Ka/Ks < 1. Twenty-three GbTub genes differed between the fiber-strength-contrasting accessions 5917 and PimaS-7, and representative expression trends were supported by RT-qPCR. Network analysis prioritized 10 GbTub candidates based on degree centrality. GbTub21 was the sole SV-associated GbTub gene displaying significant differential expression between accessions harboring versus lacking the corresponding SV. Non-Tub neighbors of the candidate hub genes were enriched for cytoskeletal, intracellular-transport, and plasma-membrane functions. Conclusions: The pan-genome analysis reveals strong conservation with limited intraspecific variation in the GbTub family. Co-expression profiles nominate candidates associated with fiber secondary-wall development, and their causal contribution to fiber strength awaits functional dissection.

Genes doi: 10.3390/genes17080872

Authors: Zhenyu Yang Wendiao Zhang Fengyi Yu Xiaomei Duan Miaojin Zhou Beisha Tang

Leukodystrophies (LDs), a group of heterogeneous genetic disorders, are characterized by selective involvement of cerebral white matter, including abnormal white matter development and/or progressive degeneration. Oligodendrocytes, astrocytes, microglia, axons, and the neurovascular unit collectively contribute to white matter homeostasis and disease progression. Recently, genomic sequencing has identified pathogenic variants in the alanyl-tRNA synthetase 1 (AARS1) and alanyl-tRNA synthetase 2, mitochondrial (AARS2) genes in LD-related phenotypes. Dysfunction of AARS1 and AARS2 proteins may impair cytosolic or mitochondrial tRNA aminoacylation, compromise editing fidelity, and disrupt mitochondrial homeostasis, which may lead to disruption of protein homeostasis, cellular stress responses, and energy failure. Alanyl-tRNA synthetase (AlaRS) impairments play an important role in the pathological processes of cytosolic and mitochondrial alanyl-tRNA synthetase-related disorders. These molecular defects are associated with characteristic neuroimaging patterns and diverse clinical manifestations observed in AARS1/AARS2-related disorders. This review summarizes current knowledge on the genetic basis, clinicopathological features, and molecular mechanisms of AARS1- and AARS2-related leukodystrophies, and discusses emerging therapeutic perspectives, with the aim of facilitating precision diagnosis and future targeted interventions.

Genes doi: 10.3390/genes17080871

Authors: Yong Shi Jiejun Liu Lei Ren Chen Feng Yuan Liu

Background/Objectives: Ficus gasparriniana var. laceratifolia (H. Lév. & Vaniot) Corner is treated as a variety of F. gasparriniana and placed in Ficus subg. Ficus on morphological grounds, but complete plastome evidence for its plastid phylogenetic placement has been lacking. We assembled and analyzed its chloroplast genome to evaluate this morphology-based placement using plastid genomic evidence and to expand genomic resources for the genus. Methods: The plastome was assembled from paired-end reads using GetOrganelle and subsequently annotated. We characterized its genome architecture, simple sequence repeats (SSRs), codon-usage bias, inverted repeat (IR) junctions, and nucleotide diversity after standardizing sequence start positions and small single-copy (SSC) region orientation. Plastid phylogenetic relationships were inferred from four single-IR datasets: whole-plastome, coding, non-coding, and partitioned. Results: The 160,476-bp plastome exhibited the typical quadripartite structure and contained 110 unique genes. Its repeat composition and preference for A/U-ending codons were consistent with an AT-rich plastome, and 61 SSRs and five candidate variable regions represented potential marker resources for future Ficus studies. In all four phylogenetic datasets, F. gasparriniana var. laceratifolia was consistently grouped with F. pumila with maximum ultrafast bootstrap support (UFBoot = 100), conflicting with its morphology-based classification. Approximately unbiased (AU) tests rejected the sampled morphology-based constraint in every dataset, indicating that this morphology–plastid discordance was robust to dataset choice. Conclusions: This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement. These findings provide a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.

Genes doi: 10.3390/genes17080870

Authors: Agata Pietras-Baczewska Adam Chmiel Katarzyna Ognik Robert Rejdak Katarzyna Nowomiejska

ROSAH syndrome is a rare autosomal dominant autoinflammatory disorder caused by gain-of-function mutations in the ALPK1 gene, characterized by retinal dystrophy, optic nerve oedema, splenomegaly, anhidrosis, and headache. We present three related female patients (two sisters and their aunt) with a long-standing history of decreased visual acuity, recurring macular oedema, and progressive retinal dystrophy, as well as systemic involvement including anhidrosis, splenomegaly, headache, and arthritis. All our patients come from one family, with a total of 11 people suffering from ophthalmologic diseases with profound vision loss. Described three patients had confirmed pathogenic variant c.710C>T; p.Thr237Met in the ALPK1 gene and extensive ophthalmic assessment. This case series highlights the importance of genetic testing and multimodal imaging in unexplained familial retinal dystrophies and underlines intrafamilial phenotypic variability. Moreover, it emphasizes ROSAH syndrome as an important differential diagnosis for inherited inflammatory vitreoretinopathies.

Genes doi: 10.3390/genes17080869

Authors: Miao Liu Feifan Wang Luying Han Feiyu Yan Yinshan Huang Yuehua Geng Chunnan Wen Luyang Song Meng Zhang Fang Liu Qingzhou Ma

Background/Objectives: Wheat root and crown rot, caused by Fusarium pseudograminearum, Fusarium graminearum, and Bipolaris sorokiniana, are devastating soil-borne diseases that cause substantial yield losses worldwide. Endophytic fungi are promising sources of bioactive metabolites for agricultural applications. This study aimed to isolate and characterize an endophytic fungus with antifungal activity against major wheat pathogens, identify its active compound, and investigate the underlying transcriptional response. Methods: An endophytic strain Y2 was isolated from Hedyotis diffusa leaves and identified through morphological and phylogenetic analysis based on TEF-1α and RPB2 sequences. Pathogenicity of strain Y2 was evaluated on wheat stem bases. The bioactive compound was purified by HPLC and identified by HR-ESI-MS and NMR. Antifungal activity was assessed using dual-culture and microbroth dilution assays. Transcriptomic analysis (RNA-seq) was performed on F. pseudograminearum treated with equisetin, with qRT-PCR validation of seven representative differentially expressed genes. Results: Strain Y2 was identified as Fusarium incarnatum or a closely related member of the F. incarnatum–equiseti species complex (FIESC) and confirmed to be non-pathogenic to wheat. The purified bioactive compound was characterized as equisetin, which exhibited significant antifungal activity with MIC values of 16, 32, and 64 μg/mL against F. pseudograminearum, B. sorokiniana, and F. graminearum, respectively. Transcriptomic analysis revealed that equisetin treatment induced a polarized transcriptional response in F. pseudograminearum, characterized by strong upregulation of ribosome and translation-related genes and widespread downregulation of other metabolic pathways, particularly nitrogen metabolism. qRT-PCR validation of seven representative genes confirmed the reliability of the RNA-seq data. Conclusions: Our findings demonstrate that equisetin is the active antifungal metabolite produced by F. incarnatum Y2, with potent in vitro activity against major wheat root and crown rot pathogens. The transcriptomic data provide insights into the potential mechanism of action, while the non-pathogenic nature of strain Y2 supports its biosafety. Although these results highlight equisetin as a promising lead compound for antifungal development, further in planta efficacy and safety studies are required before it can be considered for practical biocontrol.

Genes doi: 10.3390/genes17080868

Authors: Zhuomiaoyu Chen Fumei Cao Zhao Li

Background: PPP1R1B has been implicated in tumor progression in several malignancies; however, population-level genetic evidence supporting its role in intrahepatic cholangiocarcinoma (ICC) remains limited. This study aimed to investigate the association between PPP1R1B and ICC risk and prognosis using genetic and multi-omics analyses. Methods: Multiple public datasets were integrated, including finn-b-C3_LIVER_INTRAHEPATIC_BILE_DUCTS, ebi-a-GCST90018583, eqtl-a-ENSG00000131771, GSE138709, The Cancer Genome Atlas (TCGA)-ICC, and FU-iCCA. Two-sample Mendelian randomization (MR) was performed to evaluate the genetic association between PPP1R1B expression and ICC risk. PPP1R1B expression patterns were further characterized using single-cell and bulk transcriptomic analyses. Expression validation was conducted using TCGA-ICC data and tissue microarray immunohistochemistry. Survival analyses were performed using the FU-iCCA cohort and institutional clinical samples. Results: MR analysis identified PPP1R1B as significantly associated with increased ICC risk (p < 0.05, OR > 1), and sensitivity analyses supported the robustness of the results. Single-cell analysis demonstrated enrichment of PPP1R1B expression in malignant cell populations. Bulk transcriptomic datasets and immunohistochemical validation confirmed elevated PPP1R1B expression in tumor tissues. High PPP1R1B expression was significantly associated with poorer overall survival. Conclusions: Genetic and multi-omics evidence supports PPP1R1B as a risk-associated and potential prognostic biomarker in ICC, providing a translational genomics framework for future biomarker development. These findings complement previously reported functional studies and strengthen the biological relevance of PPP1R1B in ICC.

Genes doi: 10.3390/genes17080867

Authors: Zachary W. Nurcombe Lina Mougharbel Thomas M. Kitzler

Congenital anomalies of the kidney and urinary tract (CAKUT) are the leading cause of pediatric chronic kidney disease (CKD) and comprise a heterogeneous group of developmental disorders with a substantial genetic contribution. Advances in next-generation sequencing have facilitated the identification of numerous candidate genes and rare variants associated with CAKUT. However, establishing causality and defining the biological functions of implicated genes remain major challenges. Functional validation is therefore essential to bridge the gap between gene discovery and mechanistic understanding, enabling the interpretation of genetic variation within the context of kidney development and disease. The zebrafish (Danio rerio) has emerged as a powerful in vivo model for studying renal development and interrogating the function of CAKUT-associated genes. Its utility stems from a high degree of genetic and developmental conservation with humans, conserved nephrogenic pathways, optical transparency during embryogenesis, and the relative ease of genetic manipulation. In this review, we provide an overview of zebrafish kidney development within the broader context of vertebrate nephrogenesis, highlighting the key genetic programs governing intermediate mesoderm specification, nephron segmentation, and pronephric morphogenesis. We then systematically examine CAKUT-associated genes that have been modeled in zebrafish, focusing on studies that have linked genetic perturbations to renal development and structural phenotypes. Finally, we discuss the strengths and limitations of zebrafish models for functional genomics and variant interpretation and consider their emerging role in bridging genetic discovery with mechanistic insights into CAKUT pathogenesis.

Genes doi: 10.3390/genes17080866

Authors: Yuan Ren Junwen Meng Jin Zhang Qijian Tian Rui Huang Xin Liu

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits.

Genes doi: 10.3390/genes17080865

Authors: Xufeng Fu Bipeng Lai Rongling He Xiuji Huang Qin Jiang Hui Li

Background/Objectives: Multi-omics datasets are increasingly used for disease classification, but differences in scale, distribution, and resolution across omics layers complicate their integration. Conventional fusion approaches may overlook nonlinear cross-omics dependencies and structured sample–feature relationships. Here, we propose FastMI-HGNet, a two-stream heterogeneous graph neural network for multi-omics disease classification. Methods: The framework uses fast mutual information (FastMI) to construct dependency edge priors for a heterogeneous graph that connects sample and feature nodes. A Transformer-based data stream captures vector-level feature interactions, while a graph attention stream models structural dependencies among samples and molecular features. An uncertainty-aware ensemble further improves stability under small-sample and noisy multi-omics settings. Results: Evaluated on five public multi-omics benchmarks—ROSMAP, LGG, BRCA, and the more challenging COAD tumor-stage classification task, together with KIPAN as a ceiling-level proof-of-concept benchmark—FastMI-HGNet achieved competitive classification performance while supporting interpretable biomarker prioritization. In BRCA, SHAP-based analysis highlighted model-prioritized genes such as FOXC1 and SOX10. Conclusions: FastMI-HGNet supports interpretable multi-omics disease classification and biomarker prioritization.

Genes doi: 10.3390/genes17080864

Authors: Shibo Meng Jiajun Zhu Enmei Hu Jia Liu Yuan Cheng Meiying Ruan Chenxu Liu Qingjing Ye Rongqing Wang Zhuping Yao Zhimiao Li Guozhi Zhou Hongjian Wan Yougen Chen

Background/Objectives: Nucleotide-binding leucine-rich repeat (NLR) proteins are major intracellular immune receptors involved in effector-triggered immunity. However, the evolutionary diversity and genomic organization of NLR repertoires remain incompletely characterized in Solanaceae crops and their wild relatives. This study aimed to investigate the pan-NLRome landscape and evolutionary patterns of tomato and related species. Methods: A comparative pan-NLRome analysis was performed across five angiosperms, including cultivated tomato (Solanum lycopersicum) and four related species (Solanum chilense, Solanum lycopersicoides, Solanum pimpinellifolium, and Arabidopsis thaliana). NLR genes were identified using an integrated HMMER- and BLASTp-based pipeline, followed by chromosome anchoring, orthogroup (OG) classification, phylogenetic analysis, spatial organization analysis, and evaluation of associations with long terminal repeat (LTR) retrotransposons. Results: A total of 1566 chromosome-anchored NLR genes were assigned to 150 OGs. Core OGs represented 25.3% of total OG diversity but contained a large proportion of NLR genes. Rarefaction analysis indicated continuous accumulation of novel OGs with increasing species sampling, supporting an open pan-NLRome structure. Phylogenetic analysis identified 18 NLR subfamilies, with SF_03 and SF_01 together accounting for approximately 79% of NLR genes. Dispersed homologs represented the predominant spatial arrangement pattern, accounting for 85.1% of NLR gene pairs across Solanaceae species. Conclusions: This study provides a comparative genomic framework for understanding NLR diversity and evolution in tomato and related Solanum species, highlighting the dynamic expansion and spatial organization of plant immune receptor repertoires and providing valuable resources for resistance gene discovery.

Genes doi: 10.3390/genes17080863

Authors: Athina Theodosiou Ludmila Kousoulidou Ioannis Papaevripidou Constantia Aristidou Angelos Alexandrou Andrea Hadjipanteli Christina Votsi Marios Tomazou Styliana Menelaou Demetris Efstathiou Yiannis Ioannou Emilia Athanasiou Elena Papamichael Violetta Christophidou-Anastasiadou Sofia Ourani Paola Evangelidou George A. Tanteles Carolina Sismani

Background/Objectives: Congenital anomalies and neurodevelopmental disorders frequently co-occur and exhibit substantial genetic and phenotypic heterogeneity, posing a persistent diagnostic challenge. Exome sequencing has become an important first- or second-tier diagnostic tool for these conditions, yet diagnostic yields vary considerably depending on phenotype, ancestry, sequencing strategy, and interpretation, with over half of referrals remaining without a definitive genetic diagnosis. Methods: We analyzed data from 692 patients referred to the Department of Cytogenetics and Genomics at the Cyprus Institute of Neurology and Genetics between January 2021 and December 2025 for clinical exome sequencing or whole-exome sequencing as part of the diagnostic work-up for congenital disorders and/or syndromic or non-syndromic neurodevelopmental disorders. Results: A total of 134 distinct variants were identified, corresponding to an overall diagnostic yield of 17.9% out of which 52 (38.8%) were novel, and 50 variants (37.3%) were de novo, as expected from the high proportion of severe neurodevelopmental presentations. Missense variants were the most prevalent within our cohort, while chromatin and transcriptional regulator genes constituted the largest functional gene category, followed by variants in collagen-encoding genes. Conclusions: This study provides the first systematic, mutational-level characterization of a Cypriot Mendelian disease cohort, establishing a local baseline diagnostic yield and revealing a high proportion of novel variants that reflect the underrepresentation of Eastern Mediterranean populations in global databases. These findings underscore the value of submitting population-specific variants to public repositories and of phenotype-driven reanalysis targeting recurrent gene families, supporting more efficient diagnostics and future precision medicine initiatives in Cyprus.

Genes doi: 10.3390/genes17080862

Authors: Dario Colacurci Laura Sarno Emmanuel Fiore Francesco Raimondi Nina Martinelli Angelo Sirico Costantino Di Carlo Giuseppe Bifulco Maurizio Guida Giuseppe Maria Maruotti

Background: Neonatal encephalopathy (NE) is a major cause of neonatal mortality and long-term neurological disability. Although hypoxic–ischaemic encephalopathy (HIE) is the most common cause, several genetic disorders may mimic or coexist with hypoxic–ischaemic injury. Next-generation sequencing has emerged as a promising diagnostic tool in this setting. This systematic review evaluated the current evidence on genomic sequencing in NE. Material and methods: A systematic review was conducted according to PRISMA 2020 guidelines and prospectively registered in PROSPERO. PubMed/MEDLINE, Embase, and Scopus were searched from inception to June 2026. Eligible studies included neonates (≤28 days) with NE, suspected or confirmed HIE, HIE mimics, or unexplained NE who underwent genomic sequencing. Whole-exome sequencing (WES), whole-genome sequencing (WGS), clinical exome sequencing (CES), rapid genomic sequencing, and targeted next-generation sequencing panels were considered. Study quality was assessed using the Newcastle–Ottawa Scale. Results: Seven studies met the inclusion criteria. Considerable heterogeneity was observed regarding patient selection, sequencing strategies, and reported outcomes. Among diagnostic sequencing studies, diagnostic yield ranged from 23.5% to 53.1%. Pathogenic and likely pathogenic variants were identified in genes associated with developmental and epileptic encephalopathies, metabolic disorders, mitochondrial diseases, and neurodevelopmental syndromes, including SCN2A, KCNQ2, CACNA1A, STXBP1, PTPN11, BCOR, MMUT, COQ2, and GBE1. Genomic sequencing frequently refined or changed the initial diagnosis, improved prognostic assessment and genetic counselling, and, in selected cases, guided disease-specific treatment. One study investigated genetic susceptibility to hypoxic–ischaemic injury rather than diagnostic sequencing. Conclusions: Genomic sequencing provides clinically meaningful diagnoses in a substantial proportion of neonates with unexplained NE or atypical HIE presentations. Current evidence supports integrating genomic sequencing into the diagnostic evaluation of selected infants, although larger prospective studies are needed to define its optimal timing, clinical utility, and cost-effectiveness.