Genes doi: 10.3390/genes17091125

Authors: Yangxi Fu Zheng Wang Shan Liu Lin Liu Xudong Tang

Background: Helicobacter pylori (H. pylori) infection is a well-established risk factor for gastric cancer; however, evidence on the associations between antigen-specific antibody traits, host methylation, and gastric cancer risk remains limited. Methods: Using a forward two-sample Mendelian randomization (MR) design, we integrated methylation quantitative trait loci (mQTLs), external cohorts, The Cancer Genome Atlas–Stomach Adenocarcinoma (TCGA-STAD), and functional annotations through a three-stage framework (antibody trait screening, CpG prioritization, and external replication) to evaluate a two-step pathway from host antibody response to gastric cancer via DNA methylation. Results: Among six H. pylori antigens, antibody response to outer membrane protein (OMP) showed the strongest positive association with gastric cancer risk (OR = 1.186, 95% CI: 1.079–1.304, raw p = 4.08 × 10−4). CpG-level prioritization identified cg24290947 (annotated to HLA-DMA) as a methylation site linked to gastric cancer susceptibility, with an inverse MR association (beta = −0.2347, 95% CI: −0.3980 to −0.0713, raw p = 0.00487). External exploration showed that cg24290947 methylation was elevated in H. pylori-positive gastric mucosa; however, its direct tumor–normal difference in a 12-pair cohort was not significant, although regional methylation perturbations were observed. HLA-DMA and MHC-II expression were consistently higher in tumor versus normal tissues across three cohorts, whereas TCGA-STAD did not support a stable linear relationship between cg24290947 methylation and HLA-DMA/MHC-II expression; three of six composition-adjusted models showed nominal significance but were model-dependent. These signals were enriched in antigen processing and presentation pathways. Conclusions: cg24290947/HLA-DMA represents a hypothesis-generating regional methylation candidate for further investigation rather than a confirmed linear transcriptional regulator. The MR evidence is based on European-ancestry summary data; its generalizability and any clinical predictive value warrant independent evaluation.

Genes doi: 10.3390/genes17091122

Authors: Arnold Rojas Sahil Jethi Tulin Budak-Alpdogan Manoj K. Pandey

Acute myeloid leukemia (AML) is cytogenetically and phenotypically heterogeneous, and this diversity contributes to differences in how patients respond to therapies that target apoptosis. Venetoclax, a selective BCL-2 inhibitor, has been demonstrated to improve outcomes when combined with hypomethylating drugs (HMAs) such as azacitidine or decitabine; nonetheless, clinical trials have indicated that resistance and recurrence are prevalent. This review examines the current evidence linking chromosomal abnormalities and cellular differentiation state to mitochondrial apoptotic pathways, with an emphasis on how these factors influence dependence on certain anti-apoptotic BCL-2 family proteins. We summarize how specific cytogenetic subtypes and high-risk groups (including monosomy 7/del(7q) and complex karyotype/TP53-altered AML) frequently show stress-adaptive signaling and reliance on multiple anti-apoptotic pathways, which can limit the durability of response to BCL-2 inhibition. Lineage-associated dependencies are also examined, such as monocytic differentiation (which leads to increased MCL-1 reliance) and erythroid/megakaryocytic differentiation, which has been associated with increased BCL-XL dependence and venetoclax resistance. Finally, we discuss the therapeutic implications of dependence mapping, including venetoclax combinations and direct MCL-1/BCL-XL targeting, and propose promising biomarker strategies that can detect dependence shifts early and guide appropriate treatment selection.

Genes doi: 10.3390/genes17091123

Authors: Chunyan Yin Juan Ye Ling Hou Xiaoping Luo

Mosaic trisomy 14 is a rare chromosomal anomaly with a broad phenotypic spectrum. We report a 10-year-3-month-old girl with severe short stature, developmental delay, and repaired patent ductus arteriosus. An incompletely documented combined insulin–clonidine stimulation test yielded a peak GH concentration of 6.85 ng/mL and was not considered sufficient to establish growth hormone deficiency. Karyotyping of 100 peripheral-blood metaphases showed 47,XX,+14[6]/46,XX[94]. Initial copy-number sequencing detected a 34.37 Mb mosaic 14q gain; repeat SNP-based chromosomal microarray analysis demonstrated an approximately 86.83 Mb 14q11.2-q32.33 mosaic gain at an array-estimated fraction of approximately 50%, compatible with the cytogenetic diagnosis. Targeted 14q32.2 analysis showed increased total and methylated-allele dosage, with methylated fractions of 48.6–62.3%, interpreted as dosage imbalance within the broader 14q gain rather than an independent epimutation. Four STR loci showed biparental inheritance. Quantitative peak-height and peak-area analysis at three informative, bias-correctable STR loci demonstrated excess paternal-allele dosage, providing independent support for, but not definitive proof of, paternal origin of the additional chromosome 14. rhGH was prescribed for SGA with persistent short stature at 0.22 mg/kg/week. At three months, height was 124.7 cm (+1.9 cm); no adverse events were reported. These observations do not establish treatment efficacy or safety.

Genes doi: 10.3390/genes17091121

Authors: Yilong Lu Yong Fan Kun Liu Jian Wen Jialin Sun Wensong Sun

Background: Calcineurin B-like (CBL) protein-mediated calcium signaling represents a core regulatory pathway underlying plant abiotic stress adaptation. Ziziphus jujuba var. spinosa (sour jujube) is a perennial woody species with remarkable saline–alkali and drought tolerance, yet the CBL gene family in this species has not been systematically characterized. Methods: We performed genome-wide identification and characterization of the CBL gene family in sour jujube through integrated bioinformatic analyses, transcriptomic profiling, qRT-PCR, and yeast two-hybrid (Y2H) assays, with the annotation of one gene manually corrected based on molecular cloning and transcriptome validation. Results: Ten non-redundant ZjCBL genes were identified and grouped into three phylogenetic clades. Synteny and selection pressure analyses identified two collinear gene pairs that have undergone strong purifying selection. All ZjCBL proteins contain canonical EF-hand motifs and are predicted to be mainly localized to the plasma membrane, with ZjCBL4 and ZjCBL9 harboring additional N-terminal transmembrane helices. The promoter regions of ZjCBL genes are enriched in hormone- and stress-responsive cis-acting elements. ZjCBL1, ZjCBL2, ZjCBL3, and ZjCBL5 were highly expressed across multiple tissues, and ZjCBL1 exhibited sustained upregulation under long-term saline–alkali stress, concurrent with the accumulation of osmoprotectants. Y2H assays confirmed that ZjCBL1 interacts with two ZjCIPK proteins, exhibiting a stronger interaction signal with ZjCIPK13. Conclusions: This study provides the first systematic characterization of the CBL gene family in sour jujube and revises the annotation of ZjCBL1, establishing ZjCBL1 as an important component of the ZjCBL–ZjCIPK signaling network and offering candidate gene resources for molecular breeding to enhance stress tolerance in fruit crops.

Genes doi: 10.3390/genes17091120

Authors: David Aebisher Jakub Tylutki Angelika Myśliwiec Nazarii Kozak Dorota Bartusik-Aebisher

Despite decades of clinical validation, glioblastoma (GBM) treatment remains tethered to a dismal 15-to-16-month survival plateau, heavily thwarted by the ys blood–brain barrier (BBB) and profound cellular heterogeneity. While the 2021 World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS5) fundamentally reoriented diagnosis around definitive molecular signatures, such as isocitrate dehydrogenase (IDH)-wildtype status, epidermal growth factor receptor (EGFR) amplification, and +7/−10 chromosomal alterations, the ultimate obstacle to clinical efficacy is the tumor’s intense non-genetic plasticity. Malignant cells reject rigid hierarchies; single-nucleus insights reveal a fluid transcriptomic continuum spanning neurodevelopmental lineages, novel glia-like or neuronal-like states, and highly resilient proneural-mesenchymal (PM) hybrid populations. This intrinsic dynamism is reinforced by functional neuro-gliomal integration into the host brain via electrochemical TM synapses, an immunologically cold niche dominated by secreted phosphoprotein 1 (SPP1+) myeloid cells, and a self-reinforcing hypoxic-angiogenic loop. Under cytotoxic therapy, these networks execute rapid adaptive remodeling, selecting for hypermutator phenotypes and specialized senescence-associated secretory phenotypes (SASP) that dictate aggressive recurrence.

Genes doi: 10.3390/genes17091119

Authors: Eliezer Kopf

Background/Objectives: Retinoic acid receptor γ (RARγ), encoded by RARG, is increasingly recognized as a cancer-associated regulator through aberrant expression in multiple solid tumors and recurrent gene rearrangements in acute myeloid leukemia. While the oncogenic relevance of RARγ is well established, the potential involvement of its N-terminal activation function-1 (AF1) domain in human cancer remains poorly characterized. Previous biochemical studies demonstrated that phosphorylation of Ser66 and Ser68 in RARγ2, corresponding to Ser77 and Ser79 in canonical RARγ1, is required for ligand-dependent receptor activation, ubiquitination, and proteasome-mediated degradation. Methods: To determine whether this experimentally validated phosphoregulatory region is altered in human cancer, we interrogated the Catalogue of Somatic Mutations in Cancer (COSMIC v104, GRCh38) at single-residue resolution. Mutation data were integrated with clinical and pathological information obtained from the corresponding primary publications and public annotation resources. Results: Rare somatic mutations affecting the AF1 phosphoregulatory region were identified, including the missense variants p.S77L and p.S79L, the nonsense variant p.S79*, and the in-frame insertion p.S77_P78insLQ. These alterations occurred in independent epithelial malignancies, including cervical neuroendocrine carcinoma, head and neck squamous cell carcinoma, lung adenocarcinoma, bladder carcinoma, and gastric neuroendocrine carcinoma. Notably, the truncating p.S79* mutation was detected in five spatially distinct regions of a single EGFR-mutant lung adenocarcinoma, consistent with an early clonal event during tumor evolution. Rare cancer-associated mutations affect a previously characterized AF1 phosphoregulatory module of RARγ. These findings extend established RARγ regulatory biology into the context of human malignancy and broaden the spectrum of reported cancer-associated RARG alterations. While the functional consequences of these rare variants remain unknown, their occurrence within residues known to regulate receptor activation and turnover highlights the AF1 phosphoregulatory region as a candidate for future mechanistic investigation.

Genes doi: 10.3390/genes17091118

Authors: Predrag Noveski Natalija Jovanovska Ivana Maleva Kostovska Gjorgji Bozhinovski Sanja Kiprijanovska Marija Terzikj Marija Vujovikj Emilija Shukarova Stefanovska Aleksandar Dimovski Dijana Plaseska-Karanfilska

Background/Objectives: Expanded carrier screening (ECS) panels often rely on pan-ethnic databases, such as the ACMG Tier 3 panel, but their ability to capture population-specific reproductive risk is uncertain. We characterized pathogenic/likely pathogenic (P/LP) variants and at-risk-couple (ARC) probabilities in an underrepresented population from North Macedonia to inform ECS gene prioritization. Methods: NGS data from 1438 subjects of Macedonian, Albanian, and other local ancestry, referred for rare-disease diagnostics, were analyzed across 1795 candidate autosomal recessive/X-linked genes. P/LP variants were compared with gnomAD exomes v2.1.1 non-Finnish European frequencies (Fisher’s exact test). Gene-specific ARC probabilities ranked genes and generated cumulative ARC curves per subgroup. Results: We identified 2007 P/LP variants across 1096 genes. One hundred variants in 89 genes reached an allele frequency ≥ 1/200 in the Macedonian or Albanian subgroups; over one-third were absent from candidate ECS panels, mostly linked to severe or variable phenotypes. ARC saturated rapidly: genes with carrier counts ≥ 1/100 (ACMG Tier 2) accounted for over 85% of total ARC, and with ≥1/200 (ACMG Tier 3) for more than 93%. Total ARC among autosomal recessive panel genes (X-linked genes analyzed separately) was 3.42%, rising to 5.02% in the Albanian subgroup. Excluding top hypomorphic variants reduced ARC by 34–37%, highlighting variant-specific penetrance. The highest-ARC genes diverged between subgroups, with limited overlap with pan-ethnic panels. Conclusions: Population-specific carrier frequencies influence gene prioritization and estimated reproductive-risk probabilities for ECS. Population-tailored ECS panels that incorporate local carrier-frequency data, including embryonic/fetal-lethal genes, and account for hypomorphic alleles to avoid overestimating reproductive risk probabilities could improve the identification of couples at increased reproductive risk, particularly in underrepresented populations.

Genes doi: 10.3390/genes17091117

Authors: Alisher A. Abdullaev Darya V. Zakirova Sergei A. Kosushkin Fazliddin Z. Xonboev Guzal J. Abdullaeva Rano B. Alieva Shahlo U. Turdikulova

Background/Objectives: Central Asian populations are almost entirely absent from genomic reference resources, yet Uzbekistan has one of the fastest rates of growth in age-standardised type 2 diabetes (T2D) incidence. Allele frequencies at cardiometabolic risk loci are unknown, limiting the interpretation of polygenic risk scores (PRS) derived elsewhere. We aimed to characterise effect-allele frequencies in an Uzbek cohort from Tashkent and quantify divergence from 1000 Genomes panels to guide future PRS evaluation. Methods: We genotyped 171 adults from Tashkent (131 with T2D, 40 without) on a custom Agilent SureSelect panel of cardiometabolic candidate SNPs. After quality control, 1939 variants were analysed. Effect-allele frequencies were compared with 1000 Genomes Phase 3 superpopulations (EUR, SAS, EAS, AFR) using Hudson FST and Nei’s genetic distance with bootstrap 95% CIs (1000 replicates). Case–control association was assessed descriptively using both unadjusted and age- and sex-adjusted additive logistic regression, with the adjusted model as primary. Results: Reference frequencies were available for 1533 of 1939 variants (1363 at MAF ≥ 0.05). Frequencies clustered with South Asian (FST = 0.077, 95% CI 0.065–0.089) and European panels (FST = 0.086, 95% CI 0.072–0.099), which were indistinguishable (ΔFST = −0.010, 95% CI −0.022 to 0.003) and more divergent from East Asian and African panels. Divergence from the European and South Asian panels was unrelated to nominal association status (Mann–Whitney p = 0.99 and 0.57). In the primary age- and sex-adjusted analysis, no variant survived multiple-testing correction (minimum Bonferroni-adjusted and false-discovery-rate q = 0.28), consistent with the unadjusted sensitivity analysis. Conclusions: This study provides the first systematic allele-frequency reference for cardiometabolic risk loci in an Uzbek cohort from Tashkent. The profile is closest to South Asian and European panels and identifies PRS from these ancestries as priority candidates for future local validation in Central Asian settings. The case–control analysis was underpowered and is reported descriptively.

Genes doi: 10.3390/genes17091116

Authors: Paola D’Ambrosio Lorenzo Cipriano Alessia Pugliese Roberta Petillo Dario Ricciardi Francesco Habetswallner Carmelo Rodolico Manuela Priolo

SCN4A encodes the skeletal-muscle voltage-gated sodium channel NaV1.4. Pathogenic variation in this gene produces fundamentally different disease mechanisms, including dominant alpha-pore gain of function, dominant S4 gating-pore currents, and reduced channel availability, with severe biallelic loss of function causing congenital myopathy and fetal hypokinesia. This heterogeneity makes variant interpretation difficult because formal variant classification, the direction of channel dysfunction, and patient-level disease attribution are closely related but distinguishable conclusions. In this review, we synthesize the clinical, genetic, electrophysiological, structural, and functional evidence relevant to SCN4A variant interpretation, with particular attention to missense variants of uncertain significance. We examine how inheritance, channel topology, phenotype, population data, segregation, RNA evidence, regional and residue-level context, and mechanism-matched functional assays can be integrated within the ACMG/AMP framework. Published pathogenic-enriched regions, gnomAD regional missense constraint, and same-residue observations may contribute to variant interpretation when the requirements of an applicable ACMG/AMP criterion are met; when they have not been specifically validated or calibrated for SCN4A, they are best used as contextual information to prioritize additional evidence generation. Based on this literature, we organize these evidence domains into a practical phenotype-first, mechanism-informed workflow for SCN4A variant interpretation. This workflow is not intended as an alternative to or extension of ACMG/AMP but as an SCN4A-specific application of established variant-interpretation principles in a gene associated with multiple inheritance patterns and directionally distinct disease mechanisms. After technical confirmation of a candidate variant, as well as phenotype and inheritance context guide selection of the relevant disease model, appropriately validated functional evidence may contribute directly to ACMG/AMP classification, while functional mechanism and patient-level disease attribution are documented as related but distinguishable interpretative outputs. The same approach applies when a variant is identified through genotype-first sequencing: interpretation should return to deliberate phenotyping, inheritance assessment, electrophysiological characterization, and consideration of the differential diagnosis before disease causality is inferred.

Genes doi: 10.3390/genes17091115

Authors: Kholud R. Alrubaie Raghad A. Alzaylaee Latifah A. Alayyaf Farjah H. Algahtani Shaker A. Alomary Abdullah M. Assiri Mariam M. AlEissa

Pharmacogenomics has the potential to improve the safety and efficacy of medicines in Saudi Arabia, and has a strong basis for implementation through population-specific genomic evidence, growing laboratory capacity and national digital health investment. We undertook a structured policy analysis and evidence synthesis of Saudi, regional, and international evidence; compared selected implementation capabilities across established models; and assessed national readiness descriptively across key health system domains. Using published evidence and structured expert judgement, we propose gene–drug priority tiers according to their clinical impact, population relevance and feasibility. Saudi Arabia’s strengths are in genomic evidence and digital health infrastructure, but large gaps exist in governance, laboratory standardization, electronic health record interoperability, clinical decision support, workforce readiness, reimbursement, and outcome evaluation. Five pathways are proposed for initial implementation: CYP2C19–clopidogrel, DPYD–fluoropyrimidines, TPMT/NUDT15–thiopurines, HLA-guided anticonvulsant prescribing and HLA-B*57:01–abacavir. We propose a framework that could be supported by the Population Health Observatory and a six-phase roadmap, moving from governance and technical design to multicenter pilots, national scale-up and continuous evaluation.

Genes doi: 10.3390/genes17091114

Authors: José P. Miranda Gigliola Alberti Ana Pereira Juan Cristóbal Gana José L. Santos

Objective: To estimate the frequency and potential impact of genetic variants involved in metformin pharmacokinetics, including gastrointestinal absorption, renal elimination, and hepatic transport in the Chilean population. Subjects and methods: The frequency of metformin-related gene variants was estimated using data from a genome-wide, exome-focused genotyping array in 918 participants of the Chilean Growth and Obesity Cohort Study (GOCS). Allele frequencies in Chileans were compared with those published worldwide, and the degree of Amerindian/European ancestry was assessed. A predictive bioinformatic analysis was performed on relevant genetic variants using PolyPhen-2. Results and Discussion: The genetic polymorphism (p.Leu125Phe; p.L125F; rs77474263; C>T) in the SLC47A1 gene (MATE1 transporter) showed a much higher frequency of the 125Phe (T-allele) in the Chilean population (15.3%) than in non-American populations, being virtually absent in Africa, Europe, or Asia. The 125Phe variant was associated with a higher percentage of Amerindian ancestry in the Chilean population. This result is consistent with a previous report indicating that this variant is enriched in Native American populations, given its high frequency among Mestizo and Indigenous populations in Mexico. The functional variant p.125Phe has been previously suggested to promote plasma metformin accumulation, mitochondrial dysfunction, and increased plasma lactate concentrations by altering renal metformin elimination. Conclusions: The missense variant p.Leu125Phe (rs77474263) in SLC47A1 is frequent in Chile and Mexico, and apparently absent in non-American populations. In homozygosis, the p.125Phe variant has been previously associated with impaired renal drug elimination, metformin systemic accumulation, and hyperlactatemia.

Genes doi: 10.3390/genes17091113

Authors: Xiqing Luo Xuqi Zheng Wenyu Xu Dan Guo Xinlei Jia Jieruo Gu Xiaoyi Zhao Yutong Jiang

Objectives: We tested whether a database-derived phthalate ester (PAE)–ankylosing spondylitis (AS) candidate panel identifies an inflammatory transcriptional program and characterized its transcription-factor (TF) architecture. Methods: Machine learning prioritization and repeated nested cross-validation were followed by locked-model transfer from GSE73754 to GSE25101. Donor-level single-cell analyses included 96,746 peripheral blood mononuclear cells from 10 AS and 29 healthy-control donors (GSE194315), with corroboration assessed in 25 additional baseline AS patients (GSE277117). Results: Within classical monocytes, the continuous signature covaried with panel-excluded TNF-α/NF-κB signaling (ρ = 0.571; q = 0.000729), inflammatory response (ρ = 0.447; q = 0.0108), and eight of 10 AP-1-related TF activities. Target-excluded TF activities covaried with CXCL8 (8/10) and IL1B (10/10). AP-1-gene/CXCL8 co-expression received partial corroboration in the additional AS cohort (JUN–CXCL8: ρ = 0.92). Among 16 genes prioritized from 473 shared candidates, CXCL8, IL2RB, STAT5B and TNF were stable. The locked 14-gene model achieved an area under the receiver-operating-characteristic curve of 0.770 (DeLong 95% confidence interval, 0.596–0.943), supporting partial rank transportability. Secondary analyses showed a lower CD56bright fraction among natural killer (NK) cells in AS (−2.699 percentage points; 95% confidence interval, −4.575 to −0.611; q = 0.0498) and reduced NK-cell JUN expression (log2 fold change = −0.995; adjusted p = 0.0497). Conclusions: The PAE–AS signature identifies an AP-1/CXCL8-associated classical-monocyte inflammatory program, with partial cross-cohort corroboration and secondary NK alterations, providing candidates for exposure-informed mechanistic studies.

Genes doi: 10.3390/genes17091112

Authors: Elena Urízar Pablo Solis Nuria Puente Ana Fontalba Roberto Zarrabeitia José A. Riancho

Background: Hereditary hemorrhagic telangiectasia (HHT) is a rare autosomal dominant vascular disorder primarily caused by pathogenic variants in the ENG and ACVRL1 genes. Although genotype–phenotype correlations are well established at the population level, the degree of phenotypic similarity among relatives sharing the same variant is poorly characterized. Objective: to explore differences in expressivity and quantify the degree of phenotypic variability among individuals with HHT carrying the same pathogenic variant. Methods: We evaluated 60 patients from a reference center with recurrent ENG and ACVRL1 variants, to quantify intra-familial phenotypic heterogeneity using Shannon entropy indices, Jaccard distances, and a latent variable liability-threshold approach. Results: There was substantial phenotypic variability among individuals and families, with cutaneous telangiectasia being the most frequent manifestation. Shannon entropy and Jaccard analyses indicated broadly high variability. The shared variant accounted for only 3.3% of total variance. Age was significantly associated with disease manifestations (β = 0.027, p = 0.002; OR = 1.028, 95% CI 1.010–1.045), with each additional year increasing the odds of severe symptoms by 2.7%, particularly bleeding severity and skin telangiectasias. Conclusions: These findings suggest that the variable expressivity in HHT is predominantly driven by individual-level factors other than the specific pathogenic variant carried by each patient.

Genes doi: 10.3390/genes17091111

Authors: Caiqin Xu Tao Zhou Ying Huang Yihan Yang Jing Liu Lu Yang Qian Li Xiqiang Liu Bo Zhang

Background/Objectives: Vesicular trafficking mediates the transport of proteins and other cellular components between intracellular organelles. The MAG2 complex serves as a key tethering factor mediating ER–Golgi retrograde vesicle transport, and has been implicated in plant growth, development, and stress responses. Methods: In this study, seven MAG2 family genes were identified in Medicago sativa from the Zhongmu No. 4 reference genome using hidden Markov model searches (HMM) and BLASTP analysis. Results: Phylogenetic analysis assigned four genes to the MAG2 subfamily and three genes to the MAG2L subfamily. Chromosomal distribution and collinearity analyses indicated that segmental duplication potentially contributed to the expansion of the MAG2 family in alfalfa. Gene structure and conserved motif analyses revealed a high degree of conservation among the identified members, with Motif 10 occurring specifically in the MAG2 subfamily. Subcellular localization prediction analysis predicted that four MsMAG2 proteins were localized in chloroplasts, two in the nucleus, and one in the peroxisome. Analysis of promoter sequences identified numerous cis-regulatory elements associated with responses to hormones, light, and environmental stress, suggesting that MsMAG2 genes may participate in plant development and environmental adaptation. Furthermore, genome-wide association analysis identified MsMAG2L2 that can be associated with tillering. Conclusions: These results provide a comprehensive genome-wide characterization of the MAG2 gene family in alfalfa and establish a basis for further investigating the functional associations of MsMAG2L2 in branch development.

Genes doi: 10.3390/genes17091109

Authors: Sajid Ali Adnan Amin

Ulleungdo Island harbors several endemic plant lineages commonly interpreted as products of anagenetic speciation following long-distance colonization. Yet plastome phylogenies represent a single organellar genealogy and may conflict with nuclear genomic structure, morphology, or taxonomic boundaries. This critical mini-review evaluates whether plastid-based hypotheses for the origin and diversification of Ulleungdo endemics are supported by independent molecular and phenotypic evidence. We synthesize findings from comparative plastomics, chloroplast haplotype and network analyses, nuclear microsatellites, nrDNA sequencing, genome-wide multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) single-nucleotide polymorphisms (SNP), cytogenetics, morphology, and multicompartment phylogenomics. The evidence reveals heterogeneous evolutionary outcomes. Prunus takesimensis and Phedimus takesimensis are broadly consistent with probable single-origin scenarios, although confidence is constrained by progenitor sampling and marker resolution. Rubus takesimensis exhibits chloroplast non-monophyly and elevated haplotype diversity consistent with multiple maternal origins, whereas Acer takesimense shows signatures of historical drift and loss of rare nuclear alleles. Morphological, chromosomal, plastid, and nuclear–ribosomal evidence strongly support Allium ulleungense, while the delimitation of Viola ulleungdoensis remains unresolved. Plastid–nuclear incongruence in Hepatica maxima and Fagus multinervis further indicates that introgression, hybridization, incomplete lineage sorting, and restricted taxon sampling can complicate evolutionary inference. This comparative framework distinguishes species histories from provisional interpretations based on limited accessions or uniparentally inherited markers. The novelty of this review lies in its cross-taxon assessment of plastome–nuclear–morphological congruence rather than a descriptive plastome inventory. Ulleungdo lineages interpreted as products of anagenetic speciation do not exhibit a uniform genomic signature and that robust taxonomic, evolutionary, and conservation inference requires population-level integration of independently inherited genomic compartments with standardized morphological and reproductive data.

Genes doi: 10.3390/genes17091110

Authors: Wenqing Feng Zejun Zhang Zheng Wu Chengyu Yuan Jinlei Sun Guoqiang Wang Yunqing Liu

Background/Objectives: Large language models and automated analytical tools show potential for biomedical text understanding, knowledge integration, and single-cell data interpretation, but interpretations of specific gene regulatory relationships still require empirical grounding. For TF–target relationships, one relevant constraint is whether curated regulatory edges show detectable expression-level statistical evidence in the single-cell data being interpreted, because such evidence may vary across cellular states, conditions, and regulatory mechanisms. We therefore evaluated the statistical visibility of known transcription factor (TF)–target relationships in single-cell expression space to aid the interpretation of regulatory inference and automated-tool outputs. Methods: We performed two complementary analyses: first, testing whether curated TF–target edges showed stronger pair-level associations than matched background gene pairs; and second, assessing whether high-scoring TF–gene pairs corresponded to existing regulatory knowledge and whether their target genes showed pathway coherence. Results: Across four peripheral blood mononuclear cell (PBMC) datasets, four adult tissues, and seven adult cell types, curated TF–target relationships showed weak but reproducible statistical visibility rather than strong separation. For all five association metrics, the mean area under the precision–recall curve (AUPRC) was only slightly above the random-ranking baseline of 0.5. High-scoring pairs were more often supported by curated resources, and their target genes showed context-specific Hallmark pathway coherence. Conclusions: Single-cell expression associations can provide useful but limited statistical clues for TF–target regulation and should be interpreted as complementary rather than definitive regulatory evidence.

Genes doi: 10.3390/genes17091108

Authors: Faisal Almalki Amal Saleh Alsofyany Abdulaziz K. Almalki Ashraf Oudah Abu Shuaylan Haya Alruqi Jwaher Mesleh Althobiti

Background: The transcobalamin receptor, encoded by the CD320 gene, mediates the cellular uptake of the transcobalamin–cobalamin complex (vitamin B12). Pathogenic variants in CD320 impair the intracellular transport, resulting in methylmalonic acid (MMA) and propionylcarnitine (C3) level, despite normal circulating vitamin B12 levels, with variable clinical phenotypes. Methods: Whole-exome sequencing (WES) was carried out for a newborn screening positive proband. Further plasma metabolic investigation and blood gas analysis were carried out for the proband. Sanger sequencing was carried out to confirm the candidate variant and identify the familial segregation. Results: The proband presented with elevated C3 and MMA levels and exhibited an expanded clinical phenotype that included severe microcephaly, metabolic acidosis, low bicarbonate and pancytopenia. WES identified a homozygous missense candidate variant in the last amino acid of exon 1 in the CD320 gene (NM_016579.3: c.142G>C, p.Gly48Arg). Another adjacent synonymous homozygous candidate variant was identified (NM_016579.3: c.141A>C, p.Ala47=). Both variants were identified in a male proband from a consanguineous family. Both variants were confirmed by Sanger and segregated within the family members. During one year of follow-up, the patient showed persistent microcephaly while receiving a specialized metabolic formula and levocarnitine supplementation. Conclusions: This study identified a novel recessive missense candidate variant and an adjacent synonymous candidate variant in CD320, supported with biochemical and clinical features of CD320-associated cobalamin transport deficiency. This suggests microcephaly may be a previously unrecognized phenotype with possible association of impaired intracellular cobalamin transport, while elevated C3 detected through routine newborn screening may be the earliest biochemical indicator of CD320-associated cobalamin transport deficiency.

Genes doi: 10.3390/genes17091107

Authors: Yilin Wang Shanshan Li Xin Jin

Background/Objectives: Sleep and circadian disturbances are common in neurodevelopmental conditions, yet the developmental cortical programs linking clock-related transcriptional regulators to disease vulnerability remain unclear. Methods: Here, we integrated human developmental brain transcriptomes, weighted gene co-expression network analysis (WGCNA), human and mouse cortical single-cell atlases, prenatal immune activation transcriptomes, and ASD postmortem brain datasets to characterize the developmental architecture of BrainSpan-derived cortical programs and examine their behavior in perturbational and disease contexts. Results: In the BrainSpan frontal cortex, canonical clock-related genes followed structured but heterogeneous developmental trajectories rather than behaving as a coordinated oscillator-like unit. WGCNA identified a postnatal-rising BrainSpan-derived primary developmental module that was strongly associated with developmental age and enriched for synaptic signaling, neurotransmitter transport, ion transport, membrane excitability, cellular respiration, metabolic regulation, and proteostatic processes. Network analysis placed multiple canonical clock-related and clock-regulatory genes, including NPAS2, BHLHE40, BHLHE41, PER family members, RORA, NR1D1/2, and CLOCK, within a broader neuronal and homeostatic co-expression architecture, although their module-membership strengths varied substantially. Projection onto a human cortical developmental single-cell atlas revealed a non-uniform distribution of the corrected BrainSpan-derived developmental signature, with relatively higher scores in excitatory and inhibitory neuronal populations and lower scores in neuroblast and radial glial populations. A mouse cortical developmental single-cell atlas provided a comparative view of the stage- and cell-type-dependent expression of clock-related genes and the transferred developmental signature during corticogenesis. In a Poly(I:C)-based maternal immune activation dataset, litter-aware reanalysis identified stage-resolved genome-wide transcriptional responses following E12.5 exposure. However, neither the aggregate core clock-gene expression score nor the independently transferred BrainSpan-derived developmental signature showed a significant overall treatment effect or collection-stage-by-treatment interaction, indicating that this bulk dataset provides a perturbational context rather than evidence for selective disruption of the developmental program. An exploratory region-stratified analysis of GSE28521 yielded near-null effects for the BrainSpan-derived developmental signature, with confidence intervals crossing zero across all examined regions. These ASD postmortem findings were therefore treated as a boundary assessment rather than evidence of ASD-specific convergence. Conclusions: Collectively, these findings position clock-related genes as components of a developmentally regulated cortical maturation program enriched for neuronal signaling, synaptic maturation, metabolic regulation, and stress-response processes.

Genes doi: 10.3390/genes17091106

Authors: Mohammed Shahab Uddin Fayez AlShammari Amr Esmail Khaled Shafeen Fahad Alnajim Danah AlMohaimeed Nujud Alessa Wojod Alothman Fay Aldenaini Karthiga Gurumurthy Maryam AlQannas

Background: Infantile dilated cardiomyopathy (DCM) is uncommon but carries substantial mortality, particularly when accompanied by neurological, ocular, or metabolic abnormalities. Long–Olsen–Distelmaier syndrome is a rare mTORopathy caused by heterozygous gain-of-function variants in RRAGC and may include cortical malformations, congenital cataracts, mineral disturbances, and early-onset DCM. Case Summary: We describe a term male infant born to consanguineous parents with hypocalcemia and hyperphosphatemia, bilateral frontoparietal polymicrogyria, bilateral congenital lamellar cataracts, small patent ductus arteriosus and ventricular septal defect, and initially preserved biventricular function. At 53 days of age, he developed cardiogenic shock, severe lactic acidosis, and hyperkalemia during a rhinovirus/enterovirus-positive respiratory illness. Echocardiography showed severe DCM with marked left ventricular dilatation and an ejection fraction of 27%. Despite multi-agent inotropic support, ventricular function did not recover, and he died at approximately two months. Accordingly, the contemporaneous clinical WES record documented a heterozygous RRAGC c.343T>C, p.(Trp115Arg) variant, reported by the diagnostic laboratory as likely pathogenic. The variant was subsequently standardized in this manuscript as NM_022157.4:c.343T>C, and an independent manuscript-level ACMG/AMP reassessment was concordant. Conclusions: Because p.(Trp115Arg) was previously reported, the principal contribution is detailed documentation of rapid progression from preserved neonatal ventricular function to fatal infantile DCM, while extending the clinical and geographic spectrum of RRAGC-related Long–Olsen–Distelmaier syndrome. Respiratory viral detection should be interpreted cautiously because myocarditis was not established; early exome-based testing should be considered in infants with cardiomyopathy and multisystem abnormalities.

Genes doi: 10.3390/genes17091105

Authors: İdris Sarıkaya Recep Kılıç

Objectives: Pterygium is an invasive, hyperproliferative fibrovascular disorder of the ocular surface characterized by frequent postoperative recurrence and resistance to apoptosis. This study investigated transcriptional alterations in genes related to the regulated cell death pathways disulfidptosis and cuproptosis in pterygium and explored potential pharmacological candidates through in-silico drug repurposing. Methods: High-throughput RNA-sequencing data (GEO accession GSE155776) from primary pterygium tissues (n = 8) and healthy conjunctival controls (n = 8) were analyzed. The expression profiles of 15 disulfidptosis-related and 13 cuproptosis-related genes were evaluated. Differential expression signatures were subsequently analyzed using the L1000CDS2 platform in reverse mode to identify perturbagens with transcriptional effects opposing the pterygium-associated signature. Results: Transcriptomic analysis demonstrated marked alterations in actin-cytoskeletal genes, with profound downregulation of ACTB and WASF2 and upregulation of DSTN and CAPZA1, suggesting a potential vulnerability to disulfide stress. Cuproptosis-related analysis showed increased expression of mitochondrial metabolic genes, including PDHB and DLD, together with significant overexpression of the copper transporter SLC31A1, consistent with transcriptional remodeling of mitochondrial metabolic and copper-handling programs. In-silico drug repurposing identified several FDA-approved drugs with anti-correlative perturbational profiles, including Auranofin, Ouabain, Digitoxin, and Neratinib. Conclusions: Pterygium is associated with coordinated transcriptional alterations involving disulfidptosis- and cuproptosis-related gene networks, suggesting potential structural and metabolic vulnerabilities. In-silico drug repurposing identified several pharmacological candidates whose transcriptional effects oppose the observed disease-associated signature. These findings provide a rationale for further experimental investigation of these pathways and candidate compounds in pterygium.

Genes doi: 10.3390/genes17091104

Authors: Jingjing Li Yongjie Cheng Lin Su Chengyuan Yan Zhenhua Cao

Facioscapulohumeral muscular dystrophy (FSHD) is a genetically and epigenetically complex autosomal dominant myopathy that presents formidable challenges to molecular diagnosis and reproductive intervention. The disease is caused by aberrant derepression of the DUX4 retrogene within the D4Z4 macrosatellite repeat array at chromosome 4q35, triggered either by pathological contraction of the array on a permissive 4qA haplotype (FSHD1, ~95% of cases) or by mutations in epigenetic modifier genes SMCHD1, DNMT3B, and LRIF1 that lead to global D4Z4 hypomethylation (FSHD2, ~5% of cases). Traditional approaches (Southern blotting, optical genome mapping, bisulfite sequencing) are discontinuous and labor-intensive. Nanopore ultra-long read sequencing spans the entire D4Z4 array in single reads, simultaneously resolving repeat number, haplotype, and allele-specific CpG methylation without bisulfite conversion. With the telomere-to-telomere (T2T-CHM13) reference genome, long-range haplotype phasing enables preimplantation genetic testing for monogenic conditions (PGT-M) for families with de novo pathogenic variants and somatic mosaicism, groups previously excluded from reproductive genetic intervention. This review systematically examines FSHD molecular mechanisms, the Nanopore diagnostic workflow integrated with T2T-CHM13, Nanopore-based PGT-M clinical data, and future perspectives including R11 pore chemistry, AI-driven bioinformatics, CRISPR-targeted enrichment, and multi-omics integration.

Genes doi: 10.3390/genes17091103

Authors: Jun Yang Xinhui Li Huilin Cheng Yingfeng Luo Weifan Wu Xin Lu Chengcheng Ling

Background: Cucurbita ficifolia (figleaf gourd) is an agriculturally useful cucurbit germplasm and rootstock, but its mitochondrial genome has not been examined in a comparative family-level framework. We aimed to characterize its mitochondrial reference sequence and evaluate coding composition, repetitive DNA, plastid homology, bioinformatic RNA-editing predictions, phylogenetic placement, and genome-scale synteny. Methods: PacBio Revio sequencing generated 933,158 high-fidelity (HiFi) reads totaling 14.294 Gb, with a read N50 of 15.6 kb. The 784,544-bp mitochondrial reference (GenBank accession PZ823090) was assembled with Oatk and evaluated using graph topology, competitive read-back, and junction-spanning alignments. Codon usage, repeats, mitochondrial–plastid homologous regions, bioinformatic C-to-U RNA-editing predictions, conserved-gene phylogeny, and whole-mitogenome synteny were analyzed. Results: The reference had 43.09% GC content and contained 38 distinct protein-coding genes represented by 42 loci, 26 tRNA types represented by 37 loci, and three rRNAs. Competitive read-back retained 40,971 primary mitochondrial alignments (MAPQ ≥ 20), yielding a mean depth of 547.26× and 100% breadth at ≥100×. The terminal-to-start adjacency was supported by 366 HiFi reads with ≥2-kb anchors on each side. We identified 322 simple-sequence repeats, 115 tandem repeats, and 2374 dispersed repeat pairs. For the largest 392-bp direct repeat, the two native junctions were supported by 268 and 308 reads, whereas the two reciprocal junctions were supported by one and zero reads. Ninety-one significant plastid matches collapsed to 73 mitochondrial loci and covered 74,784 unique mitochondrial bases (9.53%). Deepred-Mt generated 494 bioinformatic C-to-U RNA-editing predictions in 37 genes, and phylogenomics placed C. ficifolia as sister to the C. pepo–C. maxima pair with maximal support despite extensive synteny turnover. Conclusions: The C. ficifolia mitogenome combines a conserved coding repertoire with abundant short repeats, appreciable plastid homology, and extensive rearrangement. Read evidence supports the submitted terminal-to-start adjacency but does not establish a unique or predominant circular molecule in vivo; likewise, the largest repeat showed no robust reciprocal-junction signal. All RNA-editing sites reported here are bioinformatic predictions rather than transcript–validated events.

Genes doi: 10.3390/genes17091101

Authors: Vasileios Konteles Ioanna Papathanasiou Maria Tzetis Eugenios Goussetis Kostantinos Malizos Aspasia Tsezou

Background/Objectives: Osteoarthritis (OA) is strongly associated with mitochondrial dysfunction, oxidative stress, and the accumulation of mitochondrial DNA (mtDNA) alterations in several joint-associated cell types, including chondrocytes, synoviocytes, and mesenchymal stromal cells (MSCs). These alterations contribute to impaired cellular homeostasis and reduced regenerative potential. In this study, we systematically characterized mtDNA heteroplasmy and variant distribution across bone marrow MSCs, induced pluripotent stem cells (iPSCs) and induced MSCs (iMSCs) derived from OA patients and healthy donors. Methods: Ultra-deep mitochondrial genome sequencing was integrated with transcriptomic and miRNome analyses to investigate mitochondrial remodeling during cellular reprogramming, encompassing changes in mtDNA heteroplasmy, variant distribution, mtDNA copy number and associated transcriptomic adaptations of nuclear-encoded mitochondrial pathways. Results: OA-derived MSCs exhibited a markedly increased heteroplasmic burden, followed by decrease in mtDNA copy number and accumulation of non-synonymous variants, particularly within OXPHOS-related genes, including MT-ND1-5, MT-ATP8, MT-CO1, and MT-RNR1/2. Reprogramming into iPSCs and subsequent differentiation into iMSCs were associated with an increase in mtDNA copy number and a progressive reduction in heteroplasmic variants predicted to have pathogenic potential, including m.7913C>T and m.7821G>A, as well as substantial reduction in heteroplasmic variant burden within several mitochondrial genes, suggesting mitochondrial genome remodeling during cellular reprogramming. Multiomic analysis further revealed coordinated deregulation of mitochondrial-associated nuclear genes and ceRNA regulatory networks involving lncRNAs MEG3 and SNHG14, along with multiple mitochondria-related miRNAs. These findings suggest post-transcriptional regulations associated with mitochondrial adaptation in iMSCs Conclusion: Collectively, our findings suggest that cellular reprogramming is associated with mitochondrial genomic reorganization in the donor-matched cell populations examined. These exploratory observations support the utility of iMSCs as a relevant model for studying OA-associated mitochondrial alterations and as a potential tool for regenerative approaches in OA.

Genes doi: 10.3390/genes17091100

Authors: Monica Giuffrida Claus Børsting Vania Pereira

Background/Objectives: This study aimed to compare the performance of four commercial bisulfite conversion kits—the Premium Bisulfite Kit, the SuperMethyl™ Fast Bisulfite Conversion Kit, the SuperMethyl™ Max Bisulfite Conversion Kit, and the EZ DNA Methylation-Gold™ Kit (hereafter: Premium, Fast, Max, and Gold)—to evaluate their impact on the age prediction accuracy at different DNA input levels. Methods: Comparisons were performed using DNA extracted from blood samples and DNA methylation standards. Different inputs of DNA were tested (1–50 ng), and all samples were analyzed twice. After bisulfite treatment, 10 targets were amplified by PCR and sequenced on a MiSeq instrument. Performance was evaluated across several metrics: DNA yield after PCR, conversion efficiency, read depth and β-value reproducibility, β-value specificity, cost, and hands-on time. Furthermore, DNA methylation levels of age-associated CpGs on the 10 PCR fragments were investigated, and the accuracy of age predictions was determined. Results: No kit was superior in performance across all metrics. Higher post-PCR DNA concentrations and more robust and reproducible results, particularly at lower DNA inputs, were obtained after treatment with the Premium and Max kits. The amplicon concentrations, read depths, and reproducibility between duplicate determinations were significantly lower with 1 ng DNA input compared to inputs of 5–50 ng DNA. Conclusions: For forensic genetic age prediction purposes, the Max or Premium kits represented more suitable options for bisulfite conversion, whereas the Fast kit may be preferable in settings where sample quantity is not a limiting factor, and cost or throughput are the primary considerations.

Genes doi: 10.3390/genes17091102

Authors: Anastasia Dell’Elice Lucia Lombardi Federico Anaclerio Claudia Palmarini Nicole Canale Lorenzo Secondi Gregorio Stratta Marco Vitali Maria Saveria Tavoletta Simona Grossi Alessandra Babore Cristina Milillo Melania Dovizio Patrizia Ballerini Valentina Gatta Liborio Stuppia Ivana Antonucci

Germline Whole-Exome Sequencing (WES) has emerged as a powerful genomic approach for investigating Hereditary Cancer predisposition through the comprehensive analysis of coding regions across the genome. Although multigene panels currently represent the standard diagnostic approach for Hereditary Cancer assessment, a substantial proportion of high-risk individuals and families remain molecularly unexplained. In this setting, germline WES may serve as a valuable second-tier strategy by identifying pathogenic variants in genes not routinely included in conventional testing panels and by addressing part of the unresolved “missing heritability” observed across Hereditary Cancer syndromes. Increasing evidence supports its application in hereditary breast and ovarian cancer, Lynch-like syndrome, colorectal polyposis, hereditary diffuse gastric cancer, and ovarian cancer predisposition, where WES has contributed to the identification of additional susceptibility genes and improved molecular characterization. Beyond Hereditary Cancer diagnostics, exome-based approaches have also been explored for tumour profiling, homologous recombination deficiency (HRD) assessment, biomarker discovery, and therapeutic stratification. However, despite its significant potential, the clinical implementation of WES remains challenging because of the high burden of variants of uncertain significance (VUS), difficulties in variant interpretation, incidental findings, and the need for robust functional validation of candidate genes. This review critically examines the current evidence supporting the clinical utility of germline WES in Hereditary Cancer syndromes, focusing on the clinical scenarios in which WES may provide meaningful additional information beyond multigene panels, its diagnostic yield, limitations, and future perspectives in precision oncology.

Genes doi: 10.3390/genes17091099

Authors: Diep Minh Quang Chi Dung Vu Khanh Ngoc Nguyen Ngoc Lan Nguyen Tran Thi Chi Mai Nguyen Thi Thanh Huong Do Thi Mo Le Thi Phuong Thinh Huy Tran Nguyen Huu Tu Ngo Xuan Khoa Vu Viet Ha Vuong Van Khanh Tran

Background/objective: Propionic acidemia (PA), an autosomal recessive metabolic disorder, is caused by biallelic pathogenic variants in the PCCA or PCCB genes. In Vietnam, molecular analyses of PA have been scarce. Hence, the objective of this study was to investigate the phenotypic and genotypic characteristics and clinical management of Vietnamese children with PA. Methods: An ambispective descriptive cohort study was conducted on 14 children who were diagnosed with PA at the Vietnam National Children’s Hospital. Collected data encompassed clinical manifestations, biochemical profiles, imaging characteristics, genetic findings, clinical management, and outcomes. Results: Symptom onset within the cohort spanned the neonatal, early infantile, and early childhood periods, with a median age at onset of 7.50 months (range 0.33–34.00 months). The clinical phenotype was characterized by acute encephalopathy, accompanied by lethargy (64.3%), vomiting (57%), and seizures (43%). Even though all tested cases exhibited abnormal urinary organic acids and elevated propionylcarnitine (C3) concentration, other key laboratory findings comprised hyperammonemia (100%), metabolic acidosis (64%), and hematological alterations (64%). The study identified eight pathogenic or likely pathogenic PCCB variants and two variants of uncertain significance, with the c.1124C>T being the most frequently identified variant. This cohort had severe clinical outcomes, as neurodevelopmental impairment was observed in 79% of cases with a mortality rate of 43%. Conclusions: This study underscores the severe clinical and biochemical characteristics of PA in 14 Vietnamese children, reinforcing the necessity of early detection and comprehensive long-term care for PA patients. Furthermore, the identification of 10 PCCB variants, including the recurrent c.1124C>T, p.(Ala375Val) variant in our cohort, broadens the known PCCB variant spectrum.

Genes doi: 10.3390/genes17091098

Authors: Pin Huang Wenxiao Wei Ying Xiao Qian Zhu

Background: More efficient and safe preventive treatments for venous thromboembolism (VTE) are warranted to decrease the incidence of hemorrhage. Emerging evidence has highlighted the pivotal role of the intestinal microbiota alterations and their metabolites in the pathophysiology of VTE process. However, the specific species involved the VTE process and the potential underlying mechanisms remain unclear. Methods: The causal relationships between 82 species and VTE were assessed using two-sample Mendelian Randomization (MR) analyses. Instrumental variables (F > 10) without horizontal pleiotropy were selected using the PhenoScanner and MR PRESSO global test. Subsequently, causal estimates were primarily derived using the inverse variance weighted method. The reliability of the results was further examined utilizing various sensitivity analyses, reverse MR analysis and multivariate MR analysis. Additionally, the potential mediated effects of gut microbiota-related metabolites were explored and replicated using the mediation MR analysis. Moreover, genome annotation and pathway enrichment analysis were conducted to investigate the role of CAG-81 sp000435795 in the related metabolites metabolism. Results: We identified independent and positive causal effects of CAG-81 sp000435795 and CAG-877 sp000433455 on VTE, which remained robust across multiple sensitivity analyses. Mediation analysis further revealed that the causal effect of CAG-81 sp000435795 on VTE risk was partially mediated by albumin, Omega-3 fatty acids and polyunsaturated fatty acids (PUFA), which were all validated in the replicated cohorts. Furthermore, CAG-81 sp000435795 might participate in the metabolism of albumin and fatty acids. Conclusions: Our findings provide evidence supporting a causal role of CAG-81 sp000435795 in the VTE pathogenesis and implicate microbes associated metabolites, albumin and Omega-3, as potential mediators.

Genes doi: 10.3390/genes17091097

Authors: Jiani Deng Boning Cao Fengjie Zheng Sinan Ai Yaoxian Wang Xu Wang

Background: Cellular heterogeneity limits causal inference in complex diseases. We applied an established cell-type-stratified Mendelian randomization (csMR) framework, originally developed by Hao et al. (2024), to investigate whether lipid phenotypes affect kidney disease through distinct brain cell populations, extended by a proteome-wide mediation component. Methods: Using Bayesian colocalization (posterior probability of hypothesis 4 [PPH4], ≥0.8) and multidimensional instrumental variable selection, we evaluated cell-type-stratified MR-supported associations of five lipid traits across ten brain cell or tissue strata with kidney disease risk. Instrumental variables were derived from published genome-wide association studies and human brain single-cell expression quantitative trait locus (eQTL) maps. An exploratory proteomic mediation analysis using the Difference Method was performed with UKB-PPP as the discovery resource and deCODE as the external validation resource, with mediation signals interpreted as hypothesis-generating. For the primary csMR analysis, multiple testing was corrected separately within each lipid trait using a Bonferroni threshold of 3.33 × 10−4, corresponding to 150 cell/tissue-by-outcome tests per lipid trait. Results: In csMR analyses, cholesterol-related lipids showed cell-type-stratified associations with kidney disease, most prominently in oligodendrocyte-related analyses (max β on the log-odds scale = 1.025). LDL-related associations with broad chronic glomerular disease were most evident in excitatory neuron-related analyses. Dual-cohort proteomic analysis prioritized plasma proteins, including SNAP29 and ICAM4, as candidate protein-associated signals for exploratory mediation analysis. These findings represent genetic colocalization and Mendelian randomization-supported associations, not experimentally established mechanisms, and should be interpreted as hypothesis-generating. Conclusions: This study provides a cell-type-resolved genetic and proteomic association map linking lipid traits, brain cell strata, and kidney disease outcomes, offering hypotheses for future experimental validation.

Genes doi: 10.3390/genes17091096

Authors: Rakesh Arya Viplov Kumar Biswas Hemlata Shakya Moumita Majumdar Jong-Joo Kim

Background: Lung adenocarcinoma (LUAD) is the most common subtype of non-small-cell lung cancer and is one of the leading causes of cancer-related deaths globally. Despite current developments, reliable biomarkers for effective diagnosis, prognosis, and patient stratification are still lacking. Methods: We analyzed publicly available TCGA-LUAD and GEO datasets using integrative bioinformatics approaches, including differential gene expression, weighted gene co-expression network analysis (WGCNA), survival modeling, mutation profiling, immune cell infiltration scores, machine learning, and bulk-RNA and single-cell RNA sequencing. Results: A total of 5581 deregulated genes were identified, with the turquoise module (298 genes) showing strong correlation with LUAD (Corr = −0.79, p < 2.2 × 10−308). The integration of two analyses yielded 281 overlapping genes, out of which nine candidates (ANO2, CHIAP2, CPED1, DNASE1L3, GSTM5, HTR3C, PRKCE, SLC14A1, and WNT3A) were selected via LASSO Cox regression to build a prognostic risk model. High-risk patients have significantly worse survival (log-rank p = 0.0027). CPED1 exhibited the highest mutation frequency, with 41% of TCGA-LUAD samples harboring mutations. Among all CPED1 mutation events, missense mutations were the most common (47%). GSEA and KEGG analysis revealed significant enrichment of pathways such as nucleocytoplasmic transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, ribosome, and ribosome biogenesis in high-risk patients. Immune infiltration analysis indicated differences in immune cell infiltration scores between high- and low-immune-score groups, with M1 macrophages showing strong statistical correlation with aDC, monocytes, and CD4+ naïve T cells. Machine learning confirmed that the combined Enet+PLS model predicted CPED1 as a core predictor, and CPED1 was successfully validated in independent GEO datasets (GSE43458 and GSE31210), showing strong diagnostic accuracy (AUCs up to 0.98). Finally, single-cell RNA sequencing revealed that CPED1 was mostly expressed in fibroblasts and myeloid cells, with CPED1 significantly downregulated in LUAD compared with normal samples. Conclusions: This study integrates multi-omics and machine learning to highlight CPED1 as a promising candidate biomarker, with potential diagnostic and prognostic relevance in LUAD. The nine-gene risk signature stratified patients by survival outcomes in the TCGA cohort. Genomic and immune analyses revealed features associated with the high-immune-score group. As the study is entirely computational and the prognostic model lacks external survival validation, these findings should be regarded as preliminary and hypothesis-generating, requiring future independent validation and functional studies to confirm the biological significance and clinical utility of CPED1 and related genes.

Genes doi: 10.3390/genes17091095

Authors: Yongjie Xia Zhuoran Huang

Background and Objectives: Codon usage bias (CUB), the non-uniform usage of synonymous codons, is prevalent in plant chloroplast genomes and plays important roles in gene expression and genome evolution. However, systematic comparisons of CUB patterns across genera in the Cucurbitaceae family remain limited. This study aimed to characterize CUB patterns and identify their driving forces in the chloroplast genomes of six Cucurbitaceae species. Methods: We analyzed the complete chloroplast genomes of six Cucurbitaceae species, watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cucumis sativus), pumpkin (Cucurbita moschata), wax gourd (Benincasa hispida), and bitter gourd (Momordica charantia). CUB patterns were assessed using ENC-plot, neutrality plot, and PR2-plot analyses, all implemented through a custom, reproducible Python-based workflow. Results: The overall codon usage bias was weak across all six species, with a clear preference for A/U-ending codons. Candidate preferred codons (hereafter referred to as optimal codons for brevity) identified independently within each species were largely shared across the six species, although species-specific codons were also detected. Combined ENC-plot, neutrality plot, and PR2-plot analyses suggest that natural selection, rather than mutation pressure, is the dominant force shaping CUB in these genomes, although these approaches provide indirect evidence. Conclusions: These findings provide a reference for codon optimization of exogenous genes in chloroplast genetic engineering of Cucurbitaceae crops. The Python-based workflow developed in this study also offers a transparent, reproducible alternative to conventional CUB analysis approaches.

Genes doi: 10.3390/genes17091094

Authors: Qingsheng Zhou Jingchong Li

Background/Objectives: Soil salinization threatens global potato production, yet the molecular mechanisms underlying salt tolerance remain poorly understood. This study aimed to elucidate dynamic transcriptomic responses to salt stress, identify key regulatory genes, and characterize the corresponding gene family and its stress-responsive roles. Methods: Potato cv. Atlantic plantlets were subjected to 150 mM NaCl stress, with samples collected at 0, 3, 12, 24, and 48 h. Physiological and transcriptomic analyses were performed. WGCNA was employed to identify salt-responsive modules. Genome-wide identification, phylogenetic analysis, gene structure characterization, conserved motif analysis, and promoter cis-element prediction of the annexin gene family were conducted. Results: Transcriptome sequencing identified 1394 differentially expressed genes (DEGs) that were consistently responsive to salt stress, with functional enrichment highlighting stress signaling, hormone transduction, and phenylpropanoid biosynthesis pathways. Weighted gene co-expression network analysis (WGCNA) revealed the MEblack module as the key salt-responsive regulatory module, in which annexin genes exhibited high intramodular connectivity. Genome-wide identification uncovered nine annexin genes (StANN1–StANN9), characterized by uneven chromosomal distribution, conserved exon–intron structures and annexin repeat domains, and expansion through tandem, proximal and segmental duplication under purifying selection. Promoter analysis revealed abundant stress-responsive cis-elements, including ABRE and DRE/CRT motifs, in salt-inducible annexins. Expression profiling demonstrated that StANN5 and StANN6 were continuously upregulated under prolonged salt stress, whereas StANN2 and StANN3 showed transient early induction. Conclusions: These findings establish the central role of annexins in calcium signaling, redox homeostasis, and hormone-mediated stress adaptation, providing candidate targets for molecular breeding of salt-tolerant potato varieties.

Genes doi: 10.3390/genes17091093

Authors: Marc Ralph M. Solomon Ma. Anita M. Bautista

Background: Arboviral transmission by Aedes aegypti is exacerbated by insecticide resistance, which undermines effective vector control strategies. In the Philippines, deltamethrin resistance in several Ae. aegypti populations has been reported and prompts an investigation into the possible molecular mechanisms involved. Methods: Two Ae. aegypti populations were subjected to susceptibility assays to deltamethrin and were RNA-sequenced for transcriptome analysis. Results: The two (2) Ae. aegypti populations were resistant to deltamethrin and had LC50 values of 1.26 and 2.15 μg/mL at the zeroth generation (G0) that shifted to 2.21 and 2.08 μg/mL at the second generation (G2) after sublethal deltamethrin exposure, although not statistically significant. Relative to a control population unexposed to any insecticide, DGE analysis of the RNA-Seq data revealed significant upregulation of cytochrome P450, glutathione S-transferase, and carboxyl/cholinesterase genes in resistant populations. Moreover, GO and KEGG analyses revealed enrichment of cytochrome P450-related terms and xenobiotic metabolism pathways. Conclusions: RNA-Seq analysis results of selected genes show concordance with their respective gene expression measured via qPCR (R = 0.89; p = 0.00049). This study provides insights into the possible molecular mechanisms of deltamethrin resistance in Philippine Ae. aegypti populations, providing informed decision-making in vector management.

Genes doi: 10.3390/genes17091092

Authors: Marisol Ibarra-Ramírez Jibran Mohamed-Noriega Joel Arenas-Estala David Asael Rodríguez-Torres Luis Daniel Campos-Acevedo Marissa L. Fernández-de-Luna

Background: Genetic eye diseases (GEDs) comprise a heterogeneous group of hereditary and de novo disorders that involve all ocular structures, including the retina, optic nerve, vitreous, anterior segment, and ocular development. Their marked clinical and genetic heterogeneity frequently delays diagnosis and access to genetic counseling, multidisciplinary management, and emerging gene-based therapies. Although ophthalmic deep phenotyping remains essential, we propose an approach that prioritizes genetic analysis, particularly in under-resourced healthcare settings with limited access to advanced imaging and electrophysiological tests. Methods: We conducted a retrospective observational study of 101 consecutive patients with suspected genetic eye diseases. All were evaluated at a tertiary referral center in northeastern Mexico between January 2020 and August 2023 through comprehensive ophthalmologic examination supplemented by optical coherence tomography, visual-field testing, and fundus photography when clinically indicated. All patients were offered early molecular testing while awaiting future tests, such as electrophysiological testing or further referral visits. Molecular testing consisted of an ophthalmology-focused next-generation sequencing multigene panel. Results: The primary outcome was molecular diagnostic yield. A clinically actionable molecular diagnosis was established in 45 patients, corresponding to an overall molecular diagnostic yield of 44.6%. A total of 165 variants were identified, including 70 pathogenic, 16 likely pathogenic, 43 variants of uncertain significance, and 36 likely benign variants. Usher syndrome was the most frequent molecular diagnosis (10/45, 22.2%), comprising nine patients with USH2A-associated Usher syndrome type 2 and one patient with MYO7A-associated Usher syndrome type 1B, followed by Stickler syndrome (8/45, 17.8%), oculocutaneous albinism (3/45, 6.7%), and Alström syndrome (2/45, 4.4%). Autosomal recessive disorders represented the predominant inheritance pattern (68.9%). Conclusions: Our findings support ophthalmology-focused multigene panels as an effective first-line diagnostic strategy for patients with suspected genetic eye diseases. Early molecular testing may shorten the diagnostic odyssey, optimize resource utilization, facilitate precision diagnosis and genetic counseling, and guide future targeted deep phenotypic evaluation, prognosis, and eligibility for emerging gene-specific therapies.

Genes doi: 10.3390/genes17091091

Authors: Sabine Vautier Corentin Levacher Florent Marguet Edwige Kasper Jean-Christophe Sabourin Stéphanie Baert-Desurmont Philippe Ruminy Claude Houdayer

Background/Objectives: Circular RNAs (circRNAs) are emerging regulators of genetic information that share the spliceosome biogenesis pathway with messenger RNAs (mRNAs), influencing their expression. There is an increasing body of evidence supporting their role in colorectal cancer (CRC) tumorigenesis. This study explored circRNAs in two distinct CRC tumorigenesis pathways: microsatellite instability (MSI) and microsatellite stability (MSS). We investigated competition between mRNA and circRNAs from their host genes, which could potentially disrupt normal gene regulation, and examined specific patterns of alterations in MSS and MSI tumors. Methods: Circular (circ) and linear (lin) exon–exon junctions were quantified using exon-specific probes targeting 48 genes involved in CRC predisposition and tumorigenesis processes. RNA was extracted from colorectal FFPE samples (stage 1 to 4 adenocarcinomas and adenomas). MSS tumors (MSS-TTs) and adjacent normal tissue (MSS-NT) were selected from 21 patients with a severe personal or family history of cancer. MSI tumors (MSI-TTs) and adjacent normal tissue (MSI-NT) were selected from 16 patients. Muscle content was also investigated as a potential confounding factor. Results: Principal component analysis distinguished NT from TT samples based on the sums of circular and linear junctions. CircRNA abundance was higher in samples with an elevated muscle content (Kruskal–Wallis test p-value = 0.034). Linear regression, adjusted for muscle content, showed significantly reduced global circRNA levels in tumors compared to in healthy tissues (MSI and MSS combined, p-value = 0.00268). In the MSS group, significant differences were observed between MSS-NT and MSS-TT in terms of circ/lin ratios and linear and circular junction counts for specific genes. MSI analysis revealed distinct gene profiles, with significant differences only in linear junction counts. Conclusions: Our results do not suggest competition between the circRNAs and mRNAs of the key oncogenic genes that we investigated, but they do reveal differences in circRNA/mRNA expression patterns within normal and tumor tissues.

Genes doi: 10.3390/genes17091090

Authors: Sushil K. Jain Rajesh Parsanathan Jeffrey Justin Margret Neslihan Gungor John A. Vanchiere Maroun J. Mhanna Robert McVie

Background: Hydrogen sulfide (H2S) is known for its significant anti-inflammatory, antioxidant, and vasculoprotective properties. In diabetic patients, blood levels of H2S are observed to be lower. Type 1 diabetic patients (T1D) often experience both hyperketonemia and hyperglycemia. Cystathionine-γ-lyase (CSE), an enzyme encoded by the CTH gene, is responsible for the biosynthesis of H2S. However, it remains uncertain whether the downregulation of CTH genes by ketones is linked to reduced levels of H2S. Objective: This study aims to test the hypothesis that ketones decrease CTH gene expression in cultured hepatocytes and that hyperketonemia negatively correlates with H2S levels in T1D. Methods: Fasting blood samples were collected from children with T1D (n = 36) and age-matched healthy controls (n = 35), following written informed consent. Plasma levels of H2S, 25(OH)VD, ketones, and inflammatory biomarkers were analyzed. To assess the effects of hyperglycemia and hyperketonemia on CTH gene expression, cultured hepatocytes were exposed to high glucose, acetoacetate, or β-hydroxybutyrate. Results: Blood levels of H2S and 25(OH)VD were significantly lower in T1D patients compared to healthy controls. Plasma H2S concentrations showed an inverse association with total ketones, BHB, acetoacetate, and MMP-9, while they were positively associated with HDL-cholesterol and 25(OH)VD. In cultured hepatocytes, exposure to acetoacetate and high glucose was linked to reduced CTH mRNA expression. Conclusions: Lower circulating H2S concentrations are associated with hyperketonemia and inflammatory/metabolic abnormalities in children and adolescents with T1D. The in vitro findings suggest that high glucose and acetoacetate may affect CTH transcription; however, further studies measuring CSE protein, enzymatic activity, and H2S production are necessary to clarify the underlying mechanism and establish causality.

Genes doi: 10.3390/genes17091089

Authors: Shengqi Ye Hongxin Ji Lianxuan Chen Jingwen Qi Haihong Chen

Background/Objectives: Neopyropia yezoensis is an economically important intertidal red alga that frequently experiences fluctuations in temperature, light intensity, and water availability. Formins are key regulators of actin nucleation and cytoskeletal dynamics, but their functions and stress-responsive roles in red algae remain poorly understood. This study aimed to systematically identify and characterize the Formin gene family in N. yezoensis and investigate their expression responses to different environmental stresses. Methods: Formin family members were identified from the N. yezoensis genome using HMMER and BLAST (2.17.0) searches based on the conserved FH2 domain, followed by domain validation. Gene structures, conserved motifs, physicochemical properties, predicted subcellular localization, protein structures, chromosomal distribution, phylogenetic relationships, and cis-acting elements in the upstream regions were analyzed. The expression patterns of the identified Formin genes were further examined by qRT-PCR under different temperature (4, 10, and 24 °C), light intensity (20, 60, and 100 μmol photons m−2 s−1), and desiccation/rehydration conditions. Results: Three Formin genes, designated NpyFormin01–03, were identified in N. yezoensis. All three encoded proteins contained the conserved FH2 domain but differed in motif composition, domain architecture, predicted subcellular localization, and structural features. NpyFormin01 contained additional PTEN_C2 and PTP_DSP_cys domains, whereas NpyFormin02 and NpyFormin03 contained only the FH2 domain. Phylogenetic analysis showed that the N. yezoensis Formins clustered with Formins from other red algae. Promoter analysis identified multiple predicted cis-acting elements associated with light, temperature, environmental, and phytohormone responses. Expression analysis revealed distinct responses among the three genes under the tested environmental conditions. Notably, NpyFormin01 was significantly upregulated under high-temperature treatment (24 °C), whereas NpyFormin02 and NpyFormin03 showed no statistically significant expression changes under the tested conditions. Conclusions: This study provides a systematic characterization of the Formin gene family in N. yezoensis. The differences in protein architecture, structural features, promoter cis-acting elements, and environmental-responsive expression patterns suggest potential functional divergence among NpyFormins. In particular, NpyFormin01 represents a potential heat-responsive candidate gene and may contribute to cytoskeletal regulation during environmental stress adaptation in N. yezoensis. These findings provide a basis for further investigation of the molecular functions of Formins in red algae.

Genes doi: 10.3390/genes17091088

Authors: Aris Kaltsas Maria-Anna Kyrgiafini Eleftheria Markou Michael Chrisofos

In non-obstructive azoospermia (NOA), microdissection testicular sperm extraction can provide sperm for intracytoplasmic sperm injection, but retrieval fails in approximately half of procedures. Genomic, transcriptomic, noncoding RNA, proteomic, metabolomic, and microbiome studies have reported molecular associations and prediction estimates. This critical narrative review examines the requirements for an assay–model system to support preoperative retrieval counseling. A focused PubMed/MEDLINE search updated on 31 August 2026 and targeted reference checking identified representative human reports and methodological guidance. Selected reports mainly illustrate discovery, development, and same-source evaluation. Common limitations include small cohorts, local assay optimization, heterogeneous outcomes, incomplete calibration, and uncertain transportability. Established karyotyping and Y-chromosome testing must be distinguished from discovery-scale genomics, which currently supports etiologic and qualified genotype-specific counseling rather than a universal calibrated retrieval model. A routine-variable multicenter model reported an external-cohort area under the receiver-operating-characteristic curve (AUC) of 0.8301, although cohort provenance, calibration, and clinical utility require independent confirmation. An author-developed seven-gate framework integrates clinical-question definition, assay specification, model development, internal validation, external evaluation, incremental value, and prospective impact. Future omics studies should test incremental value beyond a prespecified routine-variable model in the same patients and assess calibration, threshold consequences, net benefit, assay failure, cost, and patient outcomes.

Genes doi: 10.3390/genes17091087

Authors: Yuting Hu Guoqing Duan Huaxing Zhou Amei Liu Huan Wang

Background: Leptobotia tchangi is a loach species endemic to South China, but its mitochondrial genome has not yet been characterized, limiting understanding of its evolutionary relationships and conservation genetics. Methods: Here, we report the first complete mitochondrial genome of L. tchangi, using next-generation sequencing, assembly and bioinformatics analyses. Results: The double-stranded circular mitogenome has 16,590 bp and contains: 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop) containing conserved ETAS and CSB motifs. The overall base composition is 25.0% thymine (T), 27.9% cytosine (C), 31.1% adenine (A), and 16.0% guanine (G), showing a clear A + T bias (56.1%) which is consistent with other Botiidae mitogenomes. To infer the phylogenetic placement of L. tchangi within Botiidae, we conducted both Bayesian inference and maximum-likelihood phylogenetic analyses based on the concatenated PCG sequences. Our results strongly support (1) the monophyly of the subfamilies Leptobotiinae and Botiinae, as well as the monophyly of each genus within the family Botiidae; (2) three sister-group relationships within Botiinae: (Botia + Chromobotia), (Ambastaia + Sinibotia), and (Syncrossus + Yasuhikotakia), with the latter two species groups also being sister groups; (3) L. tchangi being most closely related to Leptobotia taeniops. Conclusions: These findings not only provide essential molecular markers for the species identification and conservation genetics of L. tchangi, but also clarify the taxonomic status of L. tchangi within Botiidae.

Genes doi: 10.3390/genes17091086

Authors: Chenfei Dong Ruijie Zhao Pengtao Shang Yichen Jiang Yue He Yanhong Yan Chao Chen

Background/Objectives: Using straw as feed is crucial for addressing resource scarcity and waste-based environmental pollution and alleviating the contradiction between forage production and food security. However, rice straw has disadvantages such as a high lignin, cellulose, and hemicellulose content, as well as a dense cell wall structure, which greatly limit its utilization as feed. Improving the forage quality of rice straw through genetic breeding is an important means of enhancing its utilization rate. Methods: To explore the molecular basis underlying the improved nutritional and cell wall compositional traits of the rice lines (oszfp30-1 and oszfp30-2) obtained in previous studies, we conducted phenotypic, physiological, transcriptomic, and metabolomic analyses on oszfp30-1, oszfp30-2 and the wild type (WT) after 50 days of pot cultivation. Results: oszfp30-1 and oszfp30-2 exhibited higher plant height, above-ground biomass, crude protein, and crude fat content, while their hemicellulose, cellulose, and lignin contents were significantly lower than those of the wild type. Transcriptomics was used to identify 737 common differentially expressed genes (DEGs), and metabolomics was used to identify 189 common differentially expressed metabolites (DEMs). KEGG analysis revealed that these DEGs and DEMs were significantly enriched in terpene biosynthesis, starch and sucrose metabolism, phenylpropanoid biosynthesis, and amino sugar and nucleotide sugar metabolism. Conclusions: Our research reveals that the improvement in forage-quality-related traits is closely related to key genes involved in gibberellin synthesis, including GA20ox, GA2ox, and GA3ox; key genes involved in cellulose synthesis, including OsSUS and UGPase; key genes involved in hemicellulose synthesis, including UXS and IRX10; and key genes involved in lignin synthesis, including CCR, CAD, CCoAOMT, and COMT. These identified DEGs and DEMs are associated with the OsZFP30 mutation and may be downstream targets of this transcription factor, providing a foundation for further research on the OsZFP30 regulatory network.

Genes doi: 10.3390/genes17091085

Authors: Wei Liu Xuan Liu Shuyu Zhou Kaiyang Li Xiangzhi Wang Ke Chen Lilu Guo Rui Zhang Qingzhi Su

Background: Tumor heterogeneity arises from complex interactions among diverse biological factors, posing a major challenge for the development of robust multi-omics data integration methods. While the existing Tumor Multi-Omics pre-trained Network (TMO-Net) enables the fusion of multi-omics features into unified representations, its practical utility is constrained by issues such as missing modalities, incomplete within-omics data, and high-dimensional noise. To overcome these limitations, we propose TMO-Net+, an enhanced architecture specifically designed to improve the robustness and reliability of multi-omics modeling. Methods: TMO-Net+ introduces several coordinated architectural enhancements. First, a feature attention encoder is applied to each omics data type to reduce the influence of modality-dependent input variation. Second, we combine a gated Mixture-of-Experts (MoE) module with a Product-of Experts (PoE) mechanism to capture sample-specific contributions and enable robust inference even when partial omics data are available. Additionally, a supervised deep classification head with a tailored loss function is incorporated to enhance the separability of learned embeddings in the latent space. Results: Extensive experiments on pan-cancer datasets demonstrate that TMO-Net+ consistently outperforms the original TMO-Net, as measured by LogME scores. Furthermore, in various downstream tasks (e.g., pan-cancer classification, primary/metastatic site prediction, and prognostic modeling), TMO-Net+ achieves superior performance under partial-omics settings, which proves that it enhances the robustness and cross-cancer transferability of the multi-omics representations. Conclusions: The proposed TMO-Net+ improves the robustness and cross-cancer transferability of multi-omics representations within the evaluated TCGA cohorts. Biological interpretability analyses further show that TMO-Net+ prioritizes established cancer-driver genes, preserves cancer-dependent molecular-state information, and adaptively redistributes relative modality contributions across molecular states. By addressing modality-level missingness and modality-dependent input variation, it offers a reliable framework for integrative tumor analysis within the evaluated TCGA cohorts.

Genes doi: 10.3390/genes17091084

Authors: Lei Jin Feng Wang

Background: Hyperuricemic nephropathy (UAN) involves a systemic thromboinflammatory axis, yet the role of antithrombin (AT, SERPINC1) remains incompletely defined. While AT has anticoagulant and anti-inflammatory properties, whether it contributes to UAN as a disease-responsive molecular node remains uncertain. Methods: We integrated two-sample MR of serum urate and renal traits with complementary sensitivity analyses, cis-eQTL and pQTL analyses of SERPINC1, and exploratory transcriptomic, proteomic, metabolomic, and coexpression analyses. The available data were used to assess genetic associations and to distinguish genetic evidence from cross-dataset molecular patterns. Results: Genetically predicted serum urate showed positive or negative associations with BUN and eGFR, respectively, but the primary analyses showed substantial heterogeneity. Reverse-direction estimates were also associated with serum urate, representing reciprocal genetic relationships between related renal traits and urate rather than proof of a temporal feedback cycle. Available data did not demonstrate mediation through genetically predicted whole-blood SERPINC1 expression. Three deCODE cis-pQTL instruments gave inconsistent renal estimates: nominally lower BUN (β = −0.0290, p = 0.047), null eGFR (β = −0.0036, p = 0.472), and higher CKD risk (β = +0.3361, p = 0.020) with directional pleiotropy evidence. Exploratory multi-omics analyses showed higher PBMC SERPINC1 expression during acute gout and a nominal urinary proteomic difference that did not survive multiple-testing correction (FDR = 0.998). Conclusions: SERPINC1 is best interpreted as a responsive molecular feature requiring further validation, rather than as a demonstrated genetic mediator or renal-protective therapeutic target. The transcriptomic and urinary findings represent cross-dataset, stage-associated observations and should not be interpreted as proven sequential phases.

Genes doi: 10.3390/genes17091082

Authors: Denis Fedorinov Vladimir Lyadov Marina Lyadova Sherzod Abdullaev Ivan Sychev Anna Filatova Lavrentii Danilov Oleg Glotov Iuliia Budagova Karin Mirzaev Dmitry Sychev

Background/Objectives: Pharmacogenetic testing of the dihydropyrimidine dehydrogenase gene (DPYD) is increasingly incorporated into clinical practice to identify patients at increased risk of fluoropyrimidine-related toxicity. However, most routine assays target a limited number of well-established variants, whereas the DPYD gene demonstrates substantial population variability and may harbor rare potentially functional alleles that are not detected by conventional targeted testing. Data describing coding and splice-region DPYD variants detectable by whole-exome sequencing in Russian oncology populations remain limited. This study aimed to characterize the frequency and distribution of common, clinically relevant, and rare DPYD variants in a Russian cohort of patients receiving fluoropyrimidine-containing chemotherapy and to compare the observed allele frequencies with European and East Asian reference populations. Methods: Descriptive pharmacogenetic analysis was performed in 339 patients with malignant tumors treated with fluorouracil, leucovorin, oxaliplatin, and docetaxel (FLOT), folinic acid, fluorouracil, and oxaliplatin (FOLFOX), or folinic acid, fluorouracil, irinotecan, and oxaliplatin (FOLFIRINOX) regimens. Whole-exome sequencing was performed using Illumina technology with exome enrichment by KAPA HyperExome and a sequencing depth of at least 100×. Sequence reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome, germline variants were called using Genome Analysis Toolkit (GATK), HaplotypeCaller, and functional annotation was performed with Ensembl Variant Effect Predictor. DPYD variants were classified according to their population frequency, predicted functional effect, ClinVar annotations, and current pharmacogenetic recommendations. Allele and genotype frequencies were calculated and descriptively compared with Genome Aggregation Database (gnomAD) v4.1.1 Non-Finnish European and East Asian populations. Results: Seventeen DPYD variants were identified. The most frequent alternative alleles were rs1801265 (24.93%), rs1801159 (17.70%), rs2297595 (11.06%), rs1801160 (7.08%), and rs17376848 (5.16%). Their distribution was generally closer to that observed in the Non-Finnish European population than in East Asian populations. The established reduced-function variant rs67376798 (c.2846A>T, p.Asp949Val) was detected in one heterozygous patient, corresponding to a carrier frequency of 0.29% and an allele frequency of 0.15%. The HapB3 proxy variant rs56038477 (c.1236G>A) was identified in 13 heterozygous patients, with a carrier frequency of 3.83% and an allele frequency of 1.92%; confirmation of the functional intronic variant rs75017182 would be required for definitive HapB3 assignment. Overall, rs67376798 or rs56038477 was detected in 14 patients (4.13%). In addition, rare variants with a cohort allele frequency below 1% were identified in 11 patients (3.24%). Among these, p.Thr65Ala, p.Thr65Met, p.Asn151Asp, and p.Val691Leu represented potentially relevant findings requiring further functional validation. Conclusions: Whole-exome analysis revealed a heterogeneous spectrum of DPYD variants in the studied Russian oncology cohort, including both established pharmacogenetic markers and rare variants that would not be captured by limited targeted panels. The overall allele-frequency pattern was predominantly similar to that of European reference populations, although several rare variants demonstrated distinct distributions. These findings support the value of population-specific characterization of DPYD and suggest that expanded sequencing approaches may complement conventional pharmacogenetic testing by identifying rare potentially functional alleles.

Genes doi: 10.3390/genes17091083

Authors: Katelyn N. Austin Man-Kit Lei

Background/Objectives: DNA methylation (DNAm)-based aging measures are increasingly being used in biological aging, disease vulnerability, and cancer-related risk. However, it remains unclear whether these measures capture a single generalized aging process or separable biological domains relevant to cancer-relevant biological vulnerability. Methods: Using data from the Family and Community Health Study (FACHS), we examine whether blood-based DNAm scores capture two distinct biological domains relevant to cancer susceptibility: a replication/mitotic domain, indexed by CellDRIFT, EpiTOC2, and MiAge, and an early-life systemic dysregulation domain, indexed by DunedinPACE, GrimAgeV2, and PhenoAge. Results: Regression results showed clear domain specificity. CRP, BMI, alcohol methylation, and AHRR/cg05575921 were positively associated with the early-life systemic dysregulation domain but showed weak or null associations with the replication/mitotic domain. Cross-domain tests confirmed significantly stronger associations for the early-life systemic dysregulation domain for CRP, BMI, and alcohol methylation, with a marginal difference for AHRR/cg05575921. In contrast, telomere-related methylation and immune-cell composition showed a different pattern. DNAmTL was inversely associated with both domains and did not differ significantly across domains. Conclusions: These findings suggest that blood-based DNAm aging measures do not reflect a single aging process. Instead, they distinguish at least two cancer-relevant methylation domains: one reflecting replication-driven mitotic aging and hematopoietic cell-turnover biology, and another reflecting early-life systemic dysregulation vulnerability linked to inflammation, metabolic risk, smoking methylation, and alcohol-related methylation. This two-domain framework may help clarify how blood DNAm profiles capture complementary biological processes relevant to cancer susceptibility and guide future studies of methylation-based cancer risk.

Genes doi: 10.3390/genes17091081

Authors: Yantong Luo Jingjing Deng Yuanzhan Loh Hongduo Lu Nanbu Wang Chunzhi Tang Bin Zhang

Background/Objects: Alzheimer’s disease (AD) is a chronic neurodegenerative disorder characterized by progressive cognitive decline. Although Nrf2 is a key regulator of oxidative stress in AD, the molecular factors associated with Nrf2 signaling and their potential regulatory relationships remain incompletely understood. This study aimed to systematically identify and validate a novel Nrf2-associated signaling axis in AD. Results: Slc2a1 was identified as a key Nrf2-associated candidate gene. In the SCOP-induced AD model, reduced Nrf2 expression was accompanied by decreased Slc2a1 expression, cognitive impairment, hippocampal neuronal injury, excessive ROS accumulation, and mitochondrial abnormalities. Pharmacological modulation of Nrf2 was associated with corresponding changes in Slc2a1 expression, while Nrf2 activation was accompanied by improvements in oxidative stress and neuronal injury. Conclusions: This study identifies a potential functional relationship between Nrf2 signaling and Slc2a1 expression in AD-related pathology and proposes the Nrf2/Slc2a1 pathway as a potential mechanistic framework linking oxidative stress to mitochondrial abnormalities.

Genes doi: 10.3390/genes17091080

Authors: Paul Barreau Cyril Djari John De Vos Nino-Guy Cassuto Said Assou

Infertility affects approximately one in six individuals worldwide and is a highly heterogeneous disorder resulting from the complex interplay of genetic, epigenetic, endocrine, environmental and lifestyle factors. Although numerous genes and molecular pathways involved in female and male infertility have been identified, elucidating the functional consequences of disease-associated variants remains challenging due to the lack of relevant human experimental models. In recent years, reproductive organoids have emerged as powerful three-dimensional systems that recapitulate key structural, cellular and functional characteristics of the ovary, fallopian tube, endometrium, testis and early embryo. Here, we review the current landscape of reproductive organoid models based on a focused analysis of the literature, with particular emphasis on original studies describing their generation, characterization and applications. Beyond modeling tissue development and reproductive physiology, these models provide unique opportunities to investigate infertility-associated mechanisms, gene regulatory networks, cell–cell communication and tissue-specific responses to environmental and pharmacological stimuli. Single-cell and spatial transcriptomics, multi-omics, CRISPR/Cas9 genome editing, artificial intelligence and bioengineering technologies, including organ-on-chip systems, are expanding their potential as next-generation platforms for functional genomics, disease modeling, biomarker discovery and therapeutic screening. However, current reproductive organoids remain simplified representations of native tissues, with limitations in physiological maturity, reproducibility and standardization, while their clinical predictive value remains to be established. Overall, by linking genomic variation with molecular regulation, cellular phenotypes and tissue organization, reproductive organoids represent promising preclinical platforms for understanding human infertility and may ultimately contribute to the development of precision reproductive medicine.

Genes doi: 10.3390/genes17091079

Authors: Zeran Li Shanshan Liu Quan Zhang Cuizhen Zhang Gang Peng

Background/Objectives: Precise genetic access to the zebrafish habenula remains limited by a scarcity of compact, sequence-defined cis-regulatory elements (CREs). Here, we integrated developmental expression mapping, deep-learning predictions on long-range sequences, and in vivo reporter assays to identify compact regulatory sequences driving habenular expression. Methods: Using a transgenic zebrafish line enriched for habenular reporter expression, we isolated GFP-positive cells from larval brains and profiled their transcriptomes via microarray. A subset of candidate genes enriched in this dataset was validated using whole-mount in situ hybridization across two developmental stages. This analysis identified genes with highly reproducible habenular expression, leading to the selection of the gng8 and ano2 loci for subsequent CRE characterization. We developed ZEN-former (Zebrafish EN-former), an Enformer-based sequence-to-function model trained on neuronal subclass chromatin accessibility profiles from the adult mouse brain. Results: The model demonstrated strong correlation between predicted and experimentally measured signals across held-out genomic regions. To prioritize regulatory candidates, we integrated ZEN-former predictions with available zebrafish ATAC-seq data, RepeatMasker annotations, and gene models, identifying two ~600 bp intervals at each gene locus. These selected intervals were combined to generate ~1.2 kb reporter constructs for gng8 and ano2 loci, which were then evaluated using Tol2 transposon mediated transgenesis assays in zebrafish. In transiently injected larvae, both constructs successfully drove reporter expression in the habenular region. Furthermore, the resulting stable transgenic lines displayed highly specific and reproducible habenular expression. Quantitative confocal analysis showed mean habenular labeling completeness values of 84.5% and 96.2% for the gng8- and ano2-derived lines, respectively. Conclusions: Together, these findings provide a proof of concept that sequence features learned from mammalian chromatin accessibility datasets can effectively guide the prioritization of functional regulatory elements across species in zebrafish. The compact regulatory constructs and stable transgenic lines generated here offer robust genetic tools for investigating habenular circuitry.

Genes doi: 10.3390/genes17091078

Authors: Da Hye Yoon Chang Ahn Seol Jung Woo Rhim Ji Yoon Han

Background/Objectives: Genomic reanalysis may provide additional molecular diagnoses in patients with neurodevelopmental disorders (NDDs) whose initial genetic testing was nondiagnostic. We evaluated the diagnostic yield and mechanisms of newly established diagnoses in NDDs with and without epilepsy. Methods: We retrospectively reviewed 175 patients with previously unresolved NDDs who underwent whole-exome sequencing between 2015 and 2024. Archived WES variant call format (VCF) files were reannotated using updated databases and variant prioritization criteria, followed by phenotype- and inheritance-informed clinical interpretation. Patients were classified as NDD without epilepsy (n = 133) or NDD with epilepsy (NDD+E; n = 42). Results: Five new molecular diagnoses were established, yielding an incremental diagnostic yield of 3% (5/175). The yield was numerically higher in the NDD+E group than in the NDD group (7% [3/42] vs. 2% [2/133]), although the difference was not statistically significant (p = 0.090). Newly established diagnoses involved NPRL3, RYR1, SYNGAP1, CSNK2B, and SETD5 and arose through distinct mechanisms, including complementary CNV testing with retrospective sequencing review, phenotype- and inheritance-informed reinterpretation, recognition of insufficient initial sequencing coverage, and updated variant interpretation incorporating new evidence. Conclusions: Genomic re-evaluation provided additional diagnoses in a modest but clinically relevant proportion of previously unresolved pediatric NDD cases. Periodic, phenotype-informed reassessment of existing genomic data, together with complementary testing when indicated, may resolve diagnoses missed or uninterpretable at the initial evaluation.

Genes doi: 10.3390/genes17091077

Authors: Ji Eun Kim Hyuk Lee Young Eun Oh Tae-Se Kim Yang Won Min Byung-Hoon Min Jun Haeng Lee Poong-Lyul Rhee

Background/Objectives: Observational studies in East Asia have not shown increased gastric cancer risk in ulcerative colitis, whereas a previous genetic analysis reported a positive association. Because both diseases have major histocompatibility complex (MHC) signals, we assessed whether the association was most apparent in MHC variants under ancestry-matched instrument selection. Methods: We performed a two-stage, two-sample Mendelian randomization study of 12 East Asian datasets (11 immune-related phenotypes) and a gastric cancer genome-wide association study (7921 cases; 159,201 controls), with instruments selected against the 1000 Genomes East Asian panel. For ulcerative colitis, we compared all, MHC, and non-MHC variants, evaluated signal overlap at HLA-DQA1/DQB1, and assessed cross-disease specificity. Results: Ulcerative colitis was the only phenotype associated with gastric cancer after false-discovery-rate correction (odds ratio [OR] 1.16, 95% confidence interval [CI] 1.09–1.24; q = 1.37 × 10−4). The MHC estimate was similar (OR 1.18, 95% CI 1.11–1.26), whereas the non-MHC estimate was close to 1 but rested on only two variants and remained imprecise (OR 1.00, 95% CI 0.86–1.17). The traits showed overlapping signals at HLA-DQA1/DQB1, and the MHC variants were associated with several other immune diseases. Conclusions: The positive association was most apparent in MHC variants that were not specific to ulcerative colitis. The association therefore appears to be largely carried by pleiotropic MHC variants, although these data cannot establish the pathway that explains it.

Genes doi: 10.3390/genes17091076

Authors: Aleksandra Litkowska Jan Wojtas Kaja Nadulska Grzegorz Kurec Oliwia Burdan Paweł Adam Krawczyk

Background: Precision oncology has significantly transformed the management of non-small cell lung cancer (NSCLC) through the integration of molecular diagnostics, targeted therapies, and biomarker-driven treatment selection. Advances in next-generation sequencing (NGS) and liquid biopsy have improved the identification of actionable molecular alterations and enabled dynamic monitoring of tumor evolution. Objective: To provide a structured narrative review of current evidence regarding actionable molecular biomarkers, diagnostic methodologies, targeted therapies, and future directions in NSCLC precision oncology, with a specific focus on conceptualizing acquired resistance mechanisms. Methods: A structured narrative literature review was conducted by searching PubMed and Google Scholar for English-language studies published between 2015 and 2026. Eligible publications included clinical trials, cohort studies, translational research, reviews, and clinical guidelines addressing molecular profiling, targeted treatments, diagnostic approaches, and resistance mechanisms in NSCLC. Results: A total of 99 foundational studies and clinical documents were analyzed. Key actionable biomarkers included EGFR (Epidermal Growth Factor Receptor), ALK (Anaplastic Lymphoma Kinase), ROS1 (ROS Proto-Oncogene 1, Receptor Tyrosine Kinase), KRAS (Kirsten Rat Sarcoma Viral Oncogene Homolog), RET (Rearranged during Transfection), MET (Mesenchymal–Epithelial Transition Factor), HER2 (Human Epidermal Growth Factor Receptor 2) and NTRK (Neurotrophic Tyrosine Receptor Kinase) alterations, along with emerging targets such as NRG1 (Neuregulin 1) fusions. NGS emerged as the cornerstone of comprehensive molecular profiling, while liquid biopsy enabled longitudinal monitoring of tumor dynamics and resistance development. To organize the biological complexity of treatment failure, acquired resistance mechanisms were categorized into a three-tiered conceptual framework: target-centric genetic evolution (Tier 1), cellular plasticity and intratumoral heterogeneity (Tier 2), and non-genetic/microenvironmental adaptation (Tier 3). Targeted therapies significantly improved clinical outcomes compared with conventional chemotherapy; however, acquired resistance remained a major challenge across all tiers. Conclusions: Precision oncology in NSCLC is evolving from a biomarker-focused approach toward a dynamic framework integrating molecular diagnostics, targeted therapies, and continuous resistance monitoring. The proposed three-tiered resistance framework provides a structured basis for understanding treatment failure, guiding molecular reassessment at progression, and informing future adaptive therapeutic strategies to improve long-term patient outcomes.

Genes doi: 10.3390/genes17091075

Authors: Yue Feng Haimo Zhu Shiyi Zhong Lijing Wang Yan Zhao Wei Xu Qingzhi Liu Shengkun Liu Baoshen Liu Yongzhong Zhang

Background: Leaf angle is a key determinant of plant architecture and yield under high-density planting. Loss of the ligule reduces leaf angle, offering a strategy for breeding compact maize. This study aims to identify the genetic basis of the liguleless mutant jd30 and develop a functional marker for breeding. Methods: The jd30 mutant was phenotypically characterized and compared with the wild type (WT). Genetic analysis was performed using F2 populations. Map-based cloning was conducted with simple sequence repeat (SSR) and insertion/deletion (InDel) markers. Candidate genes were annotated and sequenced. Allelism tests were performed by crossing jd30 with other lg1 mutants. A Cleaved Amplified Polymorphic Sequence (CAPS) marker was developed based on the causal mutation. Results: The jd30 mutant showed complete ligule loss from the V2 stage onward and had a significantly smaller leaf angle than the wild type. The phenotype is controlled by a single recessive nuclear gene, mapped to a 123-kb interval on chromosome 2 containing four candidate genes. A single-base cytosine (C) deletion at nucleotide 522 of ZmLG1 caused a frameshift and premature stop codon. Two other lg1 mutants, 20292 and 29163, carried distinct mutations—a C insertion and multiple base substitutions, respectively. Allelism tests confirmed jd30 as a novel allele of ZmLG1. A co-dominant CAPS marker, M5, was developed to distinguish wild-type and mutant alleles. Conclusions: This study identifies a novel loss-of-function allele of ZmLG1, designated ZmLG1-1, and the M5 marker, providing valuable genetic resources for modifying leaf architecture and improving maize plant compactness.

Genes doi: 10.3390/genes17091074

Authors: Aris Kaltsas Eleftheria Markou Athanasios Zachariou Fotios Dimitriadis Nikolaos Sofikitis

Non-coding RNAs (ncRNAs) are biologically plausible biomarkers in male infertility, but no assay is ready for routine use. This narrative review organizes human evidence by intended clinical decision and defines clinical actionability as a test’s ability to inform a specified decision through analytical reliability, clinical validity, incremental value, decision-level benefit, and feasible implementation. Evidence is most developed for obstructive versus non-obstructive azoospermia (NOA) classification and sperm-retrieval prognosis. Most reports, however, use selected case–control samples, single-center development cohorts, or same-program evaluations. Mixed biospecimens, incompletely specified RNA isoforms and normalization, uncertain cohort independence, imperfect diagnostic references, and protocol-dependent retrieval outcomes limit transportability. No independent geographic validation of a locked ncRNA assay or prospective evaluation of ncRNA-guided management was identified within the retrieved sources. Current guidelines do not recommend routine ncRNA testing. Progress requires prespecified intended uses, locked assays, representative multicenter validation, same-patient comparison with contemporary care, calibrated risk estimates, decision-curve analysis, and patient-important, couple-centered outcomes.

Genes doi: 10.3390/genes17091073

Authors: Maria Busacca Eleonora Canioni Raffaella Brugnoni

Background/Objectives: Congenital myotonia (CM) is an inherited neuromuscular disorder caused by mutations in the Chloride Voltage-Gated Channel 1 (CLCN1) gene, encoding the Chloride Channel 1 (CIC-1) in skeletal muscle. These mutations can be inherited in either an autosomal dominant (Thomsen’s disease) or recessive pattern (Becker’s disease). Within the diagnostic workflow for this pathology, gene sequencing represents one of the main analytical approaches, while Multiplex Ligation-dependent Probe Amplification (MLPA) is used as a complementary method, particularly in patients with autosomal recessive inheritance, to detect deletions or duplications involving one or more exons of the CLCN1. This study aims to highlight a specific limitation of MLPA in CLCN1 analysis. Methods: Patients carrying pathogenic CLCN1 variants, previously identified by sequencing, subsequently underwent MLPA analysis to investigate the presence of a second pathogenic allele. Results: In the analysed patients, MLPA identified apparent exon deletions involving the same exons in which the previously identified variants were present. However, no actual variation in copy number was observed at the exon level. This discrepancy is linked to the efficiency of probe hybridization and ligation to target sequences. Small sequence variations can interfere with probe binding, preventing their correct ligation and resulting in a signal pattern consistent with apparent exon loss, thereby generating false positives. Conclusions: Our findings highlight the importance of integrating sequencing and MLPA data in CLCN1 analysis. Awareness of variant-induced MLPA artefacts is essential to avoid misinterpretation of apparent exon deletions and to ensure an accurate molecular diagnosis of CM.

Genes doi: 10.3390/genes17091072

Authors: Hong Su Shiting Li Guanyang Chen Peng Bai

Background: Small-molecule-regulated gene switches are important tools for programmable mammalian cell engineering, and compact switches responsive to clinically familiar ligands that can be administered locally are particularly attractive for externally regulated transgene expression. Methods: Here, we developed ZF10–ΔVDR, a compact zinc-finger–VDR transcriptional switch, by fusing an orthogonal human-derived zinc-finger array, ZF10, to the hinge and ligand-binding domain of the vitamin D receptor. The resulting switch enabled transgene regulation by calcipotriol, a clinically used topical vitamin D analog and VDR agonist. Results: ZF10–ΔVDR maintained low basal activity, showed limited activation by the tested vitamin D species at physiologically relevant reference concentrations, and was robustly activated by calcipotriol. The system functioned across multiple human cell types. In vivo, topical calcipotriol increased serum reporter output in mice bearing subcutaneous microencapsulated-cell implants, whereas oral vitamin D3 did not measurably activate this system under the tested conditions. In a separate HaCaT implantation model, topical calcipotriol increased bioluminescence at wound-adjacent implantation sites. ZF10–ΔVDR also supported reversible ON/OFF cycling under the tested conditions and inducible secreted protein output in vitro. Conclusions: These findings establish ZF10–ΔVDR as a calcipotriol-responsive switch with limited activation by endogenous vitamin D species, activity across multiple mammalian cell types, reversible regulation under the tested conditions, and compatibility with topical induction in vivo.

Genes doi: 10.3390/genes17091071

Authors: Nikita Filatov Kirill Kokorichev Dmitry Tychinin Taisiya Voronina Elena Shagimardanova Konstantin Dergilev Pavel Makarevich Andrey Kiyasov Vsevolod Tkachuk Mary Woroncow Yelena Parfyonova Airat Bilyalov Oleg Gusev

Background/Objectives: Acomys cahirinus exhibits more favorable cardiac remodeling after ischemic injury than Mus musculus, yet the molecular organization of the intact myocardium remains poorly characterized. This study aimed to identify baseline interspecies differences in the adult left ventricle, with particular emphasis on ventricular cardiomyocyte transcriptional states. Methods: Intact left ventricles from adult male A. cahirinus and M. musculus were analyzed by single-nucleus RNA sequencing using three biological samples per species. Cross-species integration was followed by cell type annotation, pseudobulk differential expression analysis, Augur-based assessment of interspecies separability, coexpression module analysis, and focused reintegration analysis of ventricular cardiomyocytes. Cardiomyocyte profiles were further compared with published embryonic and early postnatal M. musculus heart datasets. Results: Both species contained comparable major myocardial cell populations, whereas marked interspecies transcriptional differences persisted within individual cell types. Ventricular cardiomyocytes exhibited the largest number of differentially expressed genes and were classified into three transcriptional states: contractile, matrix-associated, and alternative. Adult A. cahirinus cardiomyocytes retained a mature cardiomyocyte phenotype but showed greater enrichment of developmental, morphogenetic, and Hippo-associated gene programs than adult M. musculus cardiomyocytes. Their transcriptional profile did not correspond to embryonic or early postnatal mouse states. The integrated atlas further identified interspecies differences in fibroblast-associated and extracellular matrix-related programs. Conclusions: The intact myocardium of A. cahirinus exhibits cell type-specific transcriptional differences relative to M. musculus. Ventricular cardiomyocytes display a distinct mature transcriptional configuration rather than a direct immature state, which may contribute to the favorable response of A. cahirinus to myocardial injury.

Genes doi: 10.3390/genes17091070

Authors: Lin He Liangzhe Li Yuxiao Li Yujun Sun Zhi Zheng Chunfang Chu Shuya Chen Lin Li

Background/Objectives: Individuals with 46,XY disorders of sexual development (DSD) present with incomplete genital masculinization, aberrant gonadal development, and occasional retention of Müllerian duct remnants. Genetic factors play a substantial role in DSD pathogenesis, and whole-exome sequencing has expanded the catalog of candidate variants in recent years. However, the underlying molecular pathways remain incompletely characterized, and the functional relevance of most isolated genetic findings has not been systematically determined. This study aimed to identify and functionally characterize novel NR5A1 variants in DSD. Methods: A heterozygous missense variant NR5A1 c.88T>A (p.Cys30Ser) was identified in two patients with DSD, and initial functional characterization of the variant was performed via immunofluorescence analysis, Western Blotting, RNA sequencing, and quantitative real-time PCR analysis. Results: Wildtype NR5A1 protein localized predominantly to the nucleus, whereas the p.Cys30Ser mutant exhibited dual nuclear and cytoplasmic distribution. Compared with the wildtype, the p.Cys30Ser variant altered the expression of 642 genes, with differentially expressed genes primarily enriched in the neuroactive ligand–receptor interaction pathway. The variant impaired the transactivation of canonical NR5A1 downstream targets, resulting in the marked downregulation of 560 genes including key regulators such as KISS1R, CYP11A1, STAR, GABRP, and GRAMD1D. Conclusions: This study is the first to identify and functionally characterize the NR5A1 p.Cys30Ser variant in the context of DSD. Our findings broaden the mutational spectrum of NR5A1-related DSD and provide new insights into the molecular genetic basis of sexual development disorders.

Genes doi: 10.3390/genes17091069

Authors: John Dotis Nikoleta Printza

Pediatric nephrology is shifting from broad phenotype-based labels toward molecularly defined, genotype-guided diagnosis and management. Childhood kidney disorders are enriched for monogenic causes, yet persistent microscopic hematuria, bilateral kidney cysts, steroid-resistant nephrotic syndrome, and thrombotic microangiopathy may represent shared endpoints of biologically distinct mechanisms. Using these four scenarios, this narrative review illustrates how structured phenotyping, pedigree analysis, biochemical evaluation, and appropriately selected genomic testing can establish etiology, revise diagnoses, and guide clinical decision-making. Molecular diagnosis may support early nephroprotection, prevent ineffective immunosuppression, reveal tumor or extrarenal risks, enable mechanism-based therapy, and optimize transplantation planning. It also enables cascade testing, reproductive counseling, presymptomatic evaluation of relatives, and safer assessment of living-related donors. Genomic findings, however, require clinical context. Variants must be evaluated against gene–disease validity, inheritance, segregation, molecular mechanism, and phenotype, while variants of uncertain significance should not independently determine treatment or donor eligibility. Negative or inconclusive findings should prompt phenotypic reassessment, evaluation of analytical limitations, targeted studies, and periodic genomic reanalysis. Emerging genome and long-read sequencing, multiomics, artificial intelligence, and RNA-based therapeutics may further expand precision care, but rigorous interpretation, equitable access, appropriate counseling, and multidisciplinary collaboration remain essential. Precision nephrology derives value not from identifying variants alone, but from converting molecular etiology into safer, anticipatory, and individualized care.

Genes doi: 10.3390/genes17091068

Authors: Gang Wang Wanli Han Zhibin Zhang Xiaomei Ma Hai Zhao Yandi Yao Fuxiang Zhao Jinxin Qiao Xiang Zhang Yu Yu Hongguang Liu

Background: Drought is one of the major abiotic stresses that affect and limit cotton growth and production. However, transcriptome differences between drought-tolerant and drought-susceptible cotton lines remain largely unknown. Methods and Results: In this study, two upland cotton cultivars, the drought-tolerant XLZ80 and drought-sensitive XLZ61, were subjected to comparative phenotypic and transcriptomic analyses under drought stress. Phenotypic evaluation showed that XLZ80 exhibited only mild leaf wilting, whereas XLZ61 displayed severe wilting symptoms after drought stress. RNA-seq analysis revealed that differentially expressed genes in XLZ80 were specifically enriched in pathways related to phosphatidylinositol signaling, phenylalanine metabolism, MAPK signaling, and betaine biosynthesis, while DEGs in XLZ61 were primarily involved in basal metabolic processes. A total of 9302 core DEGs were identified across and between the cultivars and were grouped into eight dynamic expression clusters containing 841 transcription factors. Weighted gene co-expression network analysis further identified three key modules associated with drought tolerance. Twelve hub genes, including GH_D02G2153 (MADS-box) and GH_A05G1087 (bZIP), were identified as central regulators. qRT-PCR validation confirmed that these genes exhibited faster and stronger induction in the tolerant cultivar. In summary, this study deepens the transcriptional-level understanding of drought stress responses in cotton and provides valuable gene resources for breeding drought-resistant cultivars.

Genes doi: 10.3390/genes17091067

Authors: Lin Chen Ming-Juan Fang Nan Cheng Yin Xu

Background: Dystonia is a severe neurological disorder with enigmatic pathogenesis. Current treatment options are limited in preventing the disease progression, underscoring the urgent need for new targeted therapeutic agents to develop more effective therapies. Methods: We performed a proteome-wide Mendelian randomization (MR) study and sensitivity analyses to evaluate the causal relationships between dystonia and proteins. GO and KEGG enrichment analysis of dystonia-associated proteins was conducted. Then, we built PPI network and identified the expression of hub-genes in specific brain neurons in single-cell sequencing data. Additionally, we performed drug enrichment analysis of hub-genes, and employed network pharmacology and molecular docking methods to identify potential drugs for dystonia. Results: Our study identified genetically predicted associations consistent with a potential causal effect between 51 proteins and risk of dystonia. GO and KEGG enrichment analyses revealed that these proteins are involved cellular response to transforming growth factor-β stimulation and cytokine-cytokine receptor interaction. Notably, the PPI network exhibited 21 community relationships within the regulatory network among the 51 dystonia-associated proteins identified. The single-cell RNA annotations for brain cluster specificity revealed Tumor necrosis factor (TNF) was highly expressed in microglia cells. Drug enrichment analysis identified five traditional Chinese medicine monomers (paeoniflorin, artesunate, ginsenoside Rh1, psoralen, and quercetin dihydrate) as candidates for molecular docking analysis. Among these, paeoniflorin-TNF, quercetin dihydrate-TNF, and artesunate-TNF exhibited the highest binding energy (−9.1 kcal/mol). Conclusions: Our molecular-docking analysis suggested that traditional Chinese medicine monomers including paeoniflorin, quercetin dihydrate, and artesunate may serve as promising candidates for future drug development.

Genes doi: 10.3390/genes17091066

Authors: Marta Ortega-Martínez Devani Moreno-Sánchez Jenifer Hernández-Martínez María-de-Lourdes Chávez-Briones Yareth Gopar-Cuevas Jaime García-Juárez Gilberto Jaramillo-Rangel

Background/Objectives: In the identification of human remains, their genetic profile can be compared with that obtained from biological samples of the person from whom they are suspected to have come. Our aim was to evaluate the effect of storage time on DNA obtained from umbilical cord that could be used as a reference in forensic identification. Methods: Fifteen umbilical cords stored by the donors in their homes for a period of between 0.5 and 47 years were collected. Saliva samples were obtained for use as a reference. DNA extraction was performed using the PrepFiler Express BTA™ Forensic DNA Extraction Kit and quantified using the Quantifiler™ HP DNA quantification kit. STR profiling was performed using the GlobalFiler™ PCR Amplification Kit. Alleles were detected using an ABI PRISM® 3500 genetic analyzer. Results: In samples from 0.5 to 21 years of age, DNA concentration and degradation index (DI) did not follow a linear pattern over time; the genetic profiles obtained matched that of the corresponding saliva sample. Older samples showed lower DNA concentration values and higher DIs. The percentage of alleles recovered decreased to 31% in the oldest umbilical cord analyzed. However, from a sample stored for 31 years, a DNA concentration and DI similar to the younger samples were obtained, along with a complete STR profile. Conclusions: It is possible to obtain STR profiles useful for forensic identification from umbilical cords even after decades of storage; however, success is highly variable and cannot be predicted from storage time alone.

Genes doi: 10.3390/genes17091065

Authors: Ilaria Galliano Francesca Nardo Davide Tinti Cecilia Nobili Paola Montanari Cristina Calvi Michela Trada Luisa De Sanctis Massimiliano Bergallo

Background: Enteroviruses (EVs) have been proposed as environmental triggers in type 1 diabetes (T1D), potentially through activation of innate immune pathways and type I interferon (IFN) responses. However, the relationship between detectable viral infection and IFN-related transcriptional responses remains unclear. Methods: In this cross-sectional, exploratory study, peripheral blood samples from individuals with new-onset T1D, established T1D, and healthy controls were analyzed by an enterovirus 5′NCR-targeted RT-PCR assay and for the expression of innate immune receptors (TLR3, TLR7, TLR8), interferon-stimulated genes (IFI27, IFIT1, ISG15, IFI44L, RSAD2, SIGLEC1), and FOXP3, assessed as an exploratory marker related to regulatory T-cell biology potentially influenced by type I interferon signaling. Gene expression was assessed by quantitative RT-PCR, and comparisons were performed between groups. Results: Enterovirus-targeted amplification was observed in only one T1D sample under the applied assay conditions. In the setting of limited enterovirus-targeted amplification under the applied assay conditions, TLR3 was significantly increased in established T1D, while TLR7 was increased in both new-onset and established T1D, with the highest levels in established disease; these differences remained significant after correction for multiple comparisons across the full gene panel. TLR8 was unchanged. Several of the selected interferon-stimulated genes showed group-specific expression patterns: IFI27 and RSAD2 were significantly increased in new-onset T1D, whereas IFIT1 and ISG15 were more evident in established T1D. SIGLEC1 and IFI44L showed no significant differences. FOXP3 transcript abundance was also increased in both diabetic groups, a finding that correlated with lymphocyte proportion and is interpreted with caution. Conclusions: These findings indicate group-specific differences in whole-blood transcript expression of selected RNA-sensing and IFN-related genes in T1D under conditions in which enterovirus-targeted amplification was observed in only one sample. Given the cross-sectional whole-blood design and the analytical limitations of the EV assay, these results are hypothesis-generating and do not establish the presence or absence of systemic enterovirus infection or functional pathway activation.

Genes doi: 10.3390/genes17091064

Authors: Guillermo Gervasini

Tobacco use disorder (TUD) is a complex multifactorial condition resulting from the interplay between nicotine-induced neurobiological adaptations, behavioral and learning processes, environmental influences, and individual genetic susceptibility. Genetic research has progressively evolved from twin and family studies through candidate-gene approaches to large-scale genome-wide association studies (GWAS), substantially improving our understanding of the genetic architecture of tobacco use and nicotine dependence. This review summarizes the current evidence on the genetic basis of TUD, with particular emphasis on major biological pathways. We also discuss the limitations of early candidate-gene studies and the paradigm shift introduced by large GWAS and meta-analyses, and polygenic risk scores, which indicate that tobacco use and nicotine dependence have a highly polygenic and pleiotropic architecture. Finally, we review the potential clinical applications of genetic information in smoking-cessation treatment, while highlighting current limitations in clinical translation. In the future, it is clear that a multidisciplinary approach—combining genetics, clinical practice, and social sciences—will be necessary to transform tobacco use management into a precision-based model and reduce its impact on public health.

Genes doi: 10.3390/genes17091063

Authors: Tongsheng Liu Shuo Li Ke Wu Xinbin Wang Xiaoyang Sun Wenqi Ding

Rind color is an important quality trait in zucchini (Cucurbita pepo). As a core transcription factor in plant pigment biosynthesis, APRR2 plays a conserved yet mechanistically diverse regulatory role in the formation of rind color in various vegetables. However, the APRR2 transcription factor regulates rind color but has not been systematically identified in C. pepo. In this study, 50 APRR2 genes were defined by the presence of the conserved REC domain verified. These genes were identified and found to be unevenly distributed across the 20 chromosomes, primarily expanded through tandem duplication events. Phylogenetic and structural analysis classified these genes into three distinct subgroups, all featuring the conserved REC domain essential for pigment regulation but exhibiting variations in motifs and intron–exon structures. Promoter analysis revealed abundant light-responsive, hormone-responsive and stress-responsive elements that may contribute to environmental adaptation and photomorphogenesis. Crucially, transcriptome analysis during rind development (0 and 10 days after pollination) in green (GR) and white (WR) rind lines demonstrated profound functional divergence. Expression clusters indicated temporal shifts in metabolism and enriched “circadian rhythm-plant” and “photosynthesis” pathways in WR at 0 DAP. Specific APRR2 genes were tightly correlated with rind color. qPCR validation of the 24 selected APRR2 genes classified them into four trend groups based on the direction of expression change at 10 DAP. In total, 14 genes were upregulated in both GR and WR, 6 were downregulated in both lines, 1 was upregulated in GR but downregulated in WR, and 3 were downregulated in GR but upregulated in WR. Furthermore, protein–protein interaction prediction and yeast two-hybrid (Y2H) assays detected a physical interaction in yeast between a core APRR2 protein and a bHLH62 transcription factor, suggesting a potential interaction that may be involved in rind color regulation, pending in planta validation. The study first identified the members of the APRR2 gene family in C. pepo and conducted a bioinformatics analysis on them. The study establishes the molecular basis of APRR2 function and offers valuable resources for breeding improved C. pepo varieties.

Genes doi: 10.3390/genes17091062

Authors: Angran Xia Changwei Wang Yemao Xia

Background/Objectives: Cis-regulatory elements (CREs) help mediate cell-type-selective gene expression, yet sequence-to-activity models are rarely converted into compact, experimentally tractable variant panels that retain natural regulatory scaffolds. We developed SafeEdit-CRE to select minimal edits that preserve cross-model specificity while reducing predictive uncertainty, yielding an auditable CRE variant library for reporter-screening prioritization. Methods: SafeEdit-CRE combines the published Malinois sequence–activity predictor with an architecture-distinct reviewer ensemble, validation-calibrated uncertainty, sequence-domain controls, and constrained beam search. Natural 200 nt CREs were edited under fixed substitution budgets of 1, 5, 10, or 20 nucleotides and evaluated by a separately trained multi-kernel ensemble kept entirely separate from candidate generation. Results: Across 600 held-out CRE parents in K562, HepG2, and SK-N-SH cells, SafeEdit-CRE achieved a mean cross-model specificity-margin gain of 0.877 versus 0.822 for greedy editing (paired difference 0.055; 95% CI 0.040–0.071). Relative to a compute-matched primary-model beam, SafeEdit-CRE yielded a similar cross-model specificity-margin gain (difference −0.004; 95% CI −0.011–0.004) with lower ensemble uncertainty (0.314 vs. 0.335). In a locked 90-parent benchmark, 60.6% of designs passed all nine prespecified sequence and model-agreement checks, compared with 38.8% for greedy and 13.1% for random substitution (paired difference 21.8 percentage points; 95% CI 18.3–25.3). Conclusions: SafeEdit-CRE reduced 3240 designs to 74 Tier A computational candidates prioritized for reporter screening across three cell types and four edit budgets. By separating search from cross-model audit and enforcing explicit edit budgets and sequence–domain safeguards, the framework provides a reproducible and auditable approach to computational CRE prioritization, regulatory-grammar studies, and synthetic regulatory-element design.

Genes doi: 10.3390/genes17091061

Authors: Binyang Wang Yuxue Wang Yong Yin

Background/Objectives: Genetic overlap between any ischaemic stroke (AIS) and coronary artery disease (CAD) can obscure associations less closely tied to coronary risk. We aimed to separate coronary-shared from residual AIS genetic effects. Methods: We applied GWAS-by-subtraction to GIGASTROKE AIS and UK Biobank/CARDIoGRAMplusC4D CAD summary statistics. A Cholesky model separated a CAD-related shared component (F1) from a model-defined residual AIS component (F2). We tested model order, factor covariance, population prevalence, CAD input, LD reference and sample-size parameter then characterised loci using FUMA, SuSiE-RSS, genetic correlation, MAGMA, SMR/HEIDI and targeted colocalisation. Results: AIS and CAD had a genetic correlation of 0.490. F1 and F2 had SNP heritabilities of 0.0251 and 0.00414, and F2 contained 14 FUMA loci. F2 Z scores remained correlated across covariance (minimum r = 0.994), prevalence (minimum r = 0.998) and alternative-CAD analyses (r = 0.984). Reverse ordering produced reallocation of source-trait signal. At rs974819, the T allele was associated positively with CAD and negatively with marginal AIS, producing a model-derived CAD-AIS-discordant F2 association. Source-trait colocalisation showed that NBEAL1, PHACTR1 and PDGFD signals were present in one or both input-trait analyses, whereas the F11 protein signal aligned with AIS and F2. In a potentially overlapping FinnGen cross-implementation analysis, all 13 F2 lead variants showed concordant directions. Within overlapping stroke-subtype analyses, F2 showed stronger alignment with cardioembolic stroke. Conclusions: GWAS-by-subtraction resolved a model-defined residual AIS component that was stable across covariance, prevalence and CAD-input specifications, supporting a component-based view of AIS genetic effects after modelling shared coronary architecture.

Genes doi: 10.3390/genes17091060

Authors: Rong Wang Jia-Li Li Kun Liu Xuan Lu Qian-Qian Zhang Qin Zeng Yun Deng Xiao-Chao Qu Xiang-Ding Chen Li-Jun Tan

Osteoporosis (OP) is characterized by low bone mass and impaired bone microarchitecture, and the long-term use of current therapies is limited by adverse effects and poor adherence. This study sought to identify drugs that could be repurposed for glucocorticoid-induced osteoporosis. Methods: Single-cell RNA-sequencing data from two subjects with osteoporotic fractures and three control subjects were analyzed to identify transcriptional changes in osteoblasts. Candidate drugs were screened using ASGARD and L1000 drug-response signatures. Two-sample Mendelian randomization was used to examine associations between genetically predicted expression of drug-target genes and osteoporosis risk. Quinidine was tested in dexamethasone-treated Tu and Tg(Ola.Sp7:nlsGFP) zebrafish larvae using Alizarin Red staining, fluorescence imaging, and qRT-PCR. Adult zebrafish were assessed by micro-CT. Results: Four candidate drugs were identified, of which quinidine was selected for experimental evaluation. Genetically predicted SCN5A expression was positively associated with osteoporosis risk. Quinidine partially restored cranial mineralization in dexamethasone-treated larvae, with the greatest effect at 10 μmol/L; the 100 μmol/L treatment was less effective. Quinidine also altered the expression of several bone-remodeling-related genes. In adult zebrafish, quinidine treatment was associated with higher bone mineral density and bone volume fraction than dexamethasone treatment alone. Conclusions: Quinidine alleviated several dexamethasone-induced skeletal phenotypes in zebrafish and represents a candidate for further drug-repurposing studies in osteoporosis. Direct validation of its molecular mechanism and safety profile is still required.

Genes doi: 10.3390/genes17091059

Authors: Merita Xhetani Ela Zaimi Dana Dojčáková Ilir Sheraj Soňa Mačeková

Background/Objectives: The population genetic structure of Albania remains insufficiently characterized at both regional and broader European scales. This study investigated genetic variation within Albania and its relationship with neighboring and European populations using autosomal short tandem repeats (STRs). Methods: Sixteen autosomal STR loci were analyzed in 2000 unrelated individuals from 12 Albanian counties, grouped into Northern, Central, and Southern regions. Population structure was assessed using principal component analysis (PCA), pairwise Weir–Cockerham FST, hierarchical AMOVA, and Bayesian clustering (STRUCTURE Version 2.3.4). Population affinities were further evaluated using Nei’s standard genetic distance, multidimensional scaling, and neighbor-joining analysis of European reference populations. Results: PCA revealed extensive regional overlap, with PC1 and PC2 explaining 2.64% and 2.61% of variation, respectively. Pairwise FST values were close to zero, with confidence intervals overlapping zero, while AMOVA indicated negligible regional differentiation. STRUCTURE identified K = 3 as the strongest relative solution, but ancestry coefficients showed extensive admixture without discrete regional clustering. European comparisons revealed low Nei distances (approximately 0.004–0.014), with Albania showing particularly close affinity to Greece and other Southeastern European populations. Conclusions: Albanian autosomal STR variation demonstrates high regional homogeneity and limited population substructure, while broader affinities are consistent with geographic patterns across Southeastern Europe.

Genes doi: 10.3390/genes17091058

Authors: Yueyan Liu Xusheng Wang Juan Wen

Background: Secondary hair germ (SHG)-associated epithelial cells are a key progenitor population that contribute to hair follicle regeneration during early anagen. Although SHG-associated cells become activated during early anagen and contribute to the formation of regenerating follicular structures, the morphologically recognizable SHG compartment becomes less apparent as lower hair follicle structures develop during mid-anagen. However, the transcriptional changes accompanying the transition from SHG-associated states toward lower hair follicle-associated states remain poorly characterized. This study aimed to characterize the transcriptional changes associated with this transition and identify a proliferative intermediate transcriptional state during early anagen. By integrating single-cell transcriptomic analysis with regulatory and cell–cell communication analyses, we sought to improve the understanding of cellular state transitions and microenvironmental changes during early hair follicle regeneration. Methods: Hematoxylin and eosin staining (H&E) was performed to examine histological changes in mouse dorsal skin on days 0, 5, 10, 15, 20, 25, and 30 of the hair cycle. In parallel, previously published single-cell RNA sequencing data from mouse dorsal skin during early anagen were reanalyzed. Hair follicle epithelial cells were extracted and reclustered to identify cell subpopulations with distinct transcriptional characteristics. Cell types were annotated based on canonical marker genes and subpopulation-specific expression patterns. Differential expression analysis, functional enrichment analysis, cell-cycle analysis, developmental potential assessment, trajectory inference, transcription factor regulon analysis, and cell–cell communication analysis were further performed to characterize the relationships among hair germ cells, proliferative lower hair follicle-like cells (PR-loHF), and lower hair follicle cells. Results: Proliferative lower hair follicle-like cells (PR-loHF) were identified as a transcriptionally defined intermediate state associated with the transition from secondary hair germ (SHG)-associated cells toward lower hair follicle-associated cells. PR-loHF exhibited enrichment of biological programs associated with cell-cycle activity, epithelial remodeling, extracellular matrix organization, and developmental regulation. Moreover, compared with SHG-associated and lower hair follicle-associated states, PR-loHF exhibited distinct transcription factor regulon activity and cell–cell communication patterns, further supporting its characterization as a transcriptionally distinguishable intermediate state. Conclusions: PR-loHF represents a proliferative intermediate transcriptional state emerging during the transition from secondary hair germ (SHG)-associated cells toward lower hair follicle-associated states, providing new insights into transcriptional transitions and microenvironmental regulation during early hair follicle regeneration.

Genes doi: 10.3390/genes17091055

Authors: Yousef Abdulrahman E. Lawal Norman C. Garvida Christian Adam L. Espiritu James Patrick K. Peralta Ebner Bon G. Maceda Jimmbeth Zenila P. Fabia Peter James Icalia Gann

Background/Objectives: Hemoglobin is a component of the red blood cell responsible for carrying oxygen. It is composed of four chains, two of each for the alpha and beta globin. Mutations in the gene, beta-globin (HBB), coding for the beta-globin chains causes beta-thalassemia. Common diagnostic methods for this genetic disorder cover only the coding region of the HBB gene. Methods: Cis-regulatory elements within the distal HBB promoter region were predicted in silico. Promoter variants were identified through PCR amplification and Sanger sequencing, while HBB gene expression was assessed. Hematologic parameters were measured, and associations between promoter variants, gene expression, and hematologic parameters were statistically analyzed. Results: Sequencing showed varying mutations in the predicted cis-regulatory elements which suggests less binding of transcription factors leading to a potential change in HBB gene activity. This is corroborated by the gene expression analysis where the presence of more mutations in the promoter region resulted in a higher downregulation of the HBB gene which manifested in hematologic analysis as lower mean corpuscular volume (MCV) and hemoglobin (HGB). Among the cis-regulatory element mutations that potentially explain the reduced expression in HBB are binding to transcription factors such as TATA and GATA. Conclusions: Our work illuminates the importance of expanding analysis of beta-globin variations to the promoter region for understanding the causes of thalassemia traits that cannot be explained by conventional diagnostic methods to employ appropriate treatment strategies.

Genes doi: 10.3390/genes17091057

Authors: BalaSubramani Gattu Linga Faisal E. Ibrahim Nader Al-Dewik

Background: Variants of uncertain significance (VUS) in the LDLR gene remain a major barrier to the molecular diagnosis of familial hypercholesterolemia. Although computational approaches offer scalable prioritization, their clinical utility is limited by predictor discordance, incomplete annotations, and inflated performance arising from variant-type imbalance. We aimed to develop a calibrated, uncertainty-aware machine learning framework for LDLR VUS triage. Methods: We developed an end-to-end pipeline integrating multi-source variant annotations and 45 engineered features (expanded to 68 encoded features) to train RandomForest, XGBoost, and support vector machine models. The framework incorporates predictor concordance analysis, splice-aware annotation, and explicit uncertainty modeling. Models were trained using nested cross-validation and evaluated on an independent ClinGen FH-VCEP expert-panel dataset. Results: The XGBoost model achieved high discriminative performance (ROC-AUC up to 0.99 for all variants and ~0.97 for missense variants). Among 1092 LDLR VUS, 69% were assigned a directional classification, including 485 (44.4%) pathogenic-leaning and 268 (24.5%) benign-leaning variants. The remaining 31% were explicitly categorized as predictor-discordant (n = 170, 15.6%) or unresolved (n = 169, 15.5%), preserving uncertainty. Predictor discordance was particularly enriched among missense variants, indicating that naive aggregation of in silico predictors may lead to overclassification. Conclusions: This framework provides a scalable, transparent, and clinically aligned approach for LDLR VUS prioritization, generating ACMG/AMP-compatible computational evidence to support expert curation and downstream functional validation.

Genes doi: 10.3390/genes17091056

Authors: Ourayna Batta Yasmina Rahmuni Jaber Lyahyai Zineb Rchiad Yassamine Doubaj Abdelaziz Sefiani Imane Cherkaoui Jaouad

Introduction: Primary hyperoxaluria (PH) is a rare autosomal recessive disease characterized by an excess of oxalate, which results in nephrolithiasis, nephrocalcinosis, and ultimately, renal failure and systemic oxalosis. There are 3 forms of PH, named types 1, 2, and 3, caused by variants in the AGXT, GRHPR, and HOGA1 genes, respectively. In Morocco, where consanguinity is common, recurrent variants, mainly affecting the AGXT gene, have been documented; however, the overall molecular profile of PH remains poorly characterized. We aim here to describe the mutational landscape of PH in Morocco and to provide an accurate diagnostic approach. Methods: We analyzed 132 patients referred over 10 years for PH using a stepwise strategy. A step 1 test involved Sanger sequencing of exon 7 of the AGXT gene, followed by sequencing of exons 1, 2, and 10 of the AGXT gene. The step 2 analysis consists of a customized gene panel targeting the three PH-associated genes. Unresolved cases underwent whole-exome sequencing as a third step. Results: First-line Sanger sequencing identified biallelic pathogenic or likely pathogenic AGXT variants in 95 of 132 patients suspected of PH, corresponding to a diagnostic yield of 72%. Additional molecular diagnoses obtained through targeted PH panel sequencing and WES increased the final cumulative diagnostic yield to 78%. Twelve distinct variants were characterized by Sanger sequencing, with the c.731T>C in exon 7 of the AGXT gene, emerging as the most prevalent variant, supporting its founder effect in this population. Other variants were predominantly located in exons 7, 10, 2, and 1, highlighting mutation hotspots in this population. In unresolved cases, next-generation sequencing (NGS), including targeted gene panels and exome sequencing, uncovered additional pathogenic variants in the AGXT gene and variants in other genes associated with PH-like phenotypes. Conclusions: These results highlight the need for a simplified, exon-focused diagnostic strategy, particularly in resource-limited settings like Morocco.

Genes doi: 10.3390/genes17091054

Authors: Chiara Gobbetto Sofia Passarella Thomas Zoller Ruggero Lanzafame Rossella Gaudino Irene Ambrosetti Angelo Pietrobelli Franco Antoniazzi

Spondylocarpotarsal synostosis syndrome (SCT) is a rare autosomal recessive skeletal dysplasia caused by biallelic loss-of-function variants in FLNB, characterized by disproportionate short stature, progressive vertebral fusion, scoliosis, and carpal (typically capitate–hamate) synostosis, classically without rib anomalies. We performed a systematic literature search of PubMed/MEDLINE and Scopus, supplemented by citation searching, following the PRISMA 2020 statement, to identify all reports providing original, molecularly confirmed FLNB-related SCT patient data. Eleven eligible publications, spanning Taiwanese, Argentinian, Pakistani, Italian, German and Indian cohorts, were included in a qualitative synthesis together with a novel case. The novel patient, an adopted child of Indian origin, presented with severe disproportionate short stature, multisegmental vertebral fusion and posterior arch clefts extending from the cervical to the sacral spine, coccygeal dysgenesis, capitate–hamate fusion, and global developmental delay; targeted exome sequencing identified a novel homozygous frameshift FLNB variant. Integration of this case with the reviewed literature confirms disproportionate short stature, contiguous vertebral fusion, and carpal synostosis as near-universal core features, while tarsal fusion, hearing loss, and facial dysmorphism are variably present. The extent and multisegmental pattern of axial involvement in our patient appear more severe than in most previously reported cases, broadening the recognized phenotypic spectrum of FLNB-related SCT and reinforcing the need for structured, multidisciplinary long-term follow-up.

Genes doi: 10.3390/genes17091053

Authors: Qiupeng Du Lu Xing Chenchen Zhu Ping Li

Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10−5 and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini–Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray–Curtis community variance (R2 = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626–0.705, mean AUC = 0.665), all-significant-pathway model (0.645–0.712, mean AUC = 0.679), strict-pathway model (0.620–0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.

Genes doi: 10.3390/genes17091052

Authors: Zaoxia Niu Lijuan Zhang Bolin Sun Gengmei Min Zongwen Chai Yang Shao

Background: Glutathione S-transferases (GSTs) play pivotal roles in plant growth, abiotic stress responses, detoxification of xenobiotics, and maintenance of redox homeostasis. Methods: In this study, transcriptomic analysis was employed to identify differentially expressed genes (DEGs) in the pea cultivar DX27 under freezing stress (−4 °C) at 3, 6, and 12 h. Results:GO and KEGG enrichment analyses of global transcriptomic data further reveal that DEGs are significantly enriched in the following functional categories: oxidation–reduction processes, stress responses, glutathione metabolism, and secondary metabolite biosynthesis. A total of 52 PsatGST genes were identified and classified into nine subfamilies based on phylogenetic relationships. Chromosomal localization revealed a non-random distribution across seven chromosomes. Promoter cis-element analysis indicated that PsatGST genes harbor diverse regulatory elements associated with light responsiveness, hormone signaling (auxin, abscisic acid, gibberellin, salicylic acid, and MeJA), and abiotic/biotic stress responses. PsatGSTF2 expression analysis showed pronounced up-regulation under freezing stress (−4 °C) at 3, 6, and 12 h. Conclusions: These findings provide a foundational framework for understanding the evolutionary history and functional diversification of the PsatGST gene family and offer valuable candidate genes for the breeding of stress-tolerant pea varieties.

Genes doi: 10.3390/genes17091051

Authors: Siyu Liu Yuwei Hu Yueyi Li Piao Luo Yuying Liu Jixia Huang Hui Ai

Background/Objectives: Tryporyza intacta is a stem-boring pest that readily causes dead hearts in sugarcane seedlings and dead tops in mature plants, leading to large-scale yield reduction. Reverse chemical ecology studies of this pest contribute to its field biological control. During olfactory recognition, odor molecules are integrated by the olfactory nervous system after interacting with odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), thereby regulating insect behavior. Methods: Two novel full-length general odorant-binding protein (GOBP) genes were cloned from antennal tissues using reverse transcription PCR. Protein sequence analysis was conducted to determine sequence similarity and conserved structural features. The recombinant GOBP1-2 protein was expressed in Escherichia coli and purified via Ni-ion affinity chromatography. Fluorescence binding assays were performed to evaluate the binding affinities of GOBP1-2 with various volatile odorant molecules. Results: Protein sequence analysis revealed that the two identified GOBPs shared high sequence similarity with other insect GOBPs and contained the characteristic six-cysteine motif. Fluorescence binding assays demonstrated that GOBP1-2 proteins exhibited differential binding affinities to distinct volatile odorant molecules, indicating selective ligand recognition. Conclusions: These findings suggest that GOBPs and effective volatile odorants likely play a functional role in the olfactory behavioral responses of this moth. This research provides valuable insights for developing field attractants targeting this sugar borer.

Genes doi: 10.3390/genes17091050

Authors: Katharina Häusler Marta Dratwa-Kuzmin Marek Ussowicz Blanka Rybka Renata Ryczan-Krawczyk Krzysztof Kalwak Katarzyna Bogunia-Kubik

Background: Telomere length and telomerase activity are important determinants of haematopoietic cell proliferative capacity and may influence outcomes after allogeneic haematopoietic stem cell transplantation (allo-HSCT). Genetic variation within the telomerase reverse transcriptase (TERT) gene may further contribute to transplantation success and post-transplant complications. Methods: Telomere length was assessed in 98 paediatric allo-HSCT recipients and their donors using quantitative real-time PCR before allo-HSCT and at one and two years post-transplantation. Selected four TERT polymorphisms (rs2736100, rs2853669, rs2735940, and rs10069690) were genotyped in donors and recipients before allo-HSCT. Associations between telomere length, genetic variants, and clinical outcomes were analysed. Results: Telomere length did not differ between recipients and donors before transplantation; however, donors younger than 18 years exhibited significantly longer telomeres. Telomere length increased at one and two years after allo-HSCT compared with pre-transplant values, with the most pronounced changes observed in patients with acute lymphoblastic leukaemia. No direct associations were found between TERT polymorphisms and telomere length. Nevertheless, the recipient rs2735940 T allele was associated with improved survival, the donor rs2736100 G allele with the achievement of complete chimerism, and the recipient rs2853669 C allele with an increased risk of acute graft-versus-host disease (aGvHD). Haplotype analysis identified associations between TERT variants and cytomegalovirus reactivation as well as aGvHD. Conclusions: Paediatric allo-HSCT is associated with dynamic post-transplant changes in telomere length. Although TERT polymorphisms did not directly affect telomere length, several variants were linked with clinically relevant transplantation outcomes, highlighting the potential role of telomere biology in haematopoietic reconstitution and transplant-related complications.

Genes doi: 10.3390/genes17091049

Authors: Xingyu Tang Chenbo Zhao Jinquan Xi Tieshan Xu Tiantian Gu Jindong Ren Shihong Liu Lihong Gu Lizhi Lu

Background/Objectives: Shiqi and Dabao pigeons are two Chinese meat-pigeon breeds with distinct breeding backgrounds and production-related phenotypes, but whether these differences extend to ovarian physiology and molecular profiles remains unclear. This study compared ovarian physiological traits and multi-omics profiles between the breeds. Methods: Seven-month-old reproductively mature females were studied. Flock-level laying and fertilization records were obtained from 456 breeding pairs per breed and recorded every 2 days. Serum reproductive hormones were measured in 10 females per breed. Follicle numbers, atresia, and mature follicle diameter were evaluated in three females per breed. Ovarian samples from six females per breed were analyzed by paired-end RNA sequencing and untargeted LC–MS/MS metabolomics in positive- and negative-ion modes. Results: Dabao pigeons had higher serum progesterone concentrations than Shiqi pigeons (1.35 ± 0.49 vs. 0.32 ± 0.19 ng/mL, p < 0.001) and larger mature follicles (2.25 ± 0.31 vs. 1.08 ± 0.56 mm, p = 0.034), whereas follicle numbers were not significantly different. Transcriptomic analysis identified 761 DEGs (FC > 2 or < 0.5; adjusted p < 0.05), mainly involving extracellular-matrix, cholesterol-, estrogen-, PI3K–Akt-, and TGF-β-related processes. Metabolomic analysis identified five differential metabolites (VIP > 1, FC > 2 or < 0.5; adjusted p < 0.05), including three taurine-conjugated bile acids. Integrated analysis revealed exploratory gene–metabolite associations related to lipid metabolism, follicular signaling, and extracellular-matrix remodeling. Conclusions: Shiqi and Dabao pigeons differed mainly in ovarian physiological and molecular characteristics, whereas short-term flock-level reproductive records were broadly similar. Metabolomic differences were limited but concentrated in bile-acid- and lipid-related features.

Genes doi: 10.3390/genes17091048

Authors: Pedram Kharaziha Klara Junker Josefine Åhsberg Antheia Kissopoulou

Background: PRKD1-related congenital heart defects and ectodermal dysplasia syndrome (CHDED) is a rare multisystem developmental disorder caused by heterozygous gain-of-function variants in PRKD1. Reported phenotypes include congenital heart defects, ectodermal abnormalities, limb anomalies, and neurodevelopmental impairment, while vascular manifestations remain poorly characterized. We report an adult patient with a de novo PRKD1 variant and bilateral carotid artery dissections. Methods: Clinical, cardiovascular, neurological, and genetic evaluations were performed, including SNP-microarray and trio whole-exome sequencing with additional analysis of genes associated with heritable thoracic aortic and connective tissue disorders. Results: The patient was diagnosed at 35 years of age with a de novo PRKD1 c.1808G>A p.(Arg603His) variant. He had childhood-onset congenital heart disease, ectodermal and skeletal abnormalities, hearing impairment, infertility, and learning difficulties. In adulthood, he developed bilateral carotid artery dissections and mild aortic dilatation. No additional pathogenic or likely pathogenic variants were identified in the evaluated connective tissue and heritable aortic disease genes. The PRKD1 variant was absent or extremely rare in population databases and had supporting functional evidence for a gain-of-function effect. Conclusions: This case raises the possibility of a previously unrecognized vascular manifestation of PRKD1-related CHDED. Although a biological association is plausible, causality cannot be established from a single case. Further clinical and functional studies are needed to determine whether vascular fragility is a recurrent feature of PRKD1-related disease. This case also highlights the importance of considering rare genetic syndromes in patients with unexplained arteriopathy and congenital heart disease.

Genes doi: 10.3390/genes17091047

Authors: Dawid Dorna Robert Kleszcz Violetta Krajka-Kuźniak Jarosław Paluszczak

Background/Objectives: Head and neck squamous cell carcinomas (HNSCC) are a heterogenous group of tumors, which are usually treated with surgery and radiotherapy, while chemotherapy (e.g., cisplatin), anti-EGFR, or immune checkpoint inhibitors are used to treat locoregionally advanced and recurrent cases. However, survival outcomes are still unsatisfactory, and novel augmenting treatments are required. Recently, histone lysine demethylases (KDMs) emerged as promising anti-cancer targets. In order to further characterize KDM4–6 as pharmacological targets in HNSCC, we evaluated changes in KDM4/5/6 expression in HNSCC patients, and we experimentally assessed the biological effects of inhibitors of KDM4/5/6 in HNSCC cell lines. Methods: We used online tools (TIMER, GEPIA3, UALCAN) to analyze TCGA data from HNSCC patients. Then, we used resazurin assay to assess the effect of ML324, GSK-J4, and JIB-04 (the inhibitors of KDM4, KDM6, and KDM4–6, respectively) on cell viability in two-dimensional (2D) and three-dimensional (3D) culture of FaDu, SCC-152, and Detroit-562 cells. The potential for cisplatin sensitization was also assessed. Gene/protein expression was evaluated by qPCR and antibody array. Results: We found that the majority of the analyzed KDMs were overexpressed in HNSCC, except KDM4C, KDM5D, and KDM6A. All three studied inhibitors significantly reduced cell viability in 2D and 3D cell cultures. Moreover, the pre-treatment of cells with KDM inhibitors showed moderate potential for cisplatin sensitization. In addition, the chemicals significantly reduced the expression of pluripotency markers, especially SOX2. Conclusions: In conclusion, KDM4–6 inhibitors significantly affected HNSCC cell growth, and exerted the potential for epigenetic priming in combination with cisplatin.

Genes doi: 10.3390/genes17091045

Authors: Beyhan Tüysüz Evrim Çifçi Sunamak Gizem Durcan Birol Öztürk Dilek Uludağ Alkaya Hazal Cansu Çulpan Mehmet Barış Korkmaz Burak Doğangün Ertuğrul Kıykım

Background/Objectives: Autism spectrum disorder (ASD) can present with either an essential or a complex phenotype. The aim of this study was to compare clinical characteristics and the diagnostic yield of copy number variations (CNVs) in essential and complex phenotypes, and to evaluate risk factors. Methods: A total of 163 Turkish children (126 boys, 37 girls) who met the DSM-5 diagnostic criteria for ASD were evaluated. Chromosomal microarray analysis was performed. Results: Among the patients, 21.5% had a complex phenotype and 78.5% had an essential phenotype. Overall, 13.7% of the patients had a developmental/intelligence quotient (DQ/IQ) below 50, most of whom had a complex phenotype. In contrast, 15.3% of the patients had a DQ/IQ of 70 or higher, all of whom had an essential phenotype. The frequency of verbal individuals was 30.5% and did not differ between the two phenotypes. Pathogenic CNVs were identified in 7.4%; 17.1% of the complex group and 4.7% of the essential group. CNVs of uncertain significance that were potentially causal because they included an ASD-associated gene were present in 12.3% of individuals. CNV positivity was significantly higher in individuals with an IQ below 50; interestingly, it was similar between the verbal and non-verbal groups. Besides ultra-rare CNVs, recurrent CNVs associated with ASD were identified. A novel pathogenic CNV was identified at 2q13.33, including NPHP1 and BUB1, both of which are expressed in the brain and are potentially associated with ASD. Advanced parental age and preterm birth were identified as possible risk factors. Conclusions: Deep phenotyping is important for the management of both essential and complex phenotypes and allows the identification of patients with a higher probability of having CNVs. Reporting novel or rare CNVs contributes to clarifying the pathogenesis of ASD.

Genes doi: 10.3390/genes17091046

Authors: Yongle Xu Shan Shan Hanhan Liu Tao Ren

Background: Chronic obstructive pulmonary disease (COPD) is associated with systemic inflammation and increased cardiovascular comorbidity, yet peripheral blood molecular markers for cardiovascular comorbidity-related stratification in COPD remain poorly defined. Methods: In this study, PBMC transcriptomic datasets from a COPD cohort (GSE42057) and a CAD cohort (GSE113079) were analyzed using weighted gene co-expression network analysis (WGCNA) to identify disease-associated modules, followed by overlapping gene screening. Machine-learning models were then applied to prioritize the shared genes. External validation was performed in an independent COPD cohort (GSE54837) and an independent CAD cohort (GSE250283). Immune-cell deconvolution and single-cell transcriptomic analysis of a CAD dataset (GSE269269) were further used to characterize the immune and cellular context of the leading candidate. Finally, RT–qPCR was performed in an institutional PBMC cohort for experimental validation. Results: A total of 169 shared genes were identified, with enrichment in immune, mitochondrial, oxidative phosphorylation, and metabolic pathways. RTN4 was the most consistently validated candidate across COPD and CAD cohorts and was associated with poorer lung function, advanced GOLD stages, and monocyte-related immune patterns. In CAD single-cell data, RTN4-associated signals were mainly localized to monocytes, particularly intermediate monocytes under plaque rupture conditions, with enrichment of immune, antigen-presentation, oxidative-stress, and metabolic pathways. RT–qPCR confirmed increased RTN4 mRNA expression in COPD and a further increase in patients with COPD and comorbid CAD despite comparable FEV1% predicted between the two COPD groups. Conclusions: These findings suggest that elevated RTN4 expression may serve as a PBMC-derived, monocyte-associated candidate molecular feature related to COPD–CAD comorbidity.

Genes doi: 10.3390/genes17091044

Authors: Peipei Su Zhiqun Que Xin Song Gehong Wang

Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645 family in rice (Oryza sativa). Methods and Results: We identified 14 intronless, non-redundant OsDUF1645 genes distributed across eight chromosomes. Phylogenetic and collinearity analyses suggested that family expansion within Poaceae involved ancestral segmental and localized tandem duplication events. Promoter analysis identified stress- and phytohormone-responsive cis-acting elements, including ABRE, MBS, and MeJA-associated motifs. Public transcriptome datasets revealed diverse OsDUF1645 expression patterns under abiotic and hormonal treatments. Integration with the Quantitative Trait Loci Annotation Rice Online (Q-TARO) QTLome identified physical co-localization of multiple OsDUF1645 loci with stress- and agronomic-trait QTLs, including salinity-, drought-, root architecture-, and water-deficit-associated regions. On Chromosome 1, OsDUF1645.1, OsDUF1645.2, OsDUF1645.3, and OsDUF1645.4 overlapped QTL intervals associated with salinity-related physiological traits, including Na+ uptake and Na+ balance, and drought-related root traits. On Chromosome 5, the tandemly arranged OsDUF1645.8, OsDUF1645.9, and OsDUF1645.10 co-localized with QTLs related to root architecture and water-deficit responses. qRT-PCR validation under salinity, osmotic stress, and cadmium exposure confirmed distinct stress-responsive expression profiles; OsDUF1645.6 exhibited broad multi-stress responsiveness, whereas OsDUF1645.3 was downregulated under several conditions. Conclusions: The OsDUF1645 family exhibits substantial functional diversification, supported by distinct regulatory architectures, expression profiles, and QTL associations. These findings provide a framework for prioritizing OsDUF1645 candidates for functional validation and their potential application in molecular breeding and development of climate-resilient rice cultivars.

Genes doi: 10.3390/genes17091042

Authors: Ismael Ortiz Paul V. Taufalele Victor L. Dunagan Samantha S. Hodge Jing Wang Qi Liu Cynthia A. Reinhart-King

Background/Objectives: Cancer cell migration is a hallmark of cancer and is associated with metastasis. While large-scale functional screens have identified regulators of migration, less is known about how intrinsic transcriptional heterogeneity drives highly migratory phenotypes within individual cancer models or whether these transcriptional changes are conserved across different models of varying tissues of origin. This study aims to define shared and cell line-specific transcriptional programs associated with cancer cell migration and analyze their relevance to patient datasets. Methods: Five cancer cell lines across three cancer types (breast, colorectal, and melanoma) were subjected to transwell-based migratory sorting to isolate highly and weakly migratory subpopulations. Bulk RNA sequencing, differential gene expression analysis, Gene Ontology (GO) enrichment, and upstream regulator prediction were performed. Public tumor datasets were analyzed to evaluate gene expression and its association with patient survival. Results: EVA1A was consistently upregulated in all highly migratory (HM) subpopulations. Multiple GO terms were enriched across all cell lines, often driven by distinct gene signatures, indicating convergence at the level of biological processes despite transcriptional divergence. TEAD4 was predicted as an upstream regulator, and increased TEAD4 nuclear localization was observed in four of the five HM subpopulations. EVA1A and TEAD4 expression were elevated in tumors relative to normal tissues, with cancer type-dependent survival outcomes. Conclusions: Migratory selection was accompanied by extensive transcriptional change within each model, yet across five models spanning three tissue types these changes converged on shared biological processes rather than shared genes. Migration-associated phenotypes may therefore be better defined by pathway-level than single-gene analyses, and the clinical relevance of regulatory nodes such as TEAD4 appears conditional on cancer type.

Genes doi: 10.3390/genes17091043

Authors: Chun Pan Cuifang Zheng Yuhuan Wang Jieru Shi Lin Wang Ying Huang

Background/Objectives: RELA encodes the p65 subunit of NF-κB and plays a critical role in immune regulation, epithelial protection, and anti-apoptotic signaling. Pathogenic RELA variants cause monogenic immune dysregulation with heterogeneous clinical manifestations. However, genotype–phenotype relationships and optimal treatment strategies remain incompletely defined. Methods: We conducted a comprehensive literature-based analysis of reported individuals with RELA variants and additionally described a family carrying a RELA c.706C>T (p.R236*) variant, including a clinically affected proband and his variant-positive father with isolated vitiligo. Clinical, immunological, genetic, endoscopic, and therapeutic data were extracted and summarized using a module-based phenotypic framework. Exploratory analyses were performed to examine potential genotype–phenotype patterns and reported treatment responses. Results: A total of 72 individuals with RELA variants, including the proband and his variant-positive father from the present family, were analyzed. RELA-associated disease exhibited marked clinical heterogeneity, encompassing mucocutaneous, systemic inflammatory, autoimmune, gastrointestinal, hematologic, allergic/eosinophilic, and infection-related manifestations. Exploratory analyses suggested that truncating or splice-site variants were more frequently observed among individuals with mucocutaneous lesions, whereas missense variants appeared to be more common among those with autoimmune manifestations. Tumor necrosis factor (TNF) inhibitors were among the therapies associated with favorable reported responses. In the present family, the proband presented with early-onset Behçet-like intestinal inflammation and achieved clinical and endoscopic remission after thalidomide and dose-escalated infliximab treatment. Conclusions: This study expands the clinical spectrum of RELA-associated disease and highlights preliminary variant-related clinical patterns that require confirmation in larger independent cohorts. The available treatment experience suggests that TNF blockade may be considered as a therapeutic option in selected patients, although comparative efficacy cannot be established from the available data.

Genes doi: 10.3390/genes17091041

Authors: Aleksey M. Kulikov Ekaterina A. Sivoplyas Oleg E. Lazebny

Background/Objectives: The 3′ untranslated region (3′ UTR) integrates cleavage and polyadenylation signals, microRNA targets, RNA-binding-protein sites, and RNA secondary structure, but the organizational levels that remain conserved during long-term sequence evolution are poorly understood. Methods: We analyzed the ras85D 3′ UTR in 37 drosophilid taxa. Substitution rates were estimated by maximum likelihood and RelTime; insertions and deletions were reconstructed with ARPIP and summarized as insertion–deletion evolutionary localizations (IELs). Mobile-element candidates were detected with CENSOR/Repbase, and evolutionarily conserved motifs (ECMs) with MEME/MAST. Functional and structural annotations were integrated for Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis and tested using permutation-based coverage, distance, boundary-neighborhood, and multilayer architecture analyses. Results: The 2247-column alignment yielded 959 block events (710 deletions and 249 insertions). Among 63 positive-length ingroup branches, 16 were deletion-enriched, three were insertion-enriched, and one showed bidirectional turnover. Thirty-four IELs projected to 27 D. melanogaster loci and were associated with ECMs. The final registry contained 390 primary functional objects and 1135 RNAfold-predicted structural segments. Predicted weakly conserved miRNA target sites were depleted in ECM_15 and ECM_11, whereas none of 12 Functional Distance tests was significant. APA objects were enriched near predicted structural-segment boundaries (O/E = 5.21; FDR = 0.00761). SAME_MULTILOOP_INTERVAL showed reduced between-context variance (0.276× null; FDR = 0.0233), and the DIFFERENT_MULTILOOP_ARMS − SAME_MULTILOOP_INTERVAL contrast was significant (p = 0.00149; FDR = 0.00447). Conclusions: The ras85D 3′ UTR evolves as a mosaic system in which extensive deletion-biased sequence turnover coexists with conserved regulatory landmarks, recurrently remodeled local neighborhoods, and context-dependent structural–functional architectures.

Genes doi: 10.3390/genes17091038

Authors: Anna Santorek Artur Pałucki Tomasz Zwijacz-Kozica Sebastian Szczepański Michał Ciach Robert Rutkowski

Background/Objectives: The black grouse (Lyrurus tetrix) is experiencing a rapid decline across much of Europe. In Poland, the Carpathians and Sudetes constitute two of the last important strongholds of this endangered species; however, the genetic relationships between populations inhabiting these mountain systems remain poorly understood. Methods: A total of 579 non-invasive samples were collected in the Jizera Mountains and Giant Mountains (Sudetes), as well as in the Tatra Mountains and the Orava–Nowy Targ Basin (Carpathians). Microsatellite genotyping at nine loci identified 122 individuals. Genetic diversity and population genetic structure were assessed using F-statistics, AMOVA, STRUCTURE, PCoA and DAPC. Results: Significant genetic differentiation was detected among populations, with substantially lower differentiation within the mountain regions than between the Sudetes and Carpathians. Analyses consistently identified two major genetic groups corresponding to the Sudetes and Carpathians. The highest genetic diversity was recorded in the Tatra Mountains. Some individuals from this population displayed genetic signatures consistent with possible connectivity to neighbouring populations outside the study area, although this hypothesis requires testing with additional reference samples from these populations. Conclusions: The results demonstrate strong genetic structuring of black grouse populations in southern Poland and suggest limited contemporary gene flow between the Sudetes and Carpathians mountain ranges. The observed differentiation supports treating the Sudeten and Carpathian populations as separate Management Units. The Tatra Mountains constitute an important reservoir of genetic diversity and may play a key role in maintaining genetic connectivity within the Carpathian population.

Genes doi: 10.3390/genes17091039

Authors: Lin He Liangzhe Li Yuxiao Li Yujun Sun Zhi Zheng Chunfang Chu Lin Li

Background/Objectives: Müllerian duct anomalies (MDAs) are congenital structural abnormalities of the female reproductive tract with heterogeneous and incompletely defined genetic contributions. PAX8 is a developmental transcription factor implicated in thyroid and urogenital development. This study assessed the functional consequences of a rare PAX8 variant identified by whole-exome sequencing (WES) in an MDA cohort, without presuming a causal relationship. Methods: WES was performed in 150 patients with MDAs. The PAX8 c.791T>C (p.Leu264Pro) variant was evaluated using computational predictions, cellular assays, and RNA sequencing in a 293FT transient-overexpression model. Results: The heterozygous p.Leu264Pro variant was identified in one patient with a complex septate uterine, cervical, and vaginal anomaly and was absent from 120 controls. Parental samples were unavailable. No statistically significant difference in construct-derived PAX8 mRNA abundance was detected between PAX8-WT and PAX8-L264P, and both proteins showed predominantly nuclear localization. In the direct PAX8-WT-versus-L264P RNA-seq comparison, 76 transcripts had nominal p values below 0.05, but none remained significant after Benjamini–Hochberg correction, and no gene met the prespecified differential-expression criteria. AK5, RCBTB2, and IFT88 were identified as candidate PAX8-responsive genes in this experimental system. Conclusions: No major functional difference was detected between PAX8-WT and L264P under the tested conditions; however, these findings do not establish functional equivalence or exclude smaller, tissue-specific, or developmental-stage-specific effects. The p.Leu264Pro variant remains a variant of uncertain significance with respect to MDAs, and the functional results were not used as benign evidence under ACMG/AMP criterion BS3.

Genes doi: 10.3390/genes17091040

Authors: Juan Fernández-Cadena Edwin W. Naylor Arindam Bhattacharjee

Background/Objectives: Molecular autopsy increasingly identifies rare variants in heritable aortopathy and Loeys–Dietz spectrum genes among sudden-death decedents, yet classification and causal attribution remain challenging when a syndromic diagnosis was never established during life. We reviewed eight unrelated Florida medical examiner decedents ascertained by sudden or unexpected death under medical examiner jurisdiction, including laboratory-reported heterozygous missense variants spanning the Loeys–Dietz syndrome (LDS)/familial thoracic aortic aneurysm and dissection (FTAAD) gene spectrum (TGFBR1, TGFBR2, TGFB2, and SMAD3). None had a premortem clinical diagnosis of LDS; ascertainment was therefore a variant-positive molecular autopsy series, not clinically diagnosed LDS. This illustrative series of eight cases cannot estimate prevalence, diagnostic yield, penetrance, or incidental-finding frequency. Methods: Autopsy (±premortem) phenotype–variant concordance was graded as strong, limited, discordant, or not assessable without treating death as evidence of pathogenicity or equating laboratory detection with clinical LDS diagnosis. Grades were assigned by the authors using predefined rules, were not blinded to laboratory class, and were reconciled by consensus discussion; inter-rater reliability was not quantified. Population, computational, and ClinVar annotations, together with multi-axis molecular triangulation, were retained as supplementary context only. Results: Laboratory classifications were pathogenic in one case (TGFBR1 p.Arg487Gln, Case 1), likely pathogenic in another (TGFBR2 p.Glu428Asp, Case 3), and variants of uncertain significance (VUS) in the remaining cases. Strong phenotype–variant concordance mapped to two aortic-catastrophe decedents (Cases 1 and 3), limited concordance to two cases (Cases 4 and 5), and discordant presentations to four (Cases 2, 6, 7, and 8), including pulmonary thromboembolism without aortopathy, infant sudden death with competing cardiomyopathy-gene context, and ethanol-related death with a normal aorta (SMAD3 Case 8). Conclusions: In this illustrative variant-positive series, 2/8 cases had strong autopsy-led concordance, 2/8 limited, and 4/8 discordant. Autopsy-led concordance grading distinguished two LDS-spectrum variants with strong phenotype–variant concordance for fatal ascending aortic catastrophe from six variants with limited or discordant support. Rare variants in TGFBR1, TGFBR2, TGFB2, or SMAD3 should not be conflated with an LDS diagnosis or with the cause of death without concordant autopsy evidence.

Genes doi: 10.3390/genes17091037

Authors: Mingbo Li Tingting Yang Deyu Kong Jin Xu

Background/Objectives: Phytocystatins are plant-specific inhibitors of papain-like cysteine proteinases that participate in plant development and responses to biotic and abiotic stresses. The roles of rice (Oryza sativa L.) phytocystatins under cold stress remain poorly understood. Xiaomagu (XMG), a cold-tolerant japonica rice landrace, provides valuable material for exploring phytocystatin transcript responses to low-temperature stress. This study characterizes 12 rice phytocystatin genes isolated from XMG and investigates their transcript profiles under cold and abscisic acid (ABA) treatments. Methods: Twelve phytocystatin genes were isolated from the cold-tolerant japonica rice landrace Xiaomagu. Sequence characterization and conserved domain analysis were performed for these phytocystatin family members. Real-time quantitative PCR was performed to examine transcript abundance of phytocystatin genes: low-temperature stress was applied to leaf and root tissues, while ABA treatment was carried out for leaf tissues only. Results: Conserved domain analysis revealed structural differences among the identified phytocystatin members. Real-time quantitative PCR detected distinct transcriptional responses to cold stress among these phytocystatin genes. In leaves, OsCST1, OsCST8, and OsCST12 were up-regulated, whereas OsCST11 was down-regulated. In roots, OsCST2, OsCST3, OsCST6, and OsCST12 showed increased transcript levels, while OsCST1 and OsCST11 were down-regulated. OsCST2, OsCST6, and OsCST11 exhibited significantly altered transcript abundance under ABA treatment. Conclusions: This study characterizes transcript-level responses of 12 phytocystatin genes from the cold-tolerant rice landrace Xiaomagu (XMG) under cold and ABA treatments. The detected expression changes reflect stress-responsive transcriptional regulation of rice phytocystatin family genes. Further in planta functional assays and comparisons with cold-sensitive genotypes are needed to elucidate their precise roles in rice cold adaptation.

Genes doi: 10.3390/genes17091036

Authors: Ying Li Rongqin Huang Li Zhang Haiping Xu Chenglong Luo Wen Luo Zongliang Du

Background: Improving meat quality while maintaining growth efficiency remains a major challenge in poultry production. However, the molecular mechanisms underlying breed-specific meat quality variation remain unclear. This study aimed to investigate how breed-specific growth patterns influence meat quality and elucidate metabolic and transcriptional mechanisms involved. Methods: Pectoralis major meat quality traits and multi-omics profiles were characterized in three genetically distinct chicken breeds—the fast-growing Small White-Feathered chicken (XBJ), the slow-growing Huiyang Bearded chicken (HXJ), and the layer-type Hy-Line Brown chicken (HLH)—at 50, 180, and 300 days of age. Twelve birds per breed per age were used for phenotypic measurement (n = 108 in total), and eight birds per breed per age were subjected to metabolomic and transcriptomic profiling. Phenotypes were analyzed using linear mixed-effects models with breed, age, and their interaction as fixed effects and pen nested within breed as a random effect, followed by Tukey-adjusted pairwise comparisons (p < 0.05). Differential metabolites were screened by OPLS-DA (VIP > 1, p < 0.05), and differentially expressed genes were identified using DESeq2 (|log2FC| ≥ 1, FDR < 0.05). Integrative analyses were performed to identify key genes, metabolites, and pathways associated with meat quality. Results: Phenotypic evaluation revealed a breed-dependent growth–meat quality trade-off, with XBJ exhibiting superior growth but poorer water-holding capacity and meat color, whereas HXJ and HLH showed better tenderness and color at the expense of growth. Metabolomic analysis revealed lipid metabolism as a major contributor to breed-specific divergence, with triglyceride-driven divergence predominating at early and middle stages, whereas later-stage differences involved glycerophospholipid and amino acid metabolism. Transcriptomic analysis revealed significant breed-specific differences in expressed genes at 50 and 180 days, enriched in pathways related to muscle structure, ECM remodeling, and energy metabolism, consistent with metabolic and phenotypic divergence. Integrated analyses identified 28 candidate genes and 71 core metabolites associated with meat quality traits, with PLIN1 and SLC1A6 emerging as key regulators associated with TG species, drip loss, shear force, and BMW. Conclusions: These findings reveal molecular mechanisms underlying the growth–meat quality trade-off and highlight lipid metabolic regulation as a key contributor to meat quality variation. The identified gene–metabolite networks provide insights for molecular breeding to improve chicken meat quality.

Genes doi: 10.3390/genes17091035

Authors: Roxana Andra Coman Andreea Nutu Lia-Raluca Olari Stefan Strilciuc Dana Monica Iancu Ioana Berindan-Neagoe

Liquid biopsy enables minimally invasive detection and longitudinal monitoring of tumor-derived material in blood and urine. In genitourinary cancers, most applications have focused on genomic alterations in circulating tumor DNA (ctDNA), together with circulating tumor cells (CTCs), extracellular vesicles (EVs), and cell-free RNAs. These measurements are clinically informative but are often interpreted as isolated, predominantly descriptive biomarkers and therefore incompletely represent the adaptive processes that determine progression and treatment response. We propose circulating tumor function (CTF) as a systems biology framework for integrating tumor-derived and host-derived genomic, regulatory, metabolic, redox, and immune signals obtained through serial liquid biopsy. CTF is not a single analyte or assay; rather, it is an inference model intended to generate interpretable functional states, including proliferative activity, immune evasion, metastatic potential, metabolic stress, and therapeutic adaptation. We review the contributions and limitations of ctDNA, ncRNA networks, EV-mediated signaling, redox biomarkers, and tumor–host crosstalk in prostate, bladder, renal, and testicular cancers. We also outline the analytical and clinical validation required to determine whether integrated CTF models provide incremental value over established single-analyte approaches. This framework may help reposition liquid biopsy from molecular detection toward functional precision oncology.

Genes doi: 10.3390/genes17091034

Authors: Mario García-Domínguez

Pain is a complex process involving dynamic transcriptional changes in cells of the PNS and CNS following injury or inflammation. Among stress-inducible transcription factors, ATF3 has emerged as one of the most robust molecular markers of neuronal injury, particularly in sensory neurons of the DRG. Although ATF3 is widely used as an indicator of axonal damage in experimental pain models, its functional contribution to the initiation, maintenance, and resolution of pain remains poorly understood. Recent transcriptomic and functional studies suggest that ATF3 not only reflects neuronal stress but also orchestrates gene expression programs involved in axonal regeneration, neuroimmune communication, ion channel remodeling, and nociceptor plasticity. Moreover, ATF3 expression has been identified in non-neuronal cell populations, including Schwann cells and satellite glial cells, indicating broader roles in peripheral nerve repair and neuroinflammation. Despite the growing body of experimental evidence, the literature remains fragmented, and no consensus has yet been reached as to whether ATF3 primarily promotes adaptive regeneration or directly contributes to maladaptive pain signaling. This review aims to provide a comprehensive and critical overview of the current understanding of ATF3 biology in pain, building on evidence from transcriptomic and molecular analyses, experimental models of neuropathic, inflammatory, and cancer-associated pain, and emerging mechanistic insights into its role in pain-related neuronal plasticity. This review examines the regulation of ATF3 expression, its downstream transcriptional targets, its interactions with inflammatory signaling pathways, and its potential value as a therapeutic target. By consolidating current evidence and highlighting existing knowledge gaps, this review seeks to clarify the multifaceted role of ATF3 in pain pathophysiology.

Genes doi: 10.3390/genes17091033

Authors: Ragıp Onur Öztornacı

Background/Objectives: Promoter DNA methylation is conventionally summarised as a regional mean. Two alternatives have been proposed to capture information the mean discards: the concurrence ratio derived from partially methylated bisulfite reads (CAMDA) and single-CpG Shannon (β-) entropy. Benchmarks of such metrics typically report one coefficient per metric on a single gene set at a single aggregation scale. We asked how far that comparison depends on analytical choices that are rarely reported. Methods: Matched whole-genome bisulfite sequencing (WGBS) and RNA-seq from one donor of human CD3+ T cells were analysed. Promoter windows spanning −1000 to +500 bp around the transcription start site (TSS) were divided into fifteen 100 bp bins; all three metrics were computed on an identical CpG set and correlated with log2(FPKM) by Spearman’s ρ. The comparison was repeated across annotation source, quantification level, coverage threshold, aggregation scheme, the treatment of zero-expression transcripts and CpG island status, with metric differences assessed by paired bootstrap over promoters and over chromosomes. Results: Across a grid of five analytical choices, the mean methylation coefficient ranged from −0.145 to −0.593 and the ordering of the metrics reversed between configurations. At the 100 bp bin scale, the largest difference between metrics was 0.037; aggregating the same CpGs to the whole promoter opened differences of up to 0.31, so the apparent superiority of a metric is itself a function of the aggregation scale. CAMDA exceeded the regional mean consistently but modestly, with the advantage largest in distal upstream bins and indistinguishable from zero adjacent to the TSS. β-Entropy is a strictly monotone function of the folded measure 1 − 2|β − 0.5|; at the 100 bp scale, the mean of per-CpG entropy tracked the folding transform of regional mean methylation to within 0.002 in every bin, while at the whole-promoter scale, the two separated by 0.041. Within CpG islands, the regional mean weakened (ρ = −0.246) while CAMDA did not (−0.494). Conclusions: In this single-donor dataset, analytical design affected the estimated coupling more than the choice of summary metric. The observed range is dataset-specific and should not be interpreted as a transferable numerical estimate. Rather, these results show that evaluating plausible analytical configurations can provide important context when comparing promoter methylation summary metrics.

Genes doi: 10.3390/genes17091032

Authors: Ahmed M. Basudan Yazeed Alshuweishi Hamood AlSudais Mohammad A. Alfhili

Background/Objectives: Alternative splicing (AS) contributes substantially to transcriptomic diversity and has emerged as an important regulator of cancer progression. However, the genome-wide characterization of AS events specific to estrogen receptor (ER)-positive breast cancer remains limited. This study aims to comprehensively profile AS in ER-positive breast cancer and identify a prognostic AS signature associated with patient outcome. Methods: Clinical and splicing data (Percent Spliced In values) were obtained from The Cancer Genome Atlas (TCGA) for 737 ER-positive samples. Prognostic AS events were identified using Cox regression analysis. The Least Absolute Shrinkage Selection Operator (LASSO) model was used to construct an AS-based prognostic signature, and a standardized risk score was calculated for each sample. The signature was then evaluated by Kaplan–Meier (KM) analysis and receiver operating characteristic (ROC) curves, in addition to other methods to validate model performance. Furthermore, transcript-level annotation and RNA expression correlation were performed to evaluate biological relevance. Results: Profiling identified 6276 AS events across 4457 genes, with exon skipping (ES) representing the most prevalent class (34.4%). Model analysis established a novel five-event AS prognostic signature (comprising DNAJC14, BAZ2B, PCDHAC1, PCDHA7, and DAPL1). The signature significantly stratified patients into high-risk and low-risk groups for both disease-free survival (DFS; p < 0.001) and overall survival (OS; p < 0.001). HER2-specific analysis demonstrated more consistent performance in HER2-negative patients for both DFS (p < 0.001) and OS (p = 0.018). The model achieved area under the curve (AUC) of 0.804 for 60-month follow-up supporting long-term prognostic performance. Additionally, the signature demonstrated stable and reliable discrimination with a concordance index (C-index) of approximately 0.73 across multiple validation methods. Conclusions: The study identified AS signature with promising prognostic value in ER-positive breast cancer. This highlights the potential of splicing-based models to refine risk stratification beyond conventional gene expression analysis.

Genes doi: 10.3390/genes17091031

Authors: Chendong Jiang Zhan Sun Zhanyan Gao Jie Wang Jun Liang Yang Feng

Background/Objectives: Epidemiological studies link autoimmune diseases (AIDs) to follicular lymphoma (FL) risk, but their shared genetic architecture and causal mechanisms remain unclear. Methods: A two-sample Mendelian randomization (MR) analysis was employed to assess causal relationships between 15 AIDs and FL. Pleiotropic loci were identified through the Pleiotropy Analysis under Composite Null (PLACO). Bayesian colocalization analysis, functional mapping, and Multi-marker Analysis of GenoMic Annotation were applied to fine-map shared genetic variants and identify their target genes. Summary data-based MR was used with multitissue expression quantitative trait locus data to infer causal effects of gene expression. HyPrColoc analysis was applied to decipher shared genetic regulation of immune cell phenotypes. Results: MR revealed that rheumatoid arthritis increased FL risk (ORIVW = 1.55, nominal p = 7.16 × 10−5, FDR-corrected p = 1.07 × 10−3), whereas composite autoimmune disease reduced FL risk (ORIVW = 0.70, nominal p = 4.61 × 10−5, FDR-corrected p = 6.92 × 10−4). Hypothyroidism showed only a nominally suggestive protective trend (ORIVW = 0.88, nominal p = 0.015), which did not survive Benjamini–Hochberg multiple-testing correction (FDR-corrected p = 0.075). Fifty-five pleiotropic loci shared between FL and AIDs were identified, among which key loci such as 1p36.32, 6p21.32, 17p13.1, and 11q23.3 exhibited strong colocalization evidence. Core pleiotropic genes (e.g., TNFRSF14, MMEL1, CXCR5, and RNASET2) were prioritized, which implicated pathways related to MHC class II antigen presentation, interferon signaling, and T cell activation. HyPrColoc analysis demonstrated that these loci colocalized with the expression of immune receptors, including BAFF-R on B cells and HVEM (TNFRSF14) on naïve CD8+ T cells. Conclusions: Our study identifies divergent causal effects of selected AIDs on FL risk and demonstrates localized pleiotropy at key loci, providing novel insights into shared immunogenetic mechanisms.

Genes doi: 10.3390/genes17091030

Authors: Fuxiang Zhao Tao Yang Xuwen Wang Gang Wang Jinxin Qiao Xianhui Kong Li Liu Wanli Han Yu Yu

The height of the first fruiting branch node (HFFBN) is a core indicator for mechanical harvesting of cotton, and the development of molecular markers for this trait is important for accelerating the breeding process. In this study, using bulked segregant analysis coupled with whole-genome sequencing (BSA-seq), one quantitative trait locus (QTL) associated with the HFFBN was mapped; a molecular marker, qFBH7, associated with the HFFBN of cotton was developed; and its application value was systematically evaluated. A total of 20 lines with extreme phenotypes were selected from the recombinant inbred lines constructed using upland cotton Z3-146 and Z3-147 as parental lines. The screened lines with extreme phenotypes were used to construct the extreme high-HFFBN pool and the extreme low-HFFBN pool, which were subsequently used for BSA-seq. Using the upland cotton genome as a reference, relevant QTLs were mapped by BSA-seq. One relevant candidate region was identified, with a total length of 2.25 Mb. The validation experiments revealed that the genotyping results of the KASP_FBH7_03 molecular marker in the parental lines Z3-146 and Z3-147 were completely consistent with the BSA-seq data: Z3-146 had the TT genotype, and Z3-147 had the CC genotype. Among the 66 samples from the natural population, there was a significant difference (p < 0.05) in the HFFBN between the CC and TT genotypes, and the mean HFFBN of the TT genotype was greater than that of the CC genotype. In summary, the KASP_FBH7_03 molecular marker can be effectively used for selective breeding for the HFFBN of cotton, and the TT genotype has a positive regulatory effect on the HFFBN. This study not only provides resources for breeding cotton varieties suited to mechanical harvesting but also offers a robust tool for molecular marker-assisted selection.

Genes doi: 10.3390/genes17091029

Authors: Hongmei Zhang Shanshan Yang Ming Yi Qiuyue Guan Dan Ding Xiaoqian Yu Yin Liu Dan Deng Yuxi Feng Zhiguang Su

Background/Objectives: Hepatocyte proliferation during liver regeneration requires precise transcriptional coordination of metabolic reprogramming, but the key regulators governing this process remain largely unknown. Methods: Hepatocyte-specific retinoic acid receptor-related orphan receptor α (RORα) knockout (RORα-LKO) mice were generated and subjected to two-thirds partial hepatectomy (PHx). Liver regeneration was assessed by liver-to-body weight ratio, histology, and proliferation markers (PCNA, Ki67, cyclin D1). Metabolic changes were evaluated by untargeted metabolomics, Seahorse extracellular flux analysis, and glycolytic enzyme activity assays. The molecular mechanism was investigated through RNA-seq analysis, qPCR, Western blotting, dual-luciferase reporter assays, CUT&Tag-qPCR, and pharmacological inhibition. Results: RORα expression was transiently upregulated during the early phase and declined at the peak of hepatocyte proliferation. RORα-LKO mice exhibited accelerated liver recovery and increased hepatocyte proliferation following a partial hepatectomy, without enhanced inflammation or fatty acid oxidation. Mechanistically, RORα directly binds to the promoter of Me1 to repress its transcription. Loss of RORα upregulates ME1, enhances glycolysis, and increases ATP production. Pharmacological inhibition of ME1 reversed these effects. Conclusions: The RORα–ME1 axis links transcriptional repression to metabolic reprogramming and may represent a therapeutic target for liver regeneration.

Genes doi: 10.3390/genes17091028

Authors: Lucija Bavčević Anita Racetin Petar Todorović Sandra Kostić Sandra Zekić Tomaš Katarina Vukojević Nela Kelam

Background/Objectives: Congenital anomalies of the kidney and urinary tract (CAKUT) are a leading cause of pediatric kidney disease. Epithelial–mesenchymal transition (EMT), governed by SNAI1 and TGF-β, and a vascular–mesenchymal program marked by PECAM1 and VIM are central to nephrogenesis, but whether these programs are transcriptionally activated in human CAKUT is unknown. We assessed their expression and spatial organization in human fetal kidneys. Methods: We reanalyzed public transcriptomic datasets for six transcripts (SNAI1, TGFB1–3, PECAM1, VIM) and performed quantitative double immunofluorescence for four gene products (SNAIL, TGF-β1, CD31, vimentin) on formalin-fixed human fetal kidneys (20 controls, 19 CAKUT), with colocalization quantified by Pearson’s coefficient. Results: No statistically significant difference in transcript or protein abundance was detected between control and CAKUT kidneys, in either the cortex or the medulla, and abundance did not change across developmental phases. In contrast, spatial colocalization of SNAIL–TGF-β and of CD31–vimentin was increased in CAKUT kidneys. Conclusions: These findings may suggest that, in human fetal CAKUT, EMT and vascular–mesenchymal programs are not quantitatively upregulated but instead show altered spatial organization of otherwise unchanged gene products. As colocalization reflects spatial proximity rather than molecular interaction, these observations are correlative and warrant functional validation.

Genes doi: 10.3390/genes17091026

Authors: Himanshu Goel Tracy Dudding-Byth Benjamin Kamien

Despite substantial advances in genomic testing, many individuals with neurodevelopmental disorders remain without a molecular diagnosis, while others receive a genetic diagnosis that does not fully explain phenotypic variability, developmental trajectory or tissue-specific consequences. Artificial intelligence (AI)-assisted methods are increasingly used for phenotyping, variant prioritisation, splice prediction, protein modelling, DNA methylation episignature classification and multi-omic analysis. However, these approaches differ substantially in evidentiary status and are often applied as separate prediction tasks rather than as components of an explicit mechanistic model. In this targeted narrative review, focused primarily on rare and genetically enriched neurodevelopmental disorders, we examine how AI-assisted methods may contribute to systems-level interpretation while remaining anchored to established molecular diagnosis and variant-classification frameworks. We propose a hypothesis-generating load-capacity framework comprising regulatory load, network capacity, developmental buffering and regulatory network instability. These are treated as operationalisable but currently unvalidated constructs. Regulatory instability is distinguished from stable disease-associated dysregulation, and threshold-like behaviour is presented as an empirical possibility rather than an assumed property of neurodevelopmental disease. We formulate five falsifiable predictions, consider how genomic, transcriptomic, epigenomic, single-cell, spatial, imaging, neurophysiological and longitudinal phenotypic evidence can provide complementary mechanistic constraints, and outline an auditable workflow following nondiagnostic genomic testing. We distinguish clinically implemented approaches from translational, emerging and conceptual applications, and emphasise calibration, evidence traceability, domain validity, prospective validation and appropriate abstention. Finally, we describe the Instability Twin as a prospective architecture composed of independently testable patient-specific sub-models rather than an existing clinical platform. The central proposition is that systems neurogenomics should be evaluated by whether mechanistically constrained integration provides reproducible information beyond established gene-level and simpler multimodal approaches.

Genes doi: 10.3390/genes17091027

Authors: Kui Yan Shuai He Jian Peng Jianghong Qian Yunjie Gu Hongying Guo Suyuan Zhang Yulin Wei Ruiqi Wang Yu Zhou Hanbo Yang

Chalcone synthase (CHS) is a key enzyme in flavonoid biosynthesis, and its activity strongly influences the efficiency of flavonoid production in plants. By controlling the biosynthesis of secondary metabolites, CHS contributes to plant adaptation to diverse environmental stresses. Here, we identified CHS members across the Phoebe zhennan genome and systematically examined their gene structures, phylogenetic relationships, and potential roles in golden-thread wood color formation and drought response. Genome-wide screening resolved 11 putatively functional PzCHSs, which were unevenly distributed across six chromosomes. Physicochemical analyses indicated that most PzCHS proteins were hydrophilic. Phylogenetic reconstruction divided the PzCHS family into three groups, whose members generally shared similar gene structures. One tandem duplication event and five segmental duplication events were detected. Synteny analysis revealed extensive collinearity between the CHS families of P. zhennan, Phoebe bournei and Cinnamomum camphora, consistent with their close evolutionary relationships. Promoter regions of PzCHS genes were enriched for phytohormone-responsive and growth-related cis-elements, suggesting roles in development and hormonal regulation. Transcriptome profiling showed that PzCHS6 was upregulated in the transition zone of wood and under drought stress, suggesting that this gene may be associated with both golden-thread wood color formation and drought response. These results provide a framework for functional dissection of the CHS members and offer candidate genes for golden-thread wood color improvement and drought response breeding.

Genes doi: 10.3390/genes17091025

Authors: Jin Yan Ruixia Ma Yaguang Xi

Colorectal cancer (CRC) remains a major cause of cancer morbidity and mortality. Immune checkpoint inhibitors (ICIs) have transformed the treatment of microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) CRC, yet most CRCs are microsatellite-stable/mismatch repair-proficient (MSS/pMMR) and remain poorly responsive to immunotherapy. MicroRNAs (miRNAs) are well positioned to influence this biology because individual miRNAs can coordinate multiple tumor-intrinsic and microenvironmental programs that shape antitumor immunity. Rather than cataloging miRNAs one by one, this review organizes the evidence around the major barriers that sustain an immune-cold CRC microenvironment: altered checkpoint and costimulatory signaling, defective antigen presentation, impaired effector T-cell access and function, suppressive myeloid and stromal compartments, and extracellular vesicle (EV)-mediated intercellular communication. We also critically assess tissue and circulating miRNA signatures as candidate biomarkers of ICI response and discuss therapeutic approaches based on miRNA mimics, inhibitors, and targeted delivery platforms. The available evidence supports a biologically compelling role for miRNA networks in CRC immune regulation, but clinical translation remains limited by context dependence, delivery, off-target effects, and the lack of treatment-linked validation in CRC cohorts.