Genes

18 pages, 6623 KB

Open AccessArticle

Mitochondrial and Nuclear DNA Analyses of Rhipicephalus microplus from Mizoram, Northeast India: Insights into Genetic Diversity and Endosymbiont

by Khawlhring Lalawmpuii, Siju Susan Jacob, Thingujam Chaa Tolenkhomba, Parthasarathi Behera, Joy Lalmuanpuia, Hmar Tlawmte Lalremsanga, Khawlhring Lalrintluanga, Chhakchhuak Lalchhandama, Lal Biakzuala and Hmar Lalrinkima

Genes 2025, 16(10), 1216; https://doi.org/10.3390/genes16101216 (registering DOI) - 15 Oct 2025

Abstract

Background/Objectives: In this study, we conducted molecular identification of R.microplus and explored the genetic diversity of R. microplus for the first time in Mizoram, a Northeastern Hill (NEH) state of India bordering Myanmar. Methods: To assess genetic variation and evolutionary relationships, [...] Read more.

Background/Objectives: In this study, we conducted molecular identification of R.microplus and explored the genetic diversity of R. microplus for the first time in Mizoram, a Northeastern Hill (NEH) state of India bordering Myanmar. Methods: To assess genetic variation and evolutionary relationships, we employed phylogenetic analyses, genetic divergence metrics, and haplotype network construction based on mitochondrial (COX1 and 16S rDNA) and nuclear (ITS-2 and 18S rDNA) markers. Additionally, multivariate Principal Coordinate Analysis (PCoA) was used to visualize genetic differentiation among R. microplus populations. Results: Our analyses indicated that populations of R. microplus sensu lato from India, Bangladesh, and Pakistan form a closely related matrilineal lineage distinct from R. microplus sensu stricto, clustering within clade C of the COX1-based phylogeny. Globally, 24 COX1 haplotypes were recovered, with 1 haplotype identified in India. The Mizoram population exhibited a single 16S rDNA haplotype; however, intraspecific divergence was evident across India, with seven matrilineal haplotypes detected and nineteen globally. Further, five haplotypes were identified within R. microplus using the ITS-2 marker, while five haplotypes were observed within the Rhipicephalus genus using the 18S rDNA marker. Moreover, this study revealed the presence of Coxiella-like endosymbionts in 95% of the tick specimens analyzed. Conclusions: This study fills a critical knowledge gap by providing the first molecular documentation of tick diversity in Mizoram, a strategic region along the Indo–Myanmar border, and offers novel insights into the phylogeography and symbiotic associations of R. microplus and related tick taxa. Full article

(This article belongs to the Special Issue Genetics and Epidemiology of Parasites)

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17 pages, 15704 KB

Open AccessArticle

The Genome Survey Analysis of Female and Male Sepiella japonica

by Yuting Ren, Yinquan Qu, Fenglin Wang, Tianxiang Gao and Xiumei Zhang

Genes 2025, 16(10), 1215; https://doi.org/10.3390/genes16101215 - 15 Oct 2025

Abstract

Background/Objectives: Sepiella japonica is a highly adaptable cephalopod with an advanced nervous system and complex reproductive behavior, capable of reproducing two to three generations annually depending on water temperature. However, the absence of a complete genome assembly has limited molecular investigations of its [...] Read more.

Background/Objectives: Sepiella japonica is a highly adaptable cephalopod with an advanced nervous system and complex reproductive behavior, capable of reproducing two to three generations annually depending on water temperature. However, the absence of a complete genome assembly has limited molecular investigations of its unique biological characteristics. This study aimed to perform a genome survey of female and male S. japonica, systematically characterize and compare key genomic characteristics. Methods: Quality-filtered short reads enabled K-mer-based estimation of genome size, heterozygosity, repeat content, and GC content; generation of draft genome assemblies, SSR identification from the draft assemblies, complete mitogenome assemblies and annotations with ML phylogeny based on 13 concatenated PCGs, and PSMC-based demographic inference. Results: The estimated genome sizes were 4317 Mb (female) and 4222 Mb (male), with revised estimates of 4310 Mb and 4215 Mb, respectively. K-mer analysis revealed heterozygosity rates of 0.85% (female) and 0.77% (male) and repeat content of 76.05% (female) and 75.91% (male). The assembled genome sizes were 4197 Mb for females (N50: 508 bp) and 4206 Mb for males (N50: 511 bp); the GC content was 34.15% for both genomes. Deduplicated data showed GC content of 35.16% (female) and 35.27% (male). Microsatellite analysis revealed that mononucleotide repeats were the most abundant simple sequence repeat motif. The mitochondrial genome sequences measured 16,729 bp for the female genome and 16,725 bp for the male genome. Conclusions: This study provides fundamental data for subsequent high-quality whole-genome assembly and comparative analysis of female and male genomes. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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23 pages, 2734 KB

Open AccessArticle

Epigenetic Modulation and Neuroprotective Effects of Neurofabine-C in a Transgenic Model of Alzheimer’s Disease

by Ivan Carrera, Vinogran Naidoo, Lola Corzo, Olaia Martínez-Iglesias and Ramón Cacabelos

Genes 2025, 16(10), 1214; https://doi.org/10.3390/genes16101214 - 15 Oct 2025

Abstract

Background: Currently, there are limited therapeutic or preventative strategies for neurodegenerative disorders due to the challenges in alleviating the progressive neuronal loss and neuroinflammation which are the primary characteristics of these diseases, ultimately leading to cell death and functional impairment. Cocoa-derived flavanols [...] Read more.

Background: Currently, there are limited therapeutic or preventative strategies for neurodegenerative disorders due to the challenges in alleviating the progressive neuronal loss and neuroinflammation which are the primary characteristics of these diseases, ultimately leading to cell death and functional impairment. Cocoa-derived flavanols (Theobroma cacao) have been studied as potential bioactive compounds to modify and reverse various inflammation-associated diseases because of their remarkable antioxidant properties and capacity to modulate metabolic imbalance and reactive inflammatory responses. The faba bean (Vicia faba) extract obtained through nondenaturing biotechnological processes is a potent dopamine (DA) enhancer that has shown promising results as a neuroprotective agent against degeneration. Objective: This study will examine the synergistic effects of Neurofabine-C, a hybrid compound derived from cocoa and faba bean extracts, on various brain biomarkers in mice related to inflammatory, metabolic, and neurodegenerative processes. Methods: A triple-transgenic mouse model of neurodegeneration was treated with Neurofabine-C, and biomolecular data were obtained by performing biochemical and immunohistochemical analysis. Results: Neurofabine-C prevented neuronal degeneration (NeuN), mitigated the neuro-inflammatory processes triggered (decreased expression of reactive astrocytes (GFAP)), and induced an increase in neurogenesis in the treated cortical mice brain (PAX6). Epigenetic analysis revealed significant chromatin remodeling in the hippocampus. Neuroprotective genes, including FOXO3, ATM, and TRP73, were upregulated, whereas the expression of HIF1α and APOE decreased. In parallel, DNMT3A expression increased 20-fold, HDAC3 decreased by 60%, and global 5-methylcytosine levels increased four-fold. These coordinated changes suggest that Neurofabine-C promotes neuroprotective programs through enhanced DNA methylation and reduced histone deacetylation. Conclusions: The findings indicate that Neurofabine-C exhibits multiple neuroprotective mechanisms, making it a potent bioproduct for mitigating neuroinflammatory processes associated with neurodegenerative disorders. Full article

(This article belongs to the Section Neurogenomics)

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20 pages, 5947 KB

Open AccessArticle

Integrative Single-Cell and Bulk Transcriptomic Analysis Identifies Macrophage-Related Gene Signatures Predictive of Hepatocellular Carcinoma in Cirrhosis

by Zhongyuan Zhang, Chuisheng Zeng, Xuetong Yong, Wenping Zhou, Yongfang Xie and Jianzhong Shu

Genes 2025, 16(10), 1213; https://doi.org/10.3390/genes16101213 - 15 Oct 2025

Abstract

Background/Objectives: Liver cirrhosis is a major global health challenge and a key risk factor for hepatocellular carcinoma (HCC), a malignancy with high mortality due to late diagnosis. This study aimed to integrate single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) [...] Read more.

Background/Objectives: Liver cirrhosis is a major global health challenge and a key risk factor for hepatocellular carcinoma (HCC), a malignancy with high mortality due to late diagnosis. This study aimed to integrate single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) data, using single-cell data to identify macrophage-associated transcriptomic changes during the progression from cirrhosis to HCC, and using bulk data to validate these findings in independent cohorts, while developing predictive models for early risk assessment. Methods: We integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing datasets derived from liver tissues of cirrhosis and HCC patients. Single-cell data were used to identify macrophage subtypes and their dynamic transcriptional changes, while bulk data provided validation in independent cohorts. Gene expression and network analyses were performed, and candidate genes were used to construct diagnostic models with Lasso regression, Random Forest, and Extreme Gradient Boosting (XGBoost). Model performance was evaluated using receiver operating characteristic curves. Results: We identified eleven macrophage-associated genes, among which KLK11, MARCO, CFP, KRT19, GAS1, SOD3, and CYP2C8 were downregulated in HCC, indicating loss of tumor-suppressive and pro-apoptotic functions, while TOP2A, CENPF, MKI67, and NUPR1 were upregulated, reflecting enhanced cell cycle progression, proliferation, and M2 polarization. These are all associated with the progression from liver cirrhosis to HCC. Based on these findings, we established predictive models using Lasso, Random Forest, and XGBoost, which stratified cirrhotic patients into high- and low-risk groups according to cutoff values using liver tissue transcriptomic data. All three models demonstrated high diagnostic performance. Conclusions: This study highlights the critical role of macrophage-associated transcriptomic remodeling in liver disease progression. The machine learning–based predictive models offer a promising approach for early diagnosis and clinical decision-making in patients with cirrhosis. Full article

(This article belongs to the Section Bioinformatics)

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16 pages, 1868 KB

Open AccessArticle

Cystoid Macular Lesions in Inherited Retinal Diseases: Prevalence, Characteristics, and Genetic Associations in a Hungarian Cohort

by Barbara Asboth, Alessandra Sanrocco, Barbara Besztercei, Balazs Lesch, Agnes Takacs, Rita Vamos, Balazs Varsanyi, Andras Vegh, Krisztina Knezy, Viktoria Szabo, Zoltan Zsolt Nagy and Ditta Zobor

Genes 2025, 16(10), 1212; https://doi.org/10.3390/genes16101212 - 14 Oct 2025

Abstract

Background/Objectives: Cystoid macular lesion (CML) is a treatable cause of central vision loss in inherited retinal diseases (IRDs). We aimed to determine the frequency of CML in a large Hungarian IRD cohort and examine associations with causative genes. Methods: This longitudinal, [...] Read more.

Background/Objectives: Cystoid macular lesion (CML) is a treatable cause of central vision loss in inherited retinal diseases (IRDs). We aimed to determine the frequency of CML in a large Hungarian IRD cohort and examine associations with causative genes. Methods: This longitudinal, retrospective, monocentric study included patients with genetically confirmed IRD identified from our database. Targeted next-generation sequencing (351-gene panel) and comprehensive ophthalmic evaluation were performed, including best-corrected visual acuity (BCVA) and spectral domain optical coherence tomography (SD-OCT). CML was defined as intraretinal hyporeflective spaces with well-defined borders visible on at least two B-scans within the SD-OCT macular volume and was categorized as cystoid macular edema (CME) or non-CME. Results: We enrolled 430 patients with genetically confirmed IRDs. CML was detected in 93 eyes of 57 patients. Mean age at OCT was 36.6 ± 18.7 years (range, 3–76); 32 were male (56.1%). Inheritance patterns were autosomal recessive in 24 (42.1%), X-linked in 19 (33.3%), and autosomal dominant in 14 (24.6%). Frequently implicated genes were RS1 (12/57), USH2A (7/57), NR2E3 (7/57), PRPF31 (4/57), RPGR (4/57), and RHO (4/57). CME predominated in retinitis pigmentosa (32/57, 56%), with mean BCVA 0.44 ± 0.29 (decimal) and central retinal thickness (CRT) 401 ± 181 µm. Non-CME CML occurred in 25/57 (44%)—notably in X-linked retinoschisis and enhanced S-cone syndrome—with BCVA 0.40 ± 0.23 and CRT 465 ± 258 µm. BCVA did not correlate with CRT (r_S = 0.18). Conclusions: CML occurred in 13.2% of patients within a large Hungarian cohort of genetically confirmed IRDs. Patients with IRD—mainly RP—are at higher risk for CML. Gene therapy is promising for retinal diseases, but CMLs can compromise effectiveness. Reducing and managing CME before gene therapy corroborates retinal stability and the functional state essential for the proper delivery and penetration of corrective genes to the target cells. Full article

(This article belongs to the Special Issue Inherited Retinal Diseases: Genetic Research and Novel Therapeutic Prospects)

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13 pages, 1141 KB

Open AccessArticle

Pedigree-Based Estimation of Y-STR Mutation and Male Differentiation Rates: Application to Historical Remains Identification

by Jasmine R. Connell, Toni White, Thais Zielke, Luke Armstrong, Natasha Mitchell and Lyn R. Griffiths

Genes 2025, 16(10), 1211; https://doi.org/10.3390/genes16101211 - 14 Oct 2025

Abstract

Background/Objectives: High differentiation rates provided by Y-chromosomal short tandem repeats (Y-STRs) are highly advantageous in most forensic and genealogical casework, as they enhance the ability to exclude close or moderately related individuals, refine an individual’s position within a pedigree, and uncover the population [...] Read more.

Background/Objectives: High differentiation rates provided by Y-chromosomal short tandem repeats (Y-STRs) are highly advantageous in most forensic and genealogical casework, as they enhance the ability to exclude close or moderately related individuals, refine an individual’s position within a pedigree, and uncover the population substructure in otherwise homogeneous groups. However, the impact for historical remains identification casework is underexplored. Methods: We present a pedigree analysis of 366 males from 183 pedigrees, separated by 4 to 16 meioses at 27 Y-STR loci, from the Yfiler Plus kit. The differentiation rate for a given degree of separation was defined as the proportion of pairs at that specific number of meioses showing at least one allelic difference, relative to the total number of such pairs. Results: Our pedigree-based locus-specific mutation rates were consistent with published father–son values for 22 of 25 loci, with 3 loci (DYS389II, DYS449, and DYS570) being significantly different (p < 0.05). These results were consistent with previous pedigree-based estimates, and the strong agreement between father–son and pedigree-based mutation rates supports the use of pedigrees as a reliable method for estimating mutation rates. The probability of differentiating male relatives reached 60.1%, which is similar to previous studies using the Yfiler Plus kit. Conclusions: This high male differentiation rate is advantageous for distinguishing unrelated individuals within the same population, reducing false inclusions. However, when comparing distantly related individuals, excessive mutations accumulated over many generations may obscure genuine patrilineal relationships, increasing the risk of false exclusions. Our findings are likely to be highly valuable for future interpretation of Y-STR haplotypes from patrilineal relatives across a wide range of applications, with significant relevance to historical remains identification casework. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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23 pages, 3070 KB

Open AccessArticle

Genetic Interrelationship Among Newly-Bred Mutant Lines of Wheat Using Diagnostic Simple Sequence Repeat Markers and Phenotypic Traits Under Drought

by Athenkosi Makebe, Hussein Shimelis and Jacob Mashilo

Genes 2025, 16(10), 1210; https://doi.org/10.3390/genes16101210 - 14 Oct 2025

Abstract

Background/Objectives: Induced mutagenesis is vital in genetic enhancement and trait discovery, for genetic analysis and breeding of novel crop varieties with desirable product profiles. Understanding the genetic relationships among newly developed mutant genotypes enables targeted selection and genetic recombination. Therefore, the objective of [...] Read more.

Background/Objectives: Induced mutagenesis is vital in genetic enhancement and trait discovery, for genetic analysis and breeding of novel crop varieties with desirable product profiles. Understanding the genetic relationships among newly developed mutant genotypes enables targeted selection and genetic recombination. Therefore, the objective of the current study was to assess the genetic diversity among mutant bread wheat genotypes developed through ethyl methanesulfonate (EMS) mutagenesis using phenotypic traits and diagnostic simple sequence repeat (SSR) markers to identify novel mutants and traits for breeding. Methods: Sixteen advanced (M6) mutant lines, one parental genotype, and three check varieties were genetically profiled using ten diagnostic SSR markers. The genotypes were evaluated for agronomic traits under drought-stressed (DS) and non-stressed (NS) conditions using a 10 × 2 alpha lattice design with two replications. Results: The SSR markers revealed a total of 21 alleles, with an average of 2.10 alleles per locus. An average polymorphic information content (PIC) of 0.51 was computed, revealing moderate informativeness of the genetic markers. Significant (p < 0.05) differences were observed among the test genotypes for key agronomic traits under NS and DS conditions. Grain yield positively and significantly (p < 0.001) correlated with plant height (r = 0.79), number of productive tillers (r = 0.82), root biomass (r = 0.77), shoot biomass (r = 0.74), spike length (r = 0.74), total biomass (r = 0.74), and thousand-seed weight (r = 0.64), under DS conditions. Principal component analysis explained 78.03 and 87.14% genotype variation for assessed agronomic traits under DS and NS conditions, with total biomass, shoot biomass, root biomass, productive tiller, plant height and grain yield as key traits contributing the most variation in the test genotypes. Conclusions: Wheat mutants LMA16, LMA44, and LMA53 were identified as genetically distinct and high yielders under drought stress conditions and recommended for production in rain-fed environments. The selected mutants are a valuable source of genes for wheat improvement programs. Full article

(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)

10 pages, 1431 KB

Open AccessArticle

The Role of miR-326-3p in Regulating Differentiation and Thermogenesis Genes in Goat Brown Adipocytes

by Yuehua Zhu, Langda Suo, Tingting Jiang, Xinyi Jiang, Yanyan Xia and Linjie Wang

Genes 2025, 16(10), 1209; https://doi.org/10.3390/genes16101209 (registering DOI) - 14 Oct 2025

Abstract

Background: Brown adipose tissue (BAT) is indispensable for producing heat and contributes critically to the survival of neonatal mammals. MicroRNAs (miRNAs) are small noncoding RNAs that serve as key post-transcriptional regulators, playing a crucial role in regulating BAT development and thermogenesis. However, [...] Read more.

Background: Brown adipose tissue (BAT) is indispensable for producing heat and contributes critically to the survival of neonatal mammals. MicroRNAs (miRNAs) are small noncoding RNAs that serve as key post-transcriptional regulators, playing a crucial role in regulating BAT development and thermogenesis. However, the role of miR-326-3p in goat brown adipocytes remains largely unclear. Methods: Primary brown adipocytes were isolated from goat perirenal adipose tissue and subjected to gain and loss-of-function assays using miR-326-3p mimics and inhibitors. Lipid accumulation, thermogenic-related genes, and mitochondrial gene expression were quantified by Oil Red O staining and qRT-PCR. Target prediction and dual-luciferase reporter assays were performed to validate direct interaction between miR-326-3p and FGF11. Results: Expression profiling demonstrated that miR-326-3p is more enriched in brown adipose tissue (BAT) than in white adipose tissue (WAT), and the expression level gradually decreases with adipocyte differentiation. miR-326-3p overexpression significantly inhibited lipid droplet accumulation and the expression of genes associated with differentiation, thermogenesis, and mitochondria, including PPARγ, FABP4, UCP1, and PGC1α, whereas inhibition produced the opposite effect. Bioinformatic prediction and dual-luciferase reporter assays further identified fibroblast growth factor 11 (FGF11) as a direct target of miR-326-3p. Conclusions: These findings reveal that miR-326-3p negatively regulates the differentiation and expression of thermogenic-related genes of goat brown adipocytes, uncovering a novel miR-326-3p-FGF11 regulatory axis. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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16 pages, 6026 KB

Open AccessArticle

Comprehensive Identification of miRNAs and circRNAs in the Regulation of Intramuscular and Subcutaneous Fat Deposition in Meat Ducks

by Zhixiu Wang, Tingting Zhou, Wenshuang Liang, Qianqian Song, Yong Jiang, Hao Bai, Guohong Chen and Guobin Chang

Genes 2025, 16(10), 1208; https://doi.org/10.3390/genes16101208 - 14 Oct 2025

Abstract

Fat deposition is an important factor that affects meat production and its quality in livestock animals, including poultry. Non−coding RNAs (ncRNAs) play an important role in duck fat deposition. This study aims to systematically identify key regulatory molecules involved in fat deposition in [...] Read more.

Fat deposition is an important factor that affects meat production and its quality in livestock animals, including poultry. Non−coding RNAs (ncRNAs) play an important role in duck fat deposition. This study aims to systematically identify key regulatory molecules involved in fat deposition in 8−day−old Cherry Valley ducks through transcriptomic sequencing across four sample groups: intramuscular pre−adipocytes (IMP−0), intramuscular adipocytes after 4 days of induction (IMP−4), subcutaneous pre−adipocytes (SCP−0), and subcutaneous adipocytes after 4 days of induction (SCP−4). Differential expression analysis preliminarily identified several circRNAs and miRNAs differentially expressed during adipocyte differentiation, including novel_circ_000012, novel_circ_000037, novel_circ_000089, as well as miR−501−y, miR−378−y, and miR−3968−y. Further co−expression network analysis revealed that the network constructed during intramuscular adipocyte differentiation comprised 17 nodes and 39 edges, while the network constructed during subcutaneous adipocyte differentiation was larger, containing 39 nodes and 50 edges. Based on connectivity screening, we identified several key miRNAs, such as novel−m0630−5p, novel−m0485−5p, novel−m0672−5p, miR−5126−y, and miR−1408−y. Notably, this study uncovered several novel ceRNA regulatory axes during intramuscular and subcutaneous adipocyte differentiation, including novel_circ_001327/miR−141−y/Zdhhc1, novel_circ_002268/miR−2478−y/ACLY, and novel_circ_002268/miR−3963−x/ACLY. These findings provide crucial molecular insights into the specific deposition mechanisms of intramuscular versus subcutaneous fat in meat ducks, offering valuable targets for molecular breeding programs aimed at improving meat quality. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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12 pages, 1604 KB

Open AccessReview

by Sopio Gverdtsiteli, Trine Bjørg Hammer, Xenia Hermann, Noemi Becser Andersen, David Ros-Pardo, Iñigo Marcos-Alcalde, Paulino Gómez-Puertas, Alan Henry Brook, Asli Silahtaroglu and Zeynep Tümer

Genes 2025, 16(10), 1207; https://doi.org/10.3390/genes16101207 - 14 Oct 2025

Abstract

ROGDI-related neurodevelopmental and dental disorder (ROGDI-RD), also known as Kohlschütter–Tönz syndrome (KTZS, MIM #226750), is a rare condition characterized by developmental abnormalities affecting both the central nervous system (CNS) and the dentition. These phenotypes highlight the role of complex gene–environment [...] Read more.

ROGDI-related neurodevelopmental and dental disorder (ROGDI-RD), also known as Kohlschütter–Tönz syndrome (KTZS, MIM #226750), is a rare condition characterized by developmental abnormalities affecting both the central nervous system (CNS) and the dentition. These phenotypes highlight the role of complex gene–environment interactions and developmental networks shared by the nervous and stomatognathic systems, both of which originate mostly from neural crest-derived cells. In this review, we analyze clinical and genetic data from 54 previously reported ROGDI-RD patients to better define the phenotypic spectrum of the disorder. Most of the reported cases harbor protein-truncating variants. Here, we also present the first description of a patient carrying a missense variant in ROGDI atypical leucine zipper gene, ROGDI in trans to a frameshift variant. This individual presented with tooth agenesis—a dental anomaly not previously associated with the syndrome—alongside classic neurological and dental enamel features, suggesting that the phenotypic spectrum of ROGDI-RD may be broader than currently recognized. Using a complexity and network science framework, we discuss how dysregulation in multilevel, interacting developmental systems may explain the pleiotropic features of ROGDI-RD. Our findings underscore the importance of early, interdisciplinary clinical evaluation in patients with neurodevelopmental symptoms and enamel defects. As enamel phenotypes such as amelogenesis imperfecta are heterogeneous, comprehensive genomic analyses and collaborative clinical approaches are essential for accurate diagnosis and improved care. Full article

(This article belongs to the Special Issue The CranioFacial Biology Group at the University of Adelaide Collection: Genetic, Epigenetic and Environmental Factors in Complex Adaptive Systems, Multilayer Complex Interactive Networks, and Multiple Models During Oral Development)

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14 pages, 672 KB

Open AccessArticle

Rubinstein–Taybi Syndrome: A Comprehensive Analysis of a Polish Cohort with Most Cases Due to Novel CREBBP and EP300 Variants

by Agata Cieślikowska, Agnieszka Madej-Pilarczyk, Piotr Iwanowski, Katarzyna Iwanicka-Pronicka, Dorota Wicher, Maria Jędrzejowska, Dorota Jurkiewicz, Marzena Gawlik, Dorota Piekutowska-Abramczuk, Paulina Halat-Wolska, Jagoda Błaszkiewicz, Izabela Mendrek, Krystyna Chrzanowska, Marlena Młynek, Piotr Stawiński, Joanna Kosińska, Małgorzata Krajewska-Walasek and Elżbieta Ciara

Genes 2025, 16(10), 1206; https://doi.org/10.3390/genes16101206 - 14 Oct 2025

Abstract

Background: Rubinstein–Taybi syndrome (RSTS) is characterized by intellectual disability, short stature, distinctive facial dysmorphism, broad thumbs/halluces, hearing loss, congenital heart or renal defects, and cryptorchidism in males. Pathogenic variants in CREBBP (~90% of cases) or EP300 (~10%) underlie the disorder, with ~88% single [...] Read more.

Background: Rubinstein–Taybi syndrome (RSTS) is characterized by intellectual disability, short stature, distinctive facial dysmorphism, broad thumbs/halluces, hearing loss, congenital heart or renal defects, and cryptorchidism in males. Pathogenic variants in CREBBP (~90% of cases) or EP300 (~10%) underlie the disorder, with ~88% single nucleotide variants (SNVs) and ~12% copy number variants (CNVs) in CREBBP. Materials and Methods: We investigated 17 patients clinically diagnosed with RSTS at a tertiary hospital in Poland. Genetic confirmation was achieved by next-generation sequencing, multiplex ligation-dependent probe amplification (MLPA), array comparative genomic hybridization (aCGH), or Sanger sequencing. Results: Pathogenic variants were identified in CREBBP (13/17, 76%) and EP300 (4/17, 24%). Variant types included frameshift indels (6/17, 35%), missense (4/17, 24%), nonsense (3/17, 18%), splice-site (2/17, 12%), and gross deletions (2/17, 12%). Notably, 13/17 (76%) were novel: ten in CREBBP (c.−49_12del, c.289C>T, c.1093_1096del, c.1094A>G, c.3178A>T, c.3401A>T, c.(3836+1_3837−1)_(4394+1_4395−1)del, c.4133+2T>G, c.4963dup, c.5028_5029dup) and three in EP300 (c.1942C>T, c.3044_3045del, c.4713_4722del). Among the novel CREBBP variants, eight occurred de novo and two had unknown inheritance. Two novel EP300 variants occurred de novo and one was of unknown origin. Conclusions: This first Polish RSTS cohort demonstrates a considerable proportion of gross deletions (12% overall; 15% in CREBBP) and an unexpectedly high rate of novel variants (76%), suggesting possible population-specific differences. These findings underscore the genetic heterogeneity of RSTS and highlight the importance of comprehensive molecular diagnostics and studies in underrepresented populations. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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16 pages, 1338 KB

Open AccessArticle

Newly Identified TPI Deficiency Treatments Function for Novel Disease-Causing Allele, TPI1^R5G

by Joseph R. Figura, Presley Roberts, Riley Sawka, Maci Chambers, Marcelo Claudio, Laura L. Vollmer, Andreas Vogt, Gregg E. Homanics, Eduard van Beers, Mylene Donge, Emmanuel Scalais, Arthur Sorlin, Ariana J. Jou, Andrew P. VanDemark and Michael J. Palladino

Genes 2025, 16(10), 1205; https://doi.org/10.3390/genes16101205 - 14 Oct 2025

Abstract

Background/Objectives: Triosephosphate Isomerase (TPI) is a glycolytic enzyme known to be associated with TPI deficiency, a severe form of childhood-onset glycolytic enzymopathy associated with hemolytic anemia, neuromuscular impairment and early death. Most often the disease results from the common TPI1^E105D mutation, which [...] Read more.

Background/Objectives: Triosephosphate Isomerase (TPI) is a glycolytic enzyme known to be associated with TPI deficiency, a severe form of childhood-onset glycolytic enzymopathy associated with hemolytic anemia, neuromuscular impairment and early death. Most often the disease results from the common TPI1^E105D mutation, which can be either homozygous or compound heterozygous with another allele. Methods: We purified TPI^R5G protein, studied mutant protein biochemistry, established and characterized TPI^R5G/f.s.patient cells, and investigated newly identified compounds for their efficacy in vitro using Western blot and TPI activity assays. Results: We identified novel TPI1 alleles that result in TPI Deficiency with an atypical presentation lacking anemia and with more slowly developing neurologic and locomotor impairment. The patient was found to be compound heterozygous with a missense mutation resulting in an R5G amino acid substitution and a frameshift mutation that is a predicted null allele. To better understand disease pathogenesis in this patient, we expressed and purified the TPI^R5G human protein and studied it biochemically in addition to studying TPI^R5G/f.s.patient cells. We discovered that purified TPI^R5G protein has wildtype activity with modestly increased dimer stability. We also discovered that steady-state TPI protein levels were markedly reduced, suggesting that the instability of the mutant protein underlies disease pathogenesis. We tested compounds recently identified in a screen for novel TPI Df therapies for their efficacy in TPI^R5G/f.s.patient cells. All three compounds significantly increased TPI protein levels in patient cells. As expected, since the mutant protein retains essentially wild type activity, the increase in TPI protein levels also resulted in a significant increase in TPI activity. Conclusions: These results establish TPI^R5G as a TPI Df allele, demonstrate that reduced stability of the mutant protein underlies pathogenesis akin to other disease-causing alleles, and suggest that recently discovered developing therapies will likely function broadly and should be developed as potential TPI Df therapies. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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15 pages, 1167 KB

Open AccessArticle

Genome-Wide Association Study of Morphological Defects in Nellore Cattle Using a Binary Trait Framework

by Milena A. F. Campos, Hinayah Rojas de Oliveira, Henrique A. Mulim, Eduarda da Silva Oliveira, Pablo Augusto de Souza Fonseca, Gregorio M. F. de Camargo and Raphael Bermal Costa

Genes 2025, 16(10), 1204; https://doi.org/10.3390/genes16101204 - 14 Oct 2025

Abstract

Background/Objectives: Morphological defects such as limb malformations, cranial asymmetries, loin deviations, jaw misalignments, and navel irregularities are associated with early culling and reduced productivity in beef cattle. In Bos taurus indicus such as Nellore, the genetic basis of these traits remains poorly characterized. [...] Read more.

Background/Objectives: Morphological defects such as limb malformations, cranial asymmetries, loin deviations, jaw misalignments, and navel irregularities are associated with early culling and reduced productivity in beef cattle. In Bos taurus indicus such as Nellore, the genetic basis of these traits remains poorly characterized. This study aimed to investigate the genetic architecture of six morphological defects in Nellore cattle, namely feet and legs malformation, chamfer asymmetry, fallen hump, loin deviation, jaw misalignment, and navel irregularities, via a genome-wide association study (GWAS) approach tailored for binary traits. Methods: Depending on the trait, the number of genotyped animals analyzed ranged from 3369 to 23,206, using 385,079 SNPs (after quality control). Analyses were conducted using a linear mixed model framework adapted for binary outcomes. Results: Significant associations were identified for four traits: feet and legs, chamfer, hump, and loin. No significant markers were detected for jaw or navel defects, likely due to lower sample sizes and trait incidence. Gene annotation revealed 49 candidate genes related to feet and legs, 4 for chamfer, 4 for hump, and 6 for loin. Conclusions: Candidate genes were enriched for biological functions, including bone remodeling, muscle development, lipid metabolism, and epithelial organization. Overlaps with QTL related to conformation, feed intake, reproductive traits, and carcass quality were also observed. These findings provide novel insights into the genetic control of morphological defects in Nellore cattle and may inform breeding strategies aimed at improving structural soundness. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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15 pages, 1556 KB

Open AccessArticle

In Vitro Regeneration of Stevia rebaudiana Bertoni Using Somaclonal Variation as a Tool for Genetic Diversification

by Magdalena Dyduch-Siemińska and Jacek Gawroński

Genes 2025, 16(10), 1203; https://doi.org/10.3390/genes16101203 - 14 Oct 2025

Abstract

Introduction: Stevia rebaudiana Bertoni has recently gained significant attention due to the presence of intensely sweet yet low-calorie steviol glycosides (SGs) in its leaves, making it a promising natural sugar alternative with applications in the food, pharmaceutical, and cosmetics industries. The primary goal [...] Read more.

Introduction: Stevia rebaudiana Bertoni has recently gained significant attention due to the presence of intensely sweet yet low-calorie steviol glycosides (SGs) in its leaves, making it a promising natural sugar alternative with applications in the food, pharmaceutical, and cosmetics industries. The primary goal of this study was to determine whether generating somaclonal variation from plant material obtained by indirect regeneration results in further genetic changes identifiable using the SCoT marker (Start Codon Targeted). Methods: In the first stage, callus tissue was initiated from first-generation somaclones on MS medium supplemented with 4.0 mg/L 6-benzylaminopurine (BAP), 2.0 mg/L 1-naphthaleneacetic acid (NAA), and 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D). Their morphogenetic potential was analyzed on four media with different BAP and Kinetin concentrations. Donor plants, first and second generation somaclones, were also analyzed for genetic diversity using SCoT markers. Results: All first-generation somaclones demonstrated a very high callus initiation capacity, ranging from 95 to 100%. It was found that for most of the studied somaclones, the greatest number of shoots were developed by explants grown in a medium supplemented with 0.5 mg/L BAP and 0.25 mg/L Kin. The studied group of somaclones exhibits a high degree of polymorphism (55.2%). The analysis of genetic similarity of somaclones presented in the form of individual dendrograms indicates that in most cases, greater genetic diversity was revealed as a result of indirect regeneration in the first generation of somaclones compared to the second. Indirect organogenesis allows for the production of subsequent generations of genetically unstable somaclones, creating the potential for obtaining new phenotypic variants useful in plant breeding. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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27 pages, 7480 KB

Open AccessArticle

Short Inverted Repeats as Mutational Hotspots and Putative Drivers of Genome Instability in Osteosarcoma

by Minghua Li and Chun Liang

Genes 2025, 16(10), 1202; https://doi.org/10.3390/genes16101202 - 14 Oct 2025

Abstract

Background/Objectives: Short inverted repeats (SIRs) are abundant DNA motifs capable of forming secondary structures, such as hairpins and cruciforms, that can induce genome instability. However, their mutational consequences in cancer, particularly in osteosarcoma (OS), remain largely unexplored. Methods: In this study, [...] Read more.

Background/Objectives: Short inverted repeats (SIRs) are abundant DNA motifs capable of forming secondary structures, such as hairpins and cruciforms, that can induce genome instability. However, their mutational consequences in cancer, particularly in osteosarcoma (OS), remain largely unexplored. Methods: In this study, we systematically identified over 5.2 million SIRs in the human genome and analyzed their mutational patterns across six common cancer types. Results: We found that increased small insertion and deletion (INDEL) density within SIR spacer regions represents a consistent feature across cancers, whereas elevated single nucleotide variant (SNV) and structural breakpoint density is cancer-type specific. Integrating whole-genome sequencing data from 13 OS patients, we found that both SNVs and INDELs are significantly enriched within SIR spacer regions in OS. Notably, genomic regions with higher SIR density tend to accumulate more somatic mutations, suggesting a link between SIR abundance and local genome instability. SIR-associated mutations frequently occur in oncogenes and tumor suppressor genes, including TP53, NFATC2, MECOM, LRP1B, RB1, CNTNAP2, and PTPRD, as well as in long non-coding RNAs. Mutational signature analysis further suggests that defective DNA mismatch repair and homologous recombination may act in concert with SIR-induced DNA structural instability to drive OS development. Conclusions: Our findings highlight SIRs as mutational hotspots and potential drivers of osteosarcoma pathogenesis. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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8 pages, 241 KB

Open AccessArticle

The First Report of a Non-Canonical Telomeric Motif in Neuroptera: (TTGGG)n in Chromosomes of Nineta flava (Scopoli, 1763), Chrysopidae

by Desislava Stoianova and Snejana Grozeva

Genes 2025, 16(10), 1201; https://doi.org/10.3390/genes16101201 - 14 Oct 2025

Abstract

Background: Telomeres are nucleoprotein complexes that maintain chromosome integrity in eukaryotes. In insects, the canonical telomeric repeat (TTAGG)n is considered ancestral, though alternative motifs exist across various orders. Neuroptera, comprising about 5800 species, remains understudied regarding telomeric sequences, with data available for [...] Read more.

Background: Telomeres are nucleoprotein complexes that maintain chromosome integrity in eukaryotes. In insects, the canonical telomeric repeat (TTAGG)n is considered ancestral, though alternative motifs exist across various orders. Neuroptera, comprising about 5800 species, remains understudied regarding telomeric sequences, with data available for only seven species across three families. Previous studies reported the absence of (TTAGG)n in Chrysopidae species, contrasting with its presence in other Neuroptera families. This study aimed to identify and characterize telomeric motifs in Chrysopidae using chromosome-level genome assemblies and search for retrotransposon insertions. Methods: We analyzed chromosome-level genome assemblies from four Chrysopidae species: three Chrysopinae—Chrysoperla carnea (Stephens, 1836), Chrysopa pallens (Rambur, 1838), and Nineta flava (Scopoli, 1763); and one Nothochrysinae—Nothochrysa capitata (Fabricius, 1793). Terminal sequences of chromosome pseudomolecules were examined using Geneious Prime^®, applying five specific criteria for optimal telomeric sequence identification. We searched for SART and TRAS retrotransposons using the graphical sequence panel in GenBank. Results: We identified (TTGGG)n as the telomeric motif in N. flava, representing the first report of this pentanucleotide repeat in telomeres of Neuroptera. Arrays ranged from 228 to 8005 bp across seven terminal locations in five chromosome pseudomolecules. In N. capitata, we detected (TTAGG)n arrays (2316–3808 bp) at four terminal locations. No telomeric motifs meeting all criteria were found in C. carnea and C. pallens. No SART/TRAS retrotransposons were detected in any species. Conclusions: This study reveals previously unknown telomeric diversity within Chrysopidae, with both canonical (TTAGG)n and novel (TTGGG)n motifs present. The discovery of (TTGGG)n in Neuroptera expands known telomeric sequence diversity in this order. Full article

(This article belongs to the Section Animal Genetics and Genomics)

15 pages, 262 KB

Open AccessReview

How Close Are We to Achieving Durable and Efficacious Gene Therapy for Hemophilia A and B?

by Patrycja Sosnowska-Sienkiewicz and Danuta Januszkiewicz-Lewandowska

Genes 2025, 16(10), 1200; https://doi.org/10.3390/genes16101200 - 14 Oct 2025

Abstract

Hemophilia, an X-linked recessive bleeding disorder, results from mutations in the F8 or F9 genes, leading to factor VIII (hemophilia A) or factor IX (hemophilia B) deficiency. While conventional treatment relies on regular factor replacement therapy, gene therapy has emerged as a promising [...] Read more.

Hemophilia, an X-linked recessive bleeding disorder, results from mutations in the F8 or F9 genes, leading to factor VIII (hemophilia A) or factor IX (hemophilia B) deficiency. While conventional treatment relies on regular factor replacement therapy, gene therapy has emerged as a promising alternative, offering the potential for sustained endogenous factor production after a single administration. This review provides an in-depth analysis of recent advances in gene therapy for both hemophilia A and B, with a focus on AAV-mediated liver-directed approaches and other approved modalities. Key limitations—such as vector immunogenicity, hepatic toxicity, waning transgene expression, and limited re-dosing capacity—are discussed. Additional gene delivery platforms, including lentiviral and retroviral vectors, genome editing techniques (e.g., CRISPR/Cas9), and non-viral systems like transposons and lipid nanoparticles, are also examined. Although gene therapy for hemophilia B demonstrates greater clinical durability, hemophilia A presents unique challenges due to factor VIII’s size, poor expression efficiency, and the need for higher vector doses. Future efforts will focus on overcoming immune barriers, improving delivery technologies, and developing approaches suitable for pediatric patients and individuals with pre-existing immunity. This review provides not only a descriptive overview but also a critical comparison of gene therapy approaches for hemophilia A and B. We emphasize that the durability of response is currently superior in hemophilia B, whereas hemophilia A still faces unique barriers, including declining FVIII expression and higher immunogenicity. By analyzing cross-platform challenges (AAV, lentiviral, CRISPR, and emerging LNPs), we highlight the most promising strategies for overcoming these limitations and provide a forward-looking perspective on the future of gene therapy. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

17 pages, 4071 KB

Open AccessArticle

NKX6-3 in B-Cell Progenitor Differentiation and Leukemia

by Stefan Nagel, Corinna Meyer and Claudia Pommerenke

Genes 2025, 16(10), 1199; https://doi.org/10.3390/genes16101199 - 14 Oct 2025

Abstract

Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) that show aberrations of developmental transcription factors (TFs), [...] Read more.

Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) that show aberrations of developmental transcription factors (TFs), representing major oncogenic drivers. Analysis of physiological TFs in these developmental entities helps us to understand their normal and disturbed activities and regulatory connections. Here, we focused on NKL-subclass homeodomain TF NKX6-3, which is active in both normal B-cell progenitors and TCF3::PBX1 fusion gene-positive BCP-ALL cases. By performing siRNA-mediated knockdown and forced expression experiments in BCP-ALL model cell lines, we established a gene regulatory network for NKX6-3 together with TALE-class homeodomain TFs IRX1 and MEIS1, as well as ETS-TF SPIB. Importantly, NKX6-3 was activated by TCF3::PBX1, underlying their co-expression in BCP-ALL. Furthermore, comparative expression profiling analysis of public BCP-ALL patient data revealed TGFb-pathway in-hibitor CD109 as a downregulated target gene of NKX6-3. TGFb-signalling, in turn, enhanced NKX6-3 expression, indicating mutual activation. Finally, RNA-seq analysis of BCP-ALL cell line RCH-ACV after NKX6-3 knockdown revealed MPP7 as an upregulated target gene of both NKX6-3 and TCF3::PBX1, revealing a role for the HIPPO-pathway in B-cell progenitors and TCF3::PBX1-positive BCP-ALL. Collectively, our data introduce novel players and regulatory connections to normal and aberrant TF-networks in B-cell progenitors to serve as potential diagnostic markers or therapeutic targets. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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11 pages, 987 KB

Open AccessArticle

Allelic Variations of the Waxy Gene and Their Associations with Indica–Japonica Differentiation and Amylose Content in Yunnan Local Rice Germplasm

by Ying Lv, Wei Deng, Xueqian Zuo, Duo Lan, Jing Tan, Jianhua Zhang, Yangjun Dong, Yuran Xu, Jinwen Zhang, Xiao Zhang, Jian Tu, Limei Kui, Anyu Gu, Xiqiong Shen and Xiaolin Li

Genes 2025, 16(10), 1198; https://doi.org/10.3390/genes16101198 - 14 Oct 2025

Abstract

Objectives: To provide insights for breeding high-quality rice varieties, we analyzed local rice (Oryza sativa L.) germplasm from Yunnan Province, China, focusing on the relationships among Waxy gene alleles, indica–japonica differentiation, and amylose content (AC). Methods: We examined 201 local rice accessions. [...] Read more.

Objectives: To provide insights for breeding high-quality rice varieties, we analyzed local rice (Oryza sativa L.) germplasm from Yunnan Province, China, focusing on the relationships among Waxy gene alleles, indica–japonica differentiation, and amylose content (AC). Methods: We examined 201 local rice accessions. Two functional molecular markers for the Waxy gene were used to detect four alleles (Wx^a, Wx^b, Wxⁱⁿ, Wx^mw). Additionally, 33 InDel markers were employed to classify indica–japonica attributes, and AC was measured according to GB/T 15683-2008. Results: We detected 175 accessions with Wx^a, 20 with Wx^b, 4 with Wxⁱⁿ, and 2 with Wx^mw, indicating Wx^a dominance and a diverse genetic basis at the Waxy locus. Indica–japonica classification identified 180 indica-type, 19 japonica-type, and 2 intermediate-type accessions, confirming predominant indica differentiation in Yunnan rice. Integrating Waxy allele detection, indica–japonica attributes, and AC showed that Wx^a occurred primarily in indica rice with higher AC (mean 22.55%), comparable to Wxⁱⁿ (mean 24.33%); Wx^b was mainly found in japonica rice with lower AC (mean 13.46%), similar to Wx^mw (mean 15.65%). Conclusions: Local Yunnan rice exhibits Wx^a predominance at the Waxy locus and clear indica differentiation. The observed associations between Waxy alleles, subspecies attributes, and AC provide useful references for marker-assisted breeding of premium rice and for exploiting indica–japonica heterosis. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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