Genes

24 pages, 548 KiB

Open AccessSystematic Review

Understanding Glycogen Storage Disease Type IX: A Systematic Review with Clinical Focus—Why It Is Not Benign and Requires Vigilance

by Egidio Candela, Giulia Montanari, Andrea Zanaroli, Federico Baronio, Rita Ortolano, Giacomo Biasucci and Marcello Lanari

Genes 2025, 16(5), 584; https://doi.org/10.3390/genes16050584 - 15 May 2025

Abstract

Background/Objectives: Glycogen storage disease type IX (GSD IX) is a group of inherited metabolic disorders caused by phosphorylase kinase deficiency affecting the liver or muscle. Despite being relatively common among GSDs, GSD IX remains underexplored. Methods: A systematic review of GSD IX was [...] Read more.

Background/Objectives: Glycogen storage disease type IX (GSD IX) is a group of inherited metabolic disorders caused by phosphorylase kinase deficiency affecting the liver or muscle. Despite being relatively common among GSDs, GSD IX remains underexplored. Methods: A systematic review of GSD IX was conducted per PRISMA guidelines using SCOPUS and PubMed, registered with PROSPERO. Inclusion focused on human clinical studies published up to 31 December 2024. Results: A total of 400 patients with GSD IX were analyzed: 274 IXa (mean age at diagnosis 5.1 years), 72 IXc (mean age at diagnosis 4.9 years), 39 IXb (mean age at diagnosis 4.2 years), and 15 IXd (mean age at diagnosis 44.9 years). Hepatomegaly was commonly reported in types IXa, IXb, and especially IXc (91.7%), but was rare in IXd. Elevated transaminases were frequently observed in types IXa, IXb, and particularly IXc, while uncommon in IXd. Fasting hypoglycemia was occasionally observed in types IXa and IXb, more frequently in IXc (52.7%), and was not reported in IXd. Growth delay or short stature was observed in a substantial proportion of patients with types IXa (43.8%), IXb, and IXc, but was rare in IXd. Muscle involvement was prominent in IXd, with all patients showing elevated CPK (mean 1011 U/L). Neurological involvement was infrequently reported in types IXa and IXc. Conclusions: This systematic review includes the most extensive clinical case history of GSD IX described in the literature. The clinical spectrum of GSD IX varies widely among subtypes, with IXc being the most aggressive. While liver forms are generally present in early childhood, muscle-type IXd shows delayed onset and milder symptoms, often leading to diagnostic delays. For diagnosis, it is essential not to underestimate key clinical features such as hepatic involvement and hypoglycemia in a child under 5 years of age. Other manifestations, including the as-yet unexplored systemic involvement of bone and kidney, remain insufficiently understood and require further investigation. Next-generation sequencing has improved diagnostic precision over traditional biopsy. Dietary management, including uncooked cornstarch, Glycosade^®, and high-protein intake, remains the cornerstone of treatment. However, there is a paucity of well-designed, evidence-based studies to determine the most effective therapeutic approach. Despite its historically perceived benign course, the broad phenotypic variability of GSD IX, including progressive liver involvement and potential neurological complications, highlights its substantial clinical relevance and underscores the need for accurate diagnostic classification and long-term multidisciplinary follow-up. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

22 pages, 2262 KiB

Open AccessArticle

Genome-Wide Association Studies and Candidate Genes for Egg Production Traits in Layers from an F₂ Crossbred Population Produced Using Two Divergently Selected Chicken Breeds, Russian White and Cornish White

by Natalia A. Volkova, Michael N. Romanov, Alan Yu. Dzhagaev, Polina V. Larionova, Ludmila A. Volkova, Alexandra S. Abdelmanova, Anastasia N. Vetokh, Darren K. Griffin and Natalia A. Zinovieva

Genes 2025, 16(5), 583; https://doi.org/10.3390/genes16050583 - 15 May 2025

Abstract

Background/Objectives: Finding single nucleotide polymorphisms (SNPs) and candidate genes that influence the expression of key traits is essential for genomic selection and helps improve the efficiency of poultry production. Here, we aimed to conduct a genome-wide association study (GWAS) for egg production [...] Read more.

Background/Objectives: Finding single nucleotide polymorphisms (SNPs) and candidate genes that influence the expression of key traits is essential for genomic selection and helps improve the efficiency of poultry production. Here, we aimed to conduct a genome-wide association study (GWAS) for egg production traits in an F₂ resource population of chickens (Gallus gallus). Methods: The examined F₂ population was produced by crossing two divergently selected breeds with contrasting phenotypes for egg performance traits, namely Russian White (of higher egg production) and Cornish White (of lower egg production). Sampled birds (n = 142) were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. Results: In the course of the GWAS analysis, we were able to clarify significant associations with phenotypic traits of interest and economic value by using 47,432 SNPs after the genotype dataset was filtered. At the threshold p < 1.06 × 10⁻⁶, we found 23 prioritized candidate genes (PCGs) associated with egg weight at the age of 42–52 weeks (FGF14, GCK), duration of egg laying (CNTN4), egg laying cycle (SAMD12) and egg laying interval (PHF5A, AKR1B1, CALD1, ATP7B, PIK3R4, PTK2, PRKCE, FAT1, PCM1, CC2D2A, BMS1, SEMA6D, CDH13, SLIT3, ATP10B, ISCU, LRRC75A, LETM2, ANKRD24). Moreover, two SNPs were co-localized within the FGF14 gene. Conclusions: Based on our GWAS findings, the revealed SNPs and candidate genes can be used as genetic markers for egg weight and other performance characteristics in chickens to attain genetic enhancement in production and for further genomic selection. Full article

(This article belongs to the Special Issue Genetic Breeding of Poultry)

14 pages, 641 KiB

Open AccessReview

Genetic Aspects of Tooth Agenesis

by Clarissa Modafferi, Ilaria Tucci, Francesco Maria Bogliardi, Elena Gimondo, Pietro Chiurazzi, Elisabetta Tabolacci and Cristina Grippaudo

Genes 2025, 16(5), 582; https://doi.org/10.3390/genes16050582 - 15 May 2025

Abstract

Tooth agenesis is among the most prevalent congenital anomalies affecting human dentition, characterized by the developmental absence of one or more teeth. This condition may be present in either syndromic or non-syndromic forms, with significant implications for oral function, aesthetics, and craniofacial development. [...] Read more.

Tooth agenesis is among the most prevalent congenital anomalies affecting human dentition, characterized by the developmental absence of one or more teeth. This condition may be present in either syndromic or non-syndromic forms, with significant implications for oral function, aesthetics, and craniofacial development. This narrative review aims to provide a comprehensive overview of tooth agenesis, defining its classification, genetic underpinnings, epidemiological aspects, phenotypic features, and therapeutic approaches. Recent advances in genetic research have identified numerous causative genes, notably EDA, MSX1, WNT10A, and PAX9, each associated with specific patterns of missing teeth and involved in isolated and/or syndromic forms. Additionally, genes such as TSPEAR, LRP6, PITX2, and GREM2 contribute to varying degrees of severity and tooth distribution, often blurring the lines between syndromic and isolated cases. The genotype-phenotype correlations underscore the complexity of the underlying molecular pathways involved in odontogenesis. From a therapeutic perspective, the management of tooth agenesis requires a multidisciplinary approach, often involving orthodontic, prosthetic, and surgical interventions tailored to the severity of tooth loss and patient age. Early diagnosis represents a crucial role in treatment planning, facilitating timely intervention during growth and enhancing long-term outcomes. In conclusion, tooth agenesis remains a complex clinical condition with a strong genetic basis. A patient-centered and interdisciplinary strategy is essential to address both functional and psychosocial needs. Full article

(This article belongs to the Special Issue Genetic, Epigenetic and Environmental Factors in Dental Development and Pathologies: Genes, Interactions and Dental Development)

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14 pages, 638 KiB

Open AccessSystematic Review

Genetic Determinants of Colonic Diverticulosis—A Systematic Review

by Piotr Nehring and Adam Przybyłkowski

Genes 2025, 16(5), 581; https://doi.org/10.3390/genes16050581 - 15 May 2025

Abstract

Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim [...] Read more.

Background: Colonic diverticulosis is a common condition, particularly in the elderly population. While dietary habits, obesity, smoking, and physical inactivity contribute to its pathogenesis, emerging evidence highlights a genetic predisposition affecting extracellular matrix (ECM) remodeling, inflammation, and connective tissue integrity. The aim of this systematic review was to summarize genetic determinants of colonic diverticulosis. Methods: The PubMed^® database was searched for original studies in humans. The inclusion criteria were named genetic factor and confirmed diverticulosis. Patients with diverticulitis and diverticular diseases were excluded from this review. Results: Out of 137 publications, 10 articles met the inclusion criteria: six large association studies (GWAS) and four cross-sectional studies. The genes regulating ECM turnover, including TIMP1, MMP3, and MMP9, are involved in diverticulosis development. The TIMP1 (rs4898) T allele has been associated with increased susceptibility, potentially due to its role in ECM remodeling. Similarly, MMP3 (rs3025058) and MMP9 (rs3918242) polymorphisms contribute to altered collagen degradation. The COL3A1 (rs3134646) variant coding modified collagen type III may promote diverticular formation. Other genes, such as ARHGAP15 (rs4662344, rs6736741), affect cytoskeletal dynamics. Identified in GWAS studies, gene candidates may be grouped into blood group and immune system-related genes (ABO, HLA-DQA1, HLA-H, OAS1, TNFSF13, FADD), extracellular matrix and connective tissue genes (COL6A1, COLQ, EFEMP1, ELN, HAS2, TIMP2), signaling and cell communication (BMPR1B, WNT4, RHOU, PHGR1, PCSK5), nervous system and neurodevelopment (BDNF, CACNB2, GPR158, SIRT1, SCAPER, TRPS1), metabolism and transporters (SLC25A28, SLC35F3, RBKS, PPP1R14A, PPP1R16B), lipids and cholesterol (LDAH, LYPLAL1, STARD13), transcription and gene regulation (ZBTB4, UBTF, TNRC6B), apoptosis (FADD, PIAS1), and poorly characterized genes (C1TNF7, ENSG00000224849, ENSG00000251283, LINC01082, DISP2, SNX24, THEM4, UBL4B, UNC50, WDR70, SREK1IP1). Conclusions: There are a number of gene variants that probably predispose to colonic diverticulosis. Detailed characterization of the multigene background of diverticulosis will enable appropriate therapeutic or preventive interventions in the future. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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18 pages, 5893 KiB

Open AccessArticle

Analysis of Multi-Target Synergistic Mechanism of Coix Seed Therapy for Herpes Zoster Based on Machine Learning and Network Pharmacology

by Zhiqin Song, Lin Yang, Jing He, Yuchao Li, Ningxian Yang, Min Yang and Mingkai Wu

Genes 2025, 16(5), 580; https://doi.org/10.3390/genes16050580 - 14 May 2025

Abstract

Objective: To explore the efficacy and mechanism of Coix seeds in treating herpes zoster (HZ) using an integrated computational approach. Methods: Network pharmacology, molecular docking, and machine learning were employed. Disease-related targets were collected from multiple databases, and intersection targets with Coix seed [...] Read more.

Objective: To explore the efficacy and mechanism of Coix seeds in treating herpes zoster (HZ) using an integrated computational approach. Methods: Network pharmacology, molecular docking, and machine learning were employed. Disease-related targets were collected from multiple databases, and intersection targets with Coix seed were analyzed via PPI, GO, and KEGG enrichment. A “TCM-Ingredient-Target” network was constructed using Cytoscape. Molecular docking and dynamics simulations were performed for validation. Results: Fifty-five overlapping targets were identified, with core targets including TNF, EGF, and GAPDH. Enrichment analysis revealed key pathways such as inflammation and immune regulation. Molecular docking confirmed strong binding affinity between active compounds and targets. Conclusions: This study demonstrates that Coix seed exerts anti-HZ effects through multi-target mechanisms, providing a theoretical basis for developing novel multi-pathway treatment strategies. Full article

(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)

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20 pages, 2786 KiB

Open AccessArticle

Genome-Wide Identification of the Polygalacturonase Gene Family and Its Potential Association with Abscission Zone in Capsicum annuum L.

by Lei He, Chen Lu, Xi Yan, Sha Yang, Peng Zhou, Wei Lai and Jianwen He

Genes 2025, 16(5), 579; https://doi.org/10.3390/genes16050579 - 14 May 2025

Abstract

Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized [...] Read more.

Background: Polygalacturonase (PG) genes regulate plant organ abscission by degrading pectin in the cell wall. However, their association with pedicel abscission susceptibility in pepper remains poorly understood. Methods: 47 CaPG genes were identified were identified in the ‘Zunla1’ genome and characterized by structural, evolutionary, and comparative genomic analyses. Their expression profiles across various tissues and fruit development stages were examined using transcriptome data. Ethephon treatment and qRT-PCR were employed to assess gene responses during ethylene-induced pedicel abscission. Results: The 47 CaPG genes were distributed across 12 chromosomes, with CaPG1 to CaPG5 unanchored. Most proteins were hydrophilic, nuclear-localized, and had promoters enriched in light-responsive elements. Collinearity analysis revealed limited segmental duplication, and Ka/Ks values indicated strong purifying selection. Phylogenetic and collinearity analyses showed that CaPG genes are more closely related to those in tomato than in Arabidopsis or maize. Expression profiling revealed tissue- and stage-specific patterns, with 21 CaPG genes associated with pedicel abscission susceptibility. Ethephon treatment enhanced abscission and upregulated several CaPG genes. Conclusions: This study offers insights into the CaPG gene family’s structure, evolution, and function. Specific CaPG genes likely contribute to ethylene-mediated pedicel abscission, providing potential targets for improving fruit-retention traits in pepper. Full article

(This article belongs to the Special Issue Molecular Adaptation and Evolutionary Genetics in Plants)

17 pages, 688 KiB

Open AccessReview

Gene–Diet Interactions in Diabetes Mellitus: Current Insights and the Potential of Personalized Nutrition

by Angeliki Kapellou, Effie Salata, Dimitrios Miltiadis Vrachnos, Sevastiani Papailia and Spiros Vittas

Genes 2025, 16(5), 578; https://doi.org/10.3390/genes16050578 - 14 May 2025

Abstract

Type 2 diabetes mellitus (T2DM) remaina significant global health challenge, with its increasing prevalence and associated complications contributing to high morbidity and economic burden. Genetic factors play a crucial role in T2DM susceptibility, yet individual responses to dietary interventions vary widely, emphasizing the [...] Read more.

Type 2 diabetes mellitus (T2DM) remaina significant global health challenge, with its increasing prevalence and associated complications contributing to high morbidity and economic burden. Genetic factors play a crucial role in T2DM susceptibility, yet individual responses to dietary interventions vary widely, emphasizing the importance of gene–diet (G × D) interactions. This review synthesizes the current literature on the genetic basis of T2DM and the role of G × D interactions in shaping individual responses to diet. We examine the genetics implication in T2DM risk and modulation by dietary factors, with a focus on the potential of Nutrigenetics in guiding personalized nutrition (PN) strategies. Moreover, the clinical implications of these interactions for the personalized prevention and management of T2DM are explored, highlighting the promise of tailoring dietary recommendations based on genetic profiles. Critical research gaps, including the need for diverse and longitudinal studies, the integration of multi-omic data, and the inclusion of digital health technologies in PN are discussed. Finally, future directions for the field are outlined, advocating for more inclusive, large-scale studies to optimize PN approaches for diverse populations and improve the efficacy of T2DM prevention and management. This review underscores the potential of an individualized, genetically informed dietary approach in modulating the global burden of T2DM. Full article

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

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17 pages, 5019 KiB

Open AccessArticle

PAX3 Regulatory Signatures and Gene Targets in Melanoma Cells

by Stephen P. G. Moore, Shripushkar Ganesh Krishnan, Rutu Jaswanth Kothari, Noah B. Prince, Colin Kenny, Chao Zhang and Deborah Lang

Genes 2025, 16(5), 577; https://doi.org/10.3390/genes16050577 - 14 May 2025

Abstract

Background/Objectives: PAX3 is a transcription factor that drives melanoma progression by promoting cell growth, migration, and survival, while inhibiting cellular terminal differentiation. However, known PAX3 target genes are limited and cannot fully explain the wide impact of PAX3 function. The PAX3 protein can [...] Read more.

Background/Objectives: PAX3 is a transcription factor that drives melanoma progression by promoting cell growth, migration, and survival, while inhibiting cellular terminal differentiation. However, known PAX3 target genes are limited and cannot fully explain the wide impact of PAX3 function. The PAX3 protein can regulate DNA through two separate binding domains, the Paired Domain (PD) and Homeodomain (HD), which bind different DNA motifs. It is not clear if these two domains bind and work together to regulate genes and if they promote all or only a subset of downstream cellular events. Methods: PAX3 direct downstream targets were identified using Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assays in SK-MEL-5 melanoma cells. PAX3-binding genomic regions were identified through MACS2 peak calling, and peaks were categorized based on the presence of PD and/or HD binding sites (or neither) through HOMER motif analysis. The peaks were further characterized as Active, Primed, Poised, Repressed, or Closed based on ATAC-seq data and CUT&RUN for histone Post-Translational Modifications H3K4me1, H3K4me3, H3K27me3, and H3K27Ac. Results: This analysis revealed that most of the PAX3 binding sites in the SK-MEL-5 cell line were primarily through the PD and connected to Active genes. Surprisingly, PAX3 does not commonly act as a repressor in SK-MEL-5 cells. Pathway analysis identified genes involved with transcription, RNA modification, and cell growth. Peaks located in distal enhancer elements were connected to genes involved in neuronal growth, function, and signaling. Conclusions: Our results reveal novel PAX3 regulatory regions and putative genes in a melanoma cell line, with a predominance of PAX3 PD binding on active sites. Full article

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

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13 pages, 3873 KiB

Open AccessArticle

Establishment of Reference Measurement Procedure for TP53 R175H/R248W Detection and a Novel Preparation Method for ctDNA Reference Material

by Yanru Tang, Chunyan Niu, Jiejie Zhang, Lianhua Dong and Jingya Yang

Genes 2025, 16(5), 576; https://doi.org/10.3390/genes16050576 - 14 May 2025

Abstract

Background/Aims: Circulating tumor DNA (ctDNA) is becoming a valuable cancer biomarker for clinical decision-making. Nevertheless, the lack of quality control materials to assess the reliability of test results remains a challenge. This study aimed to establish digital PCR (dPCR) assays for detecting TP53 [...] Read more.

Background/Aims: Circulating tumor DNA (ctDNA) is becoming a valuable cancer biomarker for clinical decision-making. Nevertheless, the lack of quality control materials to assess the reliability of test results remains a challenge. This study aimed to establish digital PCR (dPCR) assays for detecting TP53 variants (R175H and R248W) and develop a preparation method for ctDNA reference materials to improve detection reliability. Methods: Two dPCR assays targeting TP53-R175H and TP53-R248W variants were developed and validated for repeatability, sensitivity, and linearity. Additionally, a ctDNA reference material preparation protocol was developed by digesting nucleosomes from cultured cancer cell lines with micrococcal nuclease, followed by magnetic beads purification. The size distribution and quality of the generated ctDNA fragments was analyzed, and the developed dPCR assays were applied to detect the variants in the ctDNA samples. Results: The dPCR assays demonstrated high repeatability (RSD of 0.16% to 7.65%) and excellent linearity (R² values of 1.0000 and 0.9981) across variant allele frequencies of 50%–0.1%. The limits of detection (LOD) and quantification (LOQ) were 0.143% (R175H) and 0.092% (R248W). The ctDNA reference materials exhibited single dominant peaks at 128 bp (R175H) and 143 bp (R248W). The dPCR assays successfully detected variants in these reference materials, confirming their applicability for ctDNA samples. onclusion: Firstly, accurate measurement procedures for TP53-R175H and TP53-R248W variants based on dPCR were established in this study. Furthermore, a protocol for preparing ctDNA reference material was established here. By digesting nucleosomal DNA derived from cancer cell lines with micrococcal nuclease, this method can closely mimic the properties of clinical ctDNA. The dPCR method and ctDNA reference material preparation approach established here could be used in ctDNA detection and for improving its reliability. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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17 pages, 2313 KiB

Open AccessArticle

Mapping Inherited Genetic Variation with Opposite Effects on Autoimmune Disease and Four Cancer Types Identifies Candidate Drug Targets Associated with the Anti-Tumor Immune Response

by Junyu Chen, Michael P. Epstein, Joellen M. Schildkraut and Siddhartha P. Kar

Genes 2025, 16(5), 575; https://doi.org/10.3390/genes16050575 - 14 May 2025

Abstract

Background: Germline alleles near genes encoding certain immune checkpoints (CTLA4, CD200) are associated with autoimmune/autoinflammatory disease and cancer, but in opposite ways. This motivates a systematic search for additional germline alleles with this pattern with the aim of identifying [...] Read more.

Background: Germline alleles near genes encoding certain immune checkpoints (CTLA4, CD200) are associated with autoimmune/autoinflammatory disease and cancer, but in opposite ways. This motivates a systematic search for additional germline alleles with this pattern with the aim of identifying potential cancer immunotherapeutic targets using human genetics. Methods: Pairwise fixed effect cross-disorder meta-analyses combining genome-wide association studies (GWAS) for breast, prostate, ovarian and endometrial cancers (240,540 cases/317,000 controls) and seven autoimmune/autoinflammatory diseases (112,631 cases/895,386 controls) coupled with in silico follow-up. Results: Meta-analyses followed by linkage disequilibrium clumping identified 312 unique, independent lead variants with p < 5 × 10⁻⁸ associated with at least one of the cancer types at p < 10⁻³ and one of the autoimmune/autoinflammatory diseases at p < 10⁻³. At each lead variant, the allele that conferred autoimmune/autoinflammatory disease risk was protective for cancer. Mapping led variants to nearest genes as putative functional targets and focusing on immune-related genes implicated 32 genes. Tumor bulk RNA-Seq data highlighted that the tumor expression of 5/32 genes (IRF1, IKZF1, SPI1, SH2B3, LAT) was each strongly correlated (Spearman’s ρ > 0.5) with at least one intra-tumor T/myeloid cell infiltration marker (CD4, CD8A, CD11B, CD45) in every one of the cancer types. Tumor single-cell RNA-Seq data from all cancer types showed that the five genes were more likely to be expressed in intra-tumor immune versus malignant cells. The five lead SNPs corresponding to these genes were linked to them via the expression of quantitative trait locus mechanisms and at least one additional line of functional evidence. Proteins encoded by the genes were predicted to be druggable. Conclusions: We provide population-scale germline genetic and functional genomic evidence to support further evaluation of the proteins encoded by IRF1, IKZF1, SPI1, SH2B3 and LAT as possible targets for cancer immunotherapy. Full article

(This article belongs to the Special Issue Genetics of Cancer Immunology)

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17 pages, 2090 KiB

Open AccessArticle

The Analysis of Autosomal STRs Draws the Current Genetic Map and Evolutionary History of Northernmost South America

by Julie Moncada Madero, Fernanda Mogollón Olivares, Dayana Suárez Medellín, Alejandra Coronel Guzmán, Andrea Casas-Vargas and William Usaquén Martínez

Genes 2025, 16(5), 574; https://doi.org/10.3390/genes16050574 - 14 May 2025

Abstract

Objectives: To analyze Colombia’s current human population, we employed a population genetics approach enriched by genealogical, demographic, cultural, and historical data to learn about its evolutionary history and to elucidate ethnic belonging and relationship patterns between its various population groups. Materials and Methods: [...] Read more.

Objectives: To analyze Colombia’s current human population, we employed a population genetics approach enriched by genealogical, demographic, cultural, and historical data to learn about its evolutionary history and to elucidate ethnic belonging and relationship patterns between its various population groups. Materials and Methods: This study relied on ten autosomal microsatellite markers (STRs) from 1364 individuals surveyed throughout the country. Aside from employing descriptive population genetics, substructure, and distance analysis, this investigation evaluated genealogical, demographic, cultural, and historical data gathered from fieldwork surveys. Results: We present a genetic diversity and ethnic belonging map of Colombia that suggests a nine-population classification (under Afro-descendant, Native American, and Admixed ethnicity labels) that reveals traces of evolutionary processes discussed in the light of the recent literature based on modern molecular markers. Colombia’s genetic trace from Africa varies among territories, as shown here by two differentiated Afro ancestral components, Chocó and San Andrés, in addition to the Afro admixture category. Some Native American peoples like the Wayúu, Zenú, Ticuna, Huitoto, and Cocama have a genetic configuration that remains relatively preserved. Nevertheless, other self-determined indigenous peoples who remain in their ancestral territories exhibit genetic introgression that is also reflected by their acculturation levels such as the Pijaos, Kankuamos, and Mokaná. The population classified as European admixture also shows an ancestral component that seems to be more fixed throughout neighboring territories but whose fluctuation depends on its specific demographic histories. Conclusions: This study combines STRs, a targeted sampling strategy, and advanced analytical tools to explore Colombia’s genetic diversity and evolutionary history. Locally, these findings enhance the understanding of genetics in a post-conflict society, crucial for human identification. Globally, they contribute to human population genetics, helping address evolutionary questions using data from diverse human ancestries and geographies. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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18 pages, 17046 KiB

Open AccessArticle

Olig1/2 Drive Astrocytic Glioblastoma Proliferation Through Transcriptional Co-Regulation of Various Cyclins

by Yu Tian, Ziwu Wang, Mengge Sun, Jialin Li, Wenhui Zheng, Feihong Yang and Zhuangzhi Zhang

Genes 2025, 16(5), 573; https://doi.org/10.3390/genes16050573 - 13 May 2025

Abstract

As the most aggressive primary brain tumor, glioblastoma (GBM) is considered incurable due to its molecular heterogeneity and therapy resistance. Identifying key regulatory factors in GBM is critical for developing effective therapeutic strategies. Based on the analysis of TCGA data, we confirmed a [...] Read more.

As the most aggressive primary brain tumor, glioblastoma (GBM) is considered incurable due to its molecular heterogeneity and therapy resistance. Identifying key regulatory factors in GBM is critical for developing effective therapeutic strategies. Based on the analysis of TCGA data, we confirmed a robust co-expression and correlation of OLIG1 and OLIG2 in human GBM. However, their roles in the astrocytic GBM subtype remain unclear. In this study, we first establish an astrocytic-featured GBM mouse model by introducing PiggyBac-driven hEGFRvIII plasmids and demonstrate that both OLIG1 and OLIG2 are highly expressed within this context. Next, using CRISPR/Cas9 technology to knockout Olig1/2, we found that astrocyte differentiation markers such as GFAP, SOX9, and HOPX were preserved, but tumor cell proliferation was significantly diminished. Mechanistically, CUT&Tag-seq revealed that OLIG1/2 directly binds to the promoter region of various cyclins (Cdk4, Ccne2, Ccnd3, and Ccnd1), where an enrichment of the active histone marker H3K4me3 was observed, indicating transcriptional activation of the genes. Notably, Olig1/2 knockout did not suppress tumor initiation or migration, suggesting that their primary role is to amplify proliferation rather than to drive tumorigenesis. This study defines Olig1 and Olig2 as master regulators of GBM proliferation through various cyclins, thereby offering a novel therapeutic target. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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15 pages, 2359 KiB

Open AccessArticle

The Effects of Ferulic Acid on the Growth Performance, Immune Function, Antioxidant Capacity, and Intestinal Microbiota of Broiler Chickens

by Xianguo Yi, Quanchao Ma, Zhili Li, Yuli Hu, Haigang Wu, Rui Wang, Xuyang Sun, Enen Wang, Chaofeng Ma and Qingmin Qin

Genes 2025, 16(5), 572; https://doi.org/10.3390/genes16050572 - 13 May 2025

Abstract

Objectives: Ferulic acid is a natural and safe herbal feed additive. This study aims to evaluate the effects of ferulic acid on the growth performance, anti-inflammatory and antioxidant capacities, immune function, and intestinal microbiota of broiler chickens. Methods: A total of 320 broiler [...] Read more.

Objectives: Ferulic acid is a natural and safe herbal feed additive. This study aims to evaluate the effects of ferulic acid on the growth performance, anti-inflammatory and antioxidant capacities, immune function, and intestinal microbiota of broiler chickens. Methods: A total of 320 broiler chickens, aged 14 days, were randomly divided into four groups: a blank control group (MA group), a low-concentration ferulic acid group (BM group, 10 mg/kg), a medium-concentration ferulic acid group (CM group, 30 mg/kg), and a high-concentration ferulic acid group (DM group, 90 mg/kg) after a 14-day acclimatization period. The experiment lasted for 28 days, and the chickens were dissected on day 29. Results: The results showed that compared to the MA group, the feed-to-meat ratio in the CM and DM groups was significantly reduced. The activity of duodenal trypsin in the CM and DM groups was significantly enhanced, and the activity of pancreatic protease in the DM group was significantly increased. The serum levels of urea nitrogen, creatinine, and triglycerides were significantly elevated in the CM and DM groups. The serum malondialdehyde (MDA) levels in the BM, CM, and DM groups were significantly reduced, while the activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) were significantly increased in the CM and DM groups. The serum interleukin-2 (IL-2) levels in the BM group were significantly decreased, while interferon-gamma (IFN-γ) levels in the CM group and complement component 3 (C-3) levels in the DM group were significantly increased. The mRNA expression levels of TLR4, MyD88, NF-κB, TNF-α, NLRP3, IL-1β, and IL-18 in the jejunum of the DM group were significantly reduced. The diversity of cecal microbiota in the ferulic acid groups changed, with a certain degree of increase in the relative abundance of Spirulina and Ruminococcus. The relative abundance of Escherichia coli in the DM group significantly increased, altering the metabolic function of the cecal microbiota in broiler chickens. Conclusions: The above results indicate that ferulic acid, as a novel feed additive for broiler chickens, has an impact on the growth performance, anti-inflammatory and antioxidant capacity, immune function, and intestinal microbiota of broiler chickens. Full article

(This article belongs to the Special Issue Genetic Breeding of Poultry)

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9 pages, 529 KiB

Open AccessCase Report

A Patient with a Small Deletion Affecting Only Exon 1-Intron 1 of the NXF5 Gene: Potential Evidence Supporting Its Role in Neurodevelopmental Disorders

by Yessica Yesenia Tapia, Claudia Ciaccio, Merve Begüm Bacınoğlu, Stefano D’Arrigo and Francesca Luisa Sciacca

Genes 2025, 16(5), 571; https://doi.org/10.3390/genes16050571 - 13 May 2025

Abstract

Genetic studies have identified numerous candidate genes for neurodevelopmental disorders associated with intellectual disability (ID) and autism spectrum disorders (ASD). Some genetic anomalies are very rare or challenging to detect, making it essential to validate the presence of gene mutations or copy number [...] Read more.

Genetic studies have identified numerous candidate genes for neurodevelopmental disorders associated with intellectual disability (ID) and autism spectrum disorders (ASD). Some genetic anomalies are very rare or challenging to detect, making it essential to validate the presence of gene mutations or copy number variations in additional patients with similar clinical phenotypes. Background/Objectives: Case reports play a crucial role in this process by validating rare variants in phenotypically matched patients, shedding light on novel candidate genes linked to these disorders. Methods: Patients with ID and ASD underwent neurological examinations, brain magnetic resonance imaging (MRI), sleep and wake electroencephalogram (EEG), neuropsychological evaluations, and laboratory tests including molecular analysis for fragile-X syndrome and array comparative genomic hybridization (aCGH). Results: We observed a patient with ID and ASD who carried a microdeletion in Xq22.1 that affects only exon 1 and intron 1 of the Nuclear RNA Export Factor 5 (NXF5) gene. The patient’s phenotypic features overlap with those of the only four previously reported cases of variations involving the same gene. Conclusions: Our findings suggest that NXF5 may play a role in neurodevelopmental disorders and should be considered in the spectrum of X-linked ID associated with ASD. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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11 pages, 1953 KiB

Open AccessArticle

Genetic Background and Gene Essentiality

by Paulina Gąsienica, Katarzyna Toch, Kamila Stefania Zając-Garlacz and Marta Labocha-Derkowska

Genes 2025, 16(5), 570; https://doi.org/10.3390/genes16050570 - 13 May 2025

Abstract

Background/Objectives: Essential genes are those required for an organism’s survival and reproduction. However, gene essentiality is not absolute; it can be highly context-dependent, varying across genetic and environmental conditions. Most previous studies have assessed gene essentiality in a single genetic background, limiting our [...] Read more.

Background/Objectives: Essential genes are those required for an organism’s survival and reproduction. However, gene essentiality is not absolute; it can be highly context-dependent, varying across genetic and environmental conditions. Most previous studies have assessed gene essentiality in a single genetic background, limiting our understanding of its variability. The objective of this study was to investigate how genetic background influences gene essentiality in the multicellular model organism Caenorhabditis elegans. Methods: We examined gene essentiality in three genetically distinct C. elegans strains: N2, LKC34, and MY16. A total of 294 genes were selected for RNA interference (RNAi) knockdown: 101 previously classified as essential, 175 as nonessential and 18 as conditional (condition-dependent essentiality). Each gene–strain combination was tested in multiple biological and technical replicates, and rigorous quality control and statistical analyses were used to identify strain-specific effects. Results: Our results demonstrate substantial variation in gene essentiality across genetic backgrounds. Among the 101 genes previously identified as essential in the N2 strain, only 56% were consistently essential in all three strains. We identified 23 genes that were newly essential across all strains, 13 genes essential in two strains, and 9 genes essential in only one strain. These results reveal that a significant proportion of essential genes exhibit strain-dependent essentiality. Conclusions: This study underscores the importance of genetic context in determining gene essentiality. Our findings suggest that relying on a single genetic background, such as N2, may lead to an incomplete or misleading view of gene essentiality. Understanding context-dependent gene essentiality has important implications for functional genomics, evolutionary biology, and potentially for translational research where genetic background can modulate phenotypic outcomes. Full article

(This article belongs to the Section Genes & Environments)

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20 pages, 587 KiB

Open AccessReview

Advancements in Gene Therapy for Non-Small Cell Lung Cancer: Current Approaches and Future Prospects

by Iwona Ziółkowska-Suchanek and Natalia Rozwadowska

Genes 2025, 16(5), 569; https://doi.org/10.3390/genes16050569 - 12 May 2025

Abstract

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide, characterized by late diagnosis and resistance to conventional therapies. Gene therapy has emerged as a promising alternative for NSCLC therapy, especially for patients with advanced disease who have exhausted conventional [...] Read more.

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide, characterized by late diagnosis and resistance to conventional therapies. Gene therapy has emerged as a promising alternative for NSCLC therapy, especially for patients with advanced disease who have exhausted conventional treatments. This article delved into the current developments in gene therapy for NSCLC, including gene replacement and tumor suppressor gene therapy, gene silencing, CRISPR/Cas9 gene editing, and immune modulation with CAR-T cell therapy. In addition, the challenges and future prospects of gene-based therapies for NSCLC were discussed. Full article

(This article belongs to the Special Issue Recent Advances in the Molecular Genetics of Lung Cancer)

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12 pages, 2533 KiB

Open AccessArticle

Genome-Wide Analysis of Copy Number Variations in Three Populations of Nanyang Cattle Using Whole-Genome Resequencing

by Dong Dang, Lilian Zhang, Lutao Gao, Lin Peng, Yao Rao and Linnan Yang

Genes 2025, 16(5), 568; https://doi.org/10.3390/genes16050568 - 12 May 2025

Abstract

Copy number variation (CNV) serves as a crucial contributor to genetic diversity, exerting a profound influence on phenotypic diversity, traits of economic significance, and the evolutionary trajectory of livestock species. This study aimed to dissect the genome-wide CNV landscape of the Nanyang cattle [...] Read more.

Copy number variation (CNV) serves as a crucial contributor to genetic diversity, exerting a profound influence on phenotypic diversity, traits of economic significance, and the evolutionary trajectory of livestock species. This study aimed to dissect the genome-wide CNV landscape of the Nanyang cattle line (Nanyang, Pinnan, and Xianan cattle) to identify functionally relevant CNVs associated with key economic traits and breed differentiation. In this study, 27 resequencing datasets were utilized to analyze the genome-wide distribution of CNVs in three breeds of Nanyang cattle (Nanyang cattle, Pinnan cattle, and Xianan cattle) based on the latest reference genome ARS-UCD2.0. This study identified a total of 97,564 CNVs, and after merging CNVs with overlapping genomic positions, we obtained 10,349 CNV regions (CNVRs), accounting for 1.48% of the reference genome. Functional enrichment analysis showed that CNVR genes were mainly involved in organ development, neural regulation, immune regulation, and metabolism. In addition, 131 CNVRs overlapped with 81 quantitative trait loci (QTLs), such as growth and carcass QTL, multiple birth QTL, tenderness score QTL, and antal follicle number QTL. Additionally, AOX1, KRT72, and ZBTB7C were found to overlap with body weight QTLs. Furthermore, a selective sweep analysis of CNVR revealed that numerous genes (KIF26A, SPINT4, OR5W1, etc.) exhibited divergent copy numbers between breeds. Conclusively, this study facilitates comprehension of the genetic characteristics of the Nanyang cattle line at the CNV level and furnishes valuable information for the advancement of the Nanyang cattle line breeding system. Full article

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

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14 pages, 3412 KiB

Open AccessArticle

The Complete Mitochondrial Genome of Petalocephala arcuata Cai Et Kuoh, 1992 (Hemiptera: Cicadellidae: Ledrinae: Petalocephalini) and Its Phylogenetic Implications

by Yujian Li, Yihong Guo, Ran Li, Yongcheng Liu, Chao Xue, Lina Jiang, Sai Jiang, Wei Wang and Xianfeng Yi

Genes 2025, 16(5), 567; https://doi.org/10.3390/genes16050567 - 10 May 2025

Abstract

Background/Aims: Ledrinae comprises about 460 described species across five tribes and represents an early-branching, morphologically distinctive lineage of leafhoppers, yet its intra-subfamilial relationships remain ambiguous owing to limited mitogenomic sampling. Here, we sequence and annotate the complete mitochondrial genome of Petalocephala arcuata—only [...] Read more.

Background/Aims: Ledrinae comprises about 460 described species across five tribes and represents an early-branching, morphologically distinctive lineage of leafhoppers, yet its intra-subfamilial relationships remain ambiguous owing to limited mitogenomic sampling. Here, we sequence and annotate the complete mitochondrial genome of Petalocephala arcuata—only the 18th Ledrinae mitogenome—to broaden taxon coverage within the genus and furnish critical molecular data for rigorously testing Ledrinae monophyly and refining tribal and genus level phylogenetic hypotheses. Methods: In this study, we sequenced and annotated the complete mitochondrial genome of P. arcuata via Illumina sequencing and de novo assembly, and reconstructed the phylogeny of 62 Cicadellidae species using maximum likelihood and Bayesian inference methods. Results: The 14,491 bp circular mitogenome of P. arcuata contains 37 genes with 77.4% A+T. All PCGs use ATN start codons except ND5 (TTG), and codon usage is A or U biased. Of 22 tRNAs, only trnS1 lacks a DHU arm, while the others adopt the canonical cloverleaf structure. Bayesian inference and maximum likelihood analyses produced broadly congruent topologies with mostly high nodal support, recovering Ledrinae as monophyletic and clustering all Petalocephala species into a well-supported clade. Conclusions: In this study, we enriched the molecular resources for the genus Petalocephala by sequencing, annotating, and analyzing the complete mitochondrial genome of P. arcuata. Phylogenetic reconstructions based on these genomic data align closely with previous morphological diagnoses, further confirming the monophyly of the genus Petalocephala. Full article

(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)

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34 pages, 1707 KiB

Open AccessReview

Natural Bioproducts with Epigenetic Properties for Treating Cardiovascular Disorders

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

Genes 2025, 16(5), 566; https://doi.org/10.3390/genes16050566 - 10 May 2025

Abstract

Cardiovascular disorders (CVDs) are the leading cause of mortality worldwide, highlighting an urgent need for innovative therapeutic strategies. Recent advancements highlight the potential of naturally derived bioproducts with epigenetic properties to offer protection against CVDs. These compounds act on key epigenetic mechanisms, DNA [...] Read more.

Cardiovascular disorders (CVDs) are the leading cause of mortality worldwide, highlighting an urgent need for innovative therapeutic strategies. Recent advancements highlight the potential of naturally derived bioproducts with epigenetic properties to offer protection against CVDs. These compounds act on key epigenetic mechanisms, DNA methylation, histone modifications, and non-coding RNA regulation to modulate gene expression essential for cardiovascular health. This review explores the effects of various bioproducts, such as polyphenols, flavonoids, and other natural extracts, on these epigenetic modifications and their potential benefits in preventing and managing CVDs. We discuss recent discoveries and clinical applications, providing insights into the epigenetic regulatory mechanisms of these compounds as potential epidrugs, naturally derived agents with promising therapeutic prospects in epigenetic therapy for CVDs. Full article

(This article belongs to the Section Epigenomics)

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