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Systematic Review: Fragile X Syndrome Across the Lifespan with a Focus on Genetics, Neurodevelopmental, Behavioral and Psychiatric Associations
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The Impact of Klotho in Cancer: From Development and Progression to Therapeutic Potential
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Genomic Rewilding of Domestic Animals: The Role of Hybridization and Selection in Wolfdog Breeds
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Neuronal Network Activation Induced by Forniceal Deep Brain Stimulation in Mice
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Chemical Evolution of Life on Earth
Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.9 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the second half of 2024).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.8 (2023);
5-Year Impact Factor:
3.3 (2023)
Latest Articles
Automated Quantitative Immunofluorescence Microscopy Approach for Diagnosis of Hereditary Thrombopathies: A Proof of Concept Using Bernard–Soulier Syndrome and Glanzmann Thrombasthenia
Genes 2025, 16(6), 621; https://doi.org/10.3390/genes16060621 (registering DOI) - 23 May 2025
Abstract
Inherited platelet disorders (IPDs) are rare bleeding disorders characterized by impaired platelet function and/or reduced blood platelet count. Their diagnosis typically relies on complex laboratory methods, including flow cytometry, aggregometry, and molecular genetic analysis. In recent years, immunofluorescence microscopy has been established as
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Inherited platelet disorders (IPDs) are rare bleeding disorders characterized by impaired platelet function and/or reduced blood platelet count. Their diagnosis typically relies on complex laboratory methods, including flow cytometry, aggregometry, and molecular genetic analysis. In recent years, immunofluorescence microscopy has been established as an alternative diagnostic method for IPDs. Background/Objectives: This study aims to validate a quantitative approach enhancing reproducibility through automated image analysis for diagnosing IPDs using immunofluorescence microscopy, with Bernard–Soulier Syndrome (BSS) and Glanzmann thrombasthenia (GT) as model IPDs. Methods: Native blood smears from patients with suspected BSS or GT were stained using a standardized immunofluorescence protocol targeting platelet surface glycoproteins, granules, and cytoskeletal components. The slides were analyzed using an automated fluorescence microscope, and a rule-based subpopulation analysis was implemented to quantify fluorescence signals. The results were compared to those of a healthy control group, as well as data from flow cytometry and molecular genetic testing. Results: The automated analysis successfully differentiated BSS and GT patients from healthy controls based on distinct fluorescence signal patterns. In BSS samples, CD42b (GPIbα) expression was absent or severely reduced, while GT samples showed a deficiency of CD41/CD61 (GPIIb/IIIa). The platelet size distribution confirmed macrothrombocytopenia in BSS patients. Flow cytometry and molecular genetic testing corroborated these findings, supporting the diagnostic reliability of the automated immunofluorescence microscopy approach. Conclusions: This proof-of-principle study demonstrates that automated quantitative immunofluorescence microscopy is a viable alternative for diagnosing IPDs, offering a standardized, objective, and efficient method, particularly in settings where flow cytometry is not feasible.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
Open AccessArticle
Colorectal Cancer Biomarker Identification via Joint DNA-Methylation and Transcriptomics Analysis Workflow
by
Olajumoke B. Oladapo and Marmar R. Moussa
Genes 2025, 16(6), 620; https://doi.org/10.3390/genes16060620 (registering DOI) - 23 May 2025
Abstract
Background: Colorectal cancer (CRC) is a term that refers to the combination of colon and rectal cancer as they are being treated as a single tumor. In CRC, 72% of tumors are colon cancer, while the other 28% represent rectal cancer. CRC
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Background: Colorectal cancer (CRC) is a term that refers to the combination of colon and rectal cancer as they are being treated as a single tumor. In CRC, 72% of tumors are colon cancer, while the other 28% represent rectal cancer. CRC is a multifactorial disease caused by both genetic and epigenetic changes in the colon mucosal cells, affecting the oncogenes, DNA repair genes, and tumor suppressor genes. Currently, two DNA methylation-based biomarkers for CRC have received FDA approval: SEPT9, used in blood-based screening tests, and a combination of NDRG4 and BMP3 for stool-based tests. Although DNA methylation biomarkers have been explored in colorectal cancer (CRC), the identification of robust and clinically valuable biomarkers remains a challenge, particularly for early-stage detection and precancerous lesions. Patients often receive diagnoses at the locally advanced stage, which limits the potential utility of current biomarkers in clinical settings. Methods: The datasets used in this study were retrieved from the GEO database, specifically GSE75548 and GSE75546 for rectal cancer and GSE50760 and GSE101764 for colon cancer, summing up to a total of 130 paired samples. These datasets represent expression profiling by array, methylation profiling by genome tiling array, and expression profiling by high-throughput sequencing and include rectal and colon cancer samples paired with adjacent normal tissue samples. Differential analysis was used to identify differentially methylated CPG sites (DMCs) and identify differentially expressed genes (DEGs). Results: From the integration of DMCs with DEGs in colorectal cancer, we identified 150 candidates for methylation-regulated genes (MRGs) with two genes common across all cohorts (GNG7 and PDX1) highlighted as candidate biomarkers in CRC. The functional enrichment analysis and protein–protein interactions (PPIs) identified relevant pathways involved in CRC, including the Wnt signaling pathway, extracellular matrix (ECM) organization, among other enriched pathways. Conclusions: Our findings show the strength of our in silco computational approach in jointly identifying methylation-regulated biomarkers for colon cancer and highlight several genes and pathways as biomarker candidates for further investigations.
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(This article belongs to the Special Issue Bioinformatics and Computational Genomics)
Open AccessReview
Genetics of Darier’s Disease: New Insights into Pathogenic Mechanisms
by
Barbara Moschella, Sabrina Busciglio, Enrico Ambrosini, Sofia Cesarini, Luca Caramanna, Sara Zanelli, Ilenia Rita Cannizzaro, Anita Luberto, Antonietta Taiani, Mirko Treccani, Erika De Sensi, Patrizia Caggiati, Cinzia Azzoni, Lorena Bottarelli, Bruno Lorusso, Costanza Anna Maria Lagrasta, Anna Montanaro, Luca Pagliaro, Raffaella Zamponi, Andrea Gherli, Davide Martorana, Michele Maria Dominici, Maria Beatrice De Felici Del Giudice, Paola Mozzoni, Enrico Maria Silini, Iria Neri, Claudio Feliciani, Giovanni Roti, Vera Uliana, Valeria Barili and Antonio Percesepeadd
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Genes 2025, 16(6), 619; https://doi.org/10.3390/genes16060619 - 23 May 2025
Abstract
Darier′s disease (DD) is a rare, autosomal dominant genodermatosis caused by pathogenic variants in the ATP2A2 gene, which encodes the SERCA2 protein, an endoplasmic reticulum ATPase Ca2+ transporter. These mutations impair the intracellular calcium homeostasis leading to increased protein misfolding, endoplasmic reticulum
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Darier′s disease (DD) is a rare, autosomal dominant genodermatosis caused by pathogenic variants in the ATP2A2 gene, which encodes the SERCA2 protein, an endoplasmic reticulum ATPase Ca2+ transporter. These mutations impair the intracellular calcium homeostasis leading to increased protein misfolding, endoplasmic reticulum (ER) stress response, and the activation of the unfolded protein response (UPR), culminating in keratinocyte apoptosis and anomalies in interfollicular epidermal stratification. Clinically, the disease is characterized by the presence of skin lesions with hyperkeratotic papules and an increased susceptibility to inflammatory reactions, bacterial and viral infections. The histological hallmarks include acantholysis, dyskeratosis, and increased apoptotic keratinocytes, referred to as “corp ronds”. The SERCA2b isoform is expressed not only in the epidermis but it is present ubiquitously in all tissues, suggesting that its alteration may have multi-organ effects. The review aims to provide a broad overview of the pathology, from intracellular dysfunction to the clinical manifestations, elucidating the molecular effects of SERCA2 variants found in DD patients and exploring the potential cell signaling pathways that may contribute to disease progression. Beginning with an examination of the cellular alterations, our work then shifts to exploring their impact in an organ-specific context, providing insights into new potential therapeutic strategies tailored to clinical manifestations.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Tuning Matters: Comparing Lambda Optimization Approaches for Ridge Regression in Genomic Prediction
by
Osval A. Montesinos-López, Eduardo A. Barajas-Ramirez, Abelardo Montesinos-López, Federico Lecumberry, María Inés Fariello, José Cricelio Montesinos-López, Juan Manuel Ramirez Alcaraz, José Crossa and Reka Howard
Genes 2025, 16(6), 618; https://doi.org/10.3390/genes16060618 - 23 May 2025
Abstract
Background/Objectives: Ridge regression (RR) is a widely used statistical learning method for predicting continuous response variables, particularly in high-dimensional contexts where the number of predictors (p) far exceeds the number of observations (n). RR is known for its simplicity,
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Background/Objectives: Ridge regression (RR) is a widely used statistical learning method for predicting continuous response variables, particularly in high-dimensional contexts where the number of predictors (p) far exceeds the number of observations (n). RR is known for its simplicity, as it depends on a single regularization hyperparameter (λ), and for its strong predictive performance, especially in genomic prediction applications. However, selecting the optimal value of λ remains a key challenge, with standard techniques such as cross-validation often being computationally intensive and potentially suboptimal in terms of predictive accuracy. Methods: To address this issue, recent studies have proposed alternative methods for tuning λ, aiming to enhance both predictive power and computational efficiency. In this study, we perform a comprehensive benchmarking analysis of two novel λ-selection strategies and compare them with traditional approaches. The evaluation was conducted across 14 real-world genomic selection datasets, covering diverse scenarios representative of practical breeding programs. Results: Our results demonstrate that the method proposed consistently outperforms conventional approaches in both prediction accuracy and computational speed. Additionally, we found that combining this method with another recent approach yields a hybrid strategy that, in some cases, delivers the best overall performance. These findings underscore the importance of carefully selecting the regularization parameter in ridge regression models and suggest that modern, data-driven tuning approaches can substantially improve model performance. Conclusions: This study contributes valuable insights into optimizing hyperparameter selection for high-dimensional prediction problems, with direct implications for genomic selection and other applications in the life sciences.
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(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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CCNE1 Gene Amplification Might Be Associated with Lymph Node Metastasis of Gastric Cancer
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Hinano Nishikubo, Kyoka Kawabata, Tomoya Sano, Saki Kanei, Rika Aoyama, Dongheng Ma, Daiki Imanishi, Takashi Sakuma, Koji Maruo, Yurie Yamamoto, Canfeng Fan and Masakazu Yashiro
Genes 2025, 16(6), 617; https://doi.org/10.3390/genes16060617 - 22 May 2025
Abstract
Background: Lymph node (LN) metastasis is one of the most frequent metastatic patterns in patients with gastric cancer (GC); however, few genes predictive of LN status in GC have been identified. Aims: We aimed to identify candidate genes associated with LN
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Background: Lymph node (LN) metastasis is one of the most frequent metastatic patterns in patients with gastric cancer (GC); however, few genes predictive of LN status in GC have been identified. Aims: We aimed to identify candidate genes associated with LN metastasis by analyzing the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database and performing immunohistochemical analysis of GC cases at our hospital. Patients and Methods: A total of 2028 GCs from the C-CAT database were enrolled to identify genetic alterations. A total of 360 GC patients who underwent gastrectomy at our hospital were enrolled to examine the clinical significance of CCNE1 expression via an immunohistochemical study. Results: A total of 977 cases out of 2028 GC patients showed LN metastasis. Genetic alterations of ERBB2, CCNE1, MYC, ZNF217, and GNAS were frequent in the LN metastasis group. CCNE1-positive expression was found in 108 (30.0%) of the 360 GC samples. LN metastasis was significantly (p = 0.01) more frequent in CCNE1-positive patients. In addition, the CCNE1-positive group had a significantly (p < 0.001) poorer prognosis than the CCNE1-negative group, which was especially evident for GC patients at stage I. CCNE1 positivity was significantly (p < 0.001) correlated with postoperative recurrence. Conclusions: CCNE1 gene amplification is associated with LN metastasis of GC.
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(This article belongs to the Special Issue Bioinformatics and Computational Biology for Cancer Prediction and Prognosis, 2nd Edition)
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Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Lithocarpus Species (Fagaceae) in South China
by
Shi Shi, Ziyan Zhang, Xinhao Lin, Linjing Lu, Keyi Fu, Miaoxin He, Shiou Yih Lee, Hui Yin and Jingwei Yu
Genes 2025, 16(6), 616; https://doi.org/10.3390/genes16060616 - 22 May 2025
Abstract
Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights
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Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus.
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(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)
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The Association Between Dexmedetomidine and Bradycardia: An Analysis of FDA Adverse Event Reporting System (FAERS) Data and Transcriptomic Profiles
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Robert Morris, Suguna Aishwarya Kuppa, Xinran Zhu, Kun Bu, Weiru Han and Feng Cheng
Genes 2025, 16(6), 615; https://doi.org/10.3390/genes16060615 - 22 May 2025
Abstract
Background/Objectives: Bradycardia, an uncharacteristically low heart rate below 60 bpm, is a commonly reported adverse drug event (ADE) in individuals administered dexmedetomidine for sedation. Dexmedetomidine is frequently used as a sedative and analgesic for both intubated and non-intubated patients due to its low
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Background/Objectives: Bradycardia, an uncharacteristically low heart rate below 60 bpm, is a commonly reported adverse drug event (ADE) in individuals administered dexmedetomidine for sedation. Dexmedetomidine is frequently used as a sedative and analgesic for both intubated and non-intubated patients due to its low risk of respiratory depression. The purpose of this study was to further characterize the safety profile of dexmedetomidine using safety reports collected from the FDA Adverse Event Reporting System (FAERS) and transcriptomic data. Methods: Association rule mining was used to both identify additional ADEs that presented concurrently with bradycardia in patients sedated with dexmedetomidine, as well as to characterize potential drug–drug interactions (DDIs). Furthermore, public transcriptomic data were analyzed to identify differentially expressed genes that may elucidate the genetic drivers of elevated bradycardia risk in those administered dexmedetomidine. Results: Bradycardia was the most frequently reported ADE for individuals administered dexmedetomidine. Other cardiovascular-related ADEs commonly associated with bradycardia included syncope (lift = 4.711), loss of consciousness (lift = 3.997), cardiac arrest (lift = 2.850), and hypotension (lift = 2.770). Several possible DDIs were identified, including Lactated Ringer’s solution (lift = 5.441), bupivacaine (lift = 2.984), and risperidone (lift = 2.434), which may elevate bradycardia risk. Finally, eight genes related to cardiac muscle contraction were identified as possible regulators of dexmedetomidine-induced bradycardia, including COX5B, COX6A2, COX8B, MYH7, MYH6, MYL2, UQCRQ, and UQCR11 in mouse cardiac cells. Conclusions: Key clinical takeaways include the co-presentation of multiple cardiovascular ADEs, including cardiac arrest, hypotension, and syncope, alongside dexmedetomidine-associated bradycardia. Furthermore, several possible DDIs with dexmedetomidine were also identified.
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(This article belongs to the Section Bioinformatics)
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Open AccessReview
Psychosocial Factors Involved in Genetic Testing for Rare Diseases: A Scoping Review
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Samantha Strasser, Isabella R. McDonald, Melissa K. Uveges, Sharlene Hesse-Biber, Jordan Keels, Neil Smith and Andrew A. Dwyer
Genes 2025, 16(6), 614; https://doi.org/10.3390/genes16060614 - 22 May 2025
Abstract
Background/Objectives: Rare diseases are predominantly genetic in etiology and characterized by a prolonged ‘diagnostic odyssey’. Advances in genetic testing (GT) have helped shorten the time to diagnosis for rare/undiagnosed conditions. We aimed to synthesize the evidence on psychosocial factors related to GT
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Background/Objectives: Rare diseases are predominantly genetic in etiology and characterized by a prolonged ‘diagnostic odyssey’. Advances in genetic testing (GT) have helped shorten the time to diagnosis for rare/undiagnosed conditions. We aimed to synthesize the evidence on psychosocial factors related to GT for rare diseases to inform more person-centered approaches to care. Methods: We conducted a systematic literature search in six databases using structured terms (September 2024). Retrieved articles underwent independent dual review. Data were extracted and collated in tables for analysis. Thematic analysis was used to identify promoters/barriers to GT for patients and families. Findings were validated by a patient advocate and were reported using PRISMA-ScR guidelines. Synthesized findings were mapped to the Theory of Planned Behavior to inform intervention development. Results: Of 1730 retrieved articles, 32 were included for data extraction/synthesis. Studies employed qualitative (n = 19), quantitative (n = 10), and mixed-methods (n = 3) approaches. Nearly all (29/32, 91%) were non-interventional, reporting on decision-making cognitions/processes (19/32, 59%), attitudes/preferences (15/32, 47%), psychosocial impact (6/32, 19%), and knowledge/awareness (4/32, 8%) of pre-conception/prenatal/diagnostic GT and carrier screening. Promoters included understanding GT, ending the diagnostic odyssey, actionable outcomes, personal/family history, altruism, and reproductive decision-making. Barriers included logistical (e.g., distance, cost), psychological burden, perceived lack of benefit, and discrimination/social stigma concerns. Conclusions: Some psychosocial factors related to GT for rare diseases overlap with those in literature on GT for common conditions. Identified factors represent targets for theory-informed, person-centered interventions to support high-quality GT decisions that are informed and aligned with patient/family values and preferences.
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(This article belongs to the Special Issue Genetic Counseling, Genomics, Genetic Education)
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Heterorhabditis bacteriophora Extracellular Vesicles Alter the Innate Immune Signaling in Drosophila melanogaster
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Duarte Toubarro, Eric Kenney, Christa Heryanto, Sreeradha Mallick, Nelson Simões and Ioannis Eleftherianos
Genes 2025, 16(6), 613; https://doi.org/10.3390/genes16060613 - 22 May 2025
Abstract
Background: Heterorhabditis bacteriophora entomopathogenic nematodes are commonly used in agricultural practices for the biological control of insect pests. These parasites are also used in basic research for unveiling the molecular basis of nematode parasitism in relation to the insect anti-nematode response. We
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Background: Heterorhabditis bacteriophora entomopathogenic nematodes are commonly used in agricultural practices for the biological control of insect pests. These parasites are also used in basic research for unveiling the molecular basis of nematode parasitism in relation to the insect anti-nematode response. We have recently shown that H. bacteriophora excreted–secreted products reduce the expression of the antimicrobial peptide gene Diptericin in Drosophila melanogaster, which increases fly mortality due to enhanced propagation of the mutualistic bacteria Photorhabdus luminescens. However, the effect of entomopathogenic nematode extracellular vesicles (EVs) on the insect host defense remains unknown. Methods: Here, we injected adult flies with H. bacteriophora EVs and used quantitative RT-PCR together with gene-specific primers to analyze the activity of immune-related signaling pathways. Results: We found that H. bacteriophora EVs are lethal to Drosophila melanogaster, and they downregulate the expression of Attacin, Cecropin, and Prophenoloxidase 3 in adult flies. Conclusions: These findings build on previous knowledge and strengthen the notion that H. bacteriophora entomopathogenic nematodes release a variety of effector molecules to modify the insect’s innate immune signaling. This information is important because it contributes toward clarifying the molecular interplay between entomopathogenic nematode components and the host’s innate immune system.
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(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)
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Molecular Genomics of Oral Submucous Fibrosis: A Narrative Review
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Vasileios Zisis, Stefanos Zisis, Christina Charisi, Konstantinos Poulopoulos, Aristeidis Sarkisian and Athanasios Poulopoulos
Genes 2025, 16(6), 612; https://doi.org/10.3390/genes16060612 - 22 May 2025
Abstract
Background: Oral Submucous Fibrosis (OSMF) is a chronic, progressive condition characterized by the fibrosis of the oral mucosa, often associated with the habitual consumption of areca nut and tobacco, leading to significant morbidity. Despite its prevalent occurrence in many parts of the world,
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Background: Oral Submucous Fibrosis (OSMF) is a chronic, progressive condition characterized by the fibrosis of the oral mucosa, often associated with the habitual consumption of areca nut and tobacco, leading to significant morbidity. Despite its prevalent occurrence in many parts of the world, the underlying genetic and molecular mechanisms remain poorly understood, highlighting a critical need for research into its molecular genomics. The aim of this literature review is to investigate the molecular genomics of Oral Submucous Fibrosis by analyzing the relevant literature of the past decade. Methods: The search was conducted using MEDLINE (National Library of Medicine)-PubMed, focusing on the period 2015–2025 using the following keywords: Molecular Genomics AND Oral Submucous Fibrosis. This was followed by a manual search, and references were used to identify relevant articles. Results: A total of 12 articles were included in our review according to our inclusion criteria, which illustrated the importance of TGF-β, Wnt inhibitory factor-1, CypA, Hsp-70 1B, Calreticulin, Lumican, Enolase 1, MMP-2, IGF-1R, XIST, Epigallocatechin-3-gallate, Von Hippel-Lindau, and MUC1 and 4. Conclusions: Understanding the molecular pathogenesis of OSMF involves examining the molecular interactions and the roles of specific proteins. Advanced genomic technologies have opened new frontiers in the study of OSMF. As research in OSMF continues to evolve, emerging interdisciplinary approaches may provide therapeutic strategies, aiming to improve management outcomes for the patients.
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(This article belongs to the Section Molecular Genetics and Genomics)
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The Complete Chloroplast Genome of Idesia polycarpa and Comparative Analysis of Related Species
by
Xueqian Fu, Jie Luo, Yuan Guo, Dalan Feng, Yifei Deng, Mi Kuang, Houlin Zhou, Xia Liu and Chong Sun
Genes 2025, 16(5), 611; https://doi.org/10.3390/genes16050611 - 21 May 2025
Abstract
Background/Objectives: The oil grape (Idesia polycarpa), often called the “golden tree”, is an essential woody plant valued for its edible oil. Although its economic significance is recognized, the specifics of its chloroplast genome and evolutionary connections remain unclear. This study sequenced
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Background/Objectives: The oil grape (Idesia polycarpa), often called the “golden tree”, is an essential woody plant valued for its edible oil. Although its economic significance is recognized, the specifics of its chloroplast genome and evolutionary connections remain unclear. This study sequenced the chloroplast genome of I. polycarpa and performed a comparative analysis of its genome structure, genetic diversity, and phylogenetics using chloroplast data from related species. Methods: In this study, we sequenced and annotated the whole chloroplast genome of I. polycarpa via GISEQ-500 sequencing and de novo assembly. Results: The chloroplast genome of I. polycarpa exhibits a typical tetrad structure, with a length of 155,899 bp and a GC content of 36.78%. It comprises 130 unique genes, including 85 coding genes, 37 tRNAs, and eight rRNAs, showing notable conservation in gene composition and arrangement compared to closely related species. However, the inverted repeat region boundaries are narrower. Phylogenetic analysis showed strong relationships among I. polycarpa, Bennettiodendron brevipes, Poliothyrsis sinensis, Itoa orientalis, and Carrierea calycina within the Salicaceae family. Additionally, positive selection analysis revealed that rpl16, ycf1, rps18, and rpl22 are under significant selective pressure in related species, likely linked to adaptations for photosynthesis and environmental responses. Conclusions: This research provides vital molecular foundations for the conservation, classification, and enhancement of I. polycarpa germplasm resources, advancing the study of adaptive evolutionary mechanisms and broadening the genomic database for I. polycarpa.
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(This article belongs to the Section Plant Genetics and Genomics)
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Isolation and Activity Evaluation of Callus-Specific Promoters in Rice (Oryza sativa L.)
by
Xiaojiao Ma and Chuanyin Wu
Genes 2025, 16(5), 610; https://doi.org/10.3390/genes16050610 - 21 May 2025
Abstract
Background/Objectives: In crop genetic engineering, morphogenic genes have attracted increasing attention, given their ability to facilitate the transformation of a broad range of otherwise nontransformable cultivars. However, few callus-specific promoters have been identified to date that can be employed to avoid the adverse
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Background/Objectives: In crop genetic engineering, morphogenic genes have attracted increasing attention, given their ability to facilitate the transformation of a broad range of otherwise nontransformable cultivars. However, few callus-specific promoters have been identified to date that can be employed to avoid the adverse effects resulting from the ectopic expression of morphogenic genes on shoot regeneration and growth. Methods: A set of potential callus-specific genes were initially selected based on publicly available data. These genes were then screened using quantitative real-time polymerase chain reaction (qPCR), followed by promoter activity evaluation using a transgenic approach with the GUS gene serving as a reporter. Results: Of the 24 evaluated promoters, 12 were verified as being callus-specific using qPCR. Five genes (Os11g0295900, Os10g0207500, Os01g0300000, Os02g0252200, and Os04g0488100) were chosen, and their promoters were cloned. Based on GUS staining, the pOsTDL1B (Os10g0207500) promoter showed strong callus-specific expression, pOsEDC (Os01g0300000) was a medium-level callus-specific promoter, and pOsDLN53 (Os02g0252200) was strictly callus-specific, although its activity was low. Quantification of GUS activity indicated that all three pOsTDL1B:GUS transgenic lines exhibited strong callus specificity relative to the various tissues tested. Conclusions: A callus-specific promoter was identified that can be used to drive the expression of morphogenic genes in crop transformation.
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(This article belongs to the Topic Genetic Engineering in Agriculture)
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Functional and Bioinformatic Analysis of PDX2 from Ginkgo biloba
by
Yifan Xiao, Zhi Feng, Zhi Yao, Hailan Jiang, Yiqiang Wang and Meng Li
Genes 2025, 16(5), 609; https://doi.org/10.3390/genes16050609 - 21 May 2025
Abstract
Background: The PDX2 gene serves as a critical catalytic component in vitamin B6 (VB6) biosynthesis pathways and plays pivotal regulatory roles in plant growth. Methods: To investigate the metabolic regulation of PDX2 (GbPDX2) from Ginkgo biloba in VB6 biosynthesis
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Background: The PDX2 gene serves as a critical catalytic component in vitamin B6 (VB6) biosynthesis pathways and plays pivotal regulatory roles in plant growth. Methods: To investigate the metabolic regulation of PDX2 (GbPDX2) from Ginkgo biloba in VB6 biosynthesis during kernel development, we successfully cloned this gene and conducted systematic expression profiling through qRT-PCR across multiple tissues and developmental stages. Results: Bioinformatic characterization revealed that GbPDX2 contains a 765-bp coding sequence encoding a 254-amino acid polypeptide. The encoded protein displays typical hydrophilic properties (average hydrophobicity index: −0.32) and was predicted to be an unstable cytosolic protein (instability index: 45.7) lacking signal peptides or transmembrane domains with cytoplasmic localization. Phylogenetic analysis demonstrated that GbPDX2’s closest evolutionary relationship was with its ortholog in Picea sitchensis, which had an amino acid sequence similarity of 83.7% with spruce PsPDX2. Tissue-specific expression analysis revealed a gradient expression profile of Kernel > Exocarp > Leaves > Stems > Roots. The expression level in kernels was significantly higher than that in other tissues (19.7 times that in roots, 8.3 times that in stems, and 5.9 times that in leaves; p < 0.01), with peak transcript levels observed in mature kernels. HPLC quantification established a strong positive correlation between GbPDX2 expression dynamics and VB6 accumulation patterns during kernel maturation (r = 0.92, p < 0.01), and the peak period of VB6 reached 288.9 ± 7.1 μg/g. Conclusions: Our findings provide the first experimental evidence that GbPDX2 spatiotemporally regulates VB6 biosynthesis in ginkgo kernels, offering novel insights into the evolutionary adaptation of vitamin metabolism in gymnosperms.
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(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)
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Analysis of Codon Usage Bias of 30 Chloroplast Genomes in Ulva (Ulvophyceae, Chlorophyta)
by
Jiao Fang, Liming Qin, Hongni Liu and Zhangfeng Hu
Genes 2025, 16(5), 608; https://doi.org/10.3390/genes16050608 - 21 May 2025
Abstract
Background: Ulva is a globally distributed genus with ecological and economic significance, yet the codon usage bias of the Ulva chloroplast genome remains poorly understood. Methods: We assessed the Ulva chloroplast genome codon usage patterns and their drivers by analyzing 30 genomes across
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Background: Ulva is a globally distributed genus with ecological and economic significance, yet the codon usage bias of the Ulva chloroplast genome remains poorly understood. Methods: We assessed the Ulva chloroplast genome codon usage patterns and their drivers by analyzing 30 genomes across 16 Ulva species. Results: The nucleotide composition analysis demonstrated that Ulva chloroplast genomes are rich in A/T, and prefer to use codons that ended with A/T. The relative synonymous codon usage analysis suggested that related species have similar codon usage patterns. A total of 25 high-frequency codons and 7–14 optimal codons were identified in these chloroplast genomes. The ENC values ranged from 31.40 to 32.76, all of which are less than 35, illustrating a strong codon bias of the Ulva genus. Our comparative analyses suggested that natural selection played the main role in the formation of the codon usage bias. Furthermore, the correlation analysis indicated that an influence of the base composition and gene expression levels on the codon usage bias. Conclusions: This study provides the first comprehensive analysis of the codon usage patterns in Ulva chloroplast genomes, improving our understanding of the genetics and evolution of these economically and ecologically important macroalgae.
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(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)
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Open AccessArticle
Comparative Analysis of the Genetic Composition of Minorities in the Carpathian Basin Through Genome-Wide Autosomal Data
by
András Szabó, Katalin Sümegi, Zsolt Bánfai, Kinga Hadzsiev, Ferenc Gallyas, Attila Miseta, Miklós Kásler and Béla Melegh
Genes 2025, 16(5), 607; https://doi.org/10.3390/genes16050607 - 21 May 2025
Abstract
Background/Objectives: The Carpathian Basin is a genetically and culturally diverse region shaped by complex historical migrations and various ethnic groups. While studies based on Y-chromosomal and mitochondrial DNA have provided valuable insights into the genetic diversity of these populations, genome-wide autosomal SNP data
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Background/Objectives: The Carpathian Basin is a genetically and culturally diverse region shaped by complex historical migrations and various ethnic groups. While studies based on Y-chromosomal and mitochondrial DNA have provided valuable insights into the genetic diversity of these populations, genome-wide autosomal SNP data remain underutilized in understanding the genetic structure of these groups. This study presents the first genome-wide autosomal SNP-based analysis of key Hungarian-speaking ethnic groups in the region, focusing on admixture patterns and the extent of preserved historical genetic components. Methods: We analyzed genome-wide autosomal SNP data from 597 individuals representing several ethnic groups in the Carpathian Basin. Standard population genetic methods were applied to assess genetic structure, admixture and differentiation, with comparisons to broader European reference populations. Results: Most ethnic groups displayed genetic affinities with Eastern European populations, consistent with historical and geographical proximity. The Swabian group, of German descent, exhibited a distinct Western European genetic component, likely due to historical isolation. Transylvanian populations appeared relatively homogeneous, indicating a shared ancestral background. In contrast, Csangos showed distinct sub-clusters, suggesting population isolation and distinct histories. Overall, genetic homogeneity characterizes the region, though certain isolated groups retain distinct ancestral signatures. Conclusions: Autosomal SNP analysis revealed mild overall genetic structuring among Carpathian Basin ethnic groups. However, historical isolation has preserved unique genetic components in specific groups, highlighting the value of genome-wide data in uncovering fine-scale population structure. These findings contribute to a deeper understanding of regional genetic diversity, which has implications for both population history and health-related genetic research.
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(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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Open AccessArticle
Deciphering the First Mitochondrial Genome of the Liolophura Pilsbry, 1893 Genus: An Extensive Phylogenetic Study Within the Chitonidae Family
by
Qianqian Zhou, Zhiyong Liu, Weifeng Dong, Bingpeng Xing, Site Luo and Peng Xiang
Genes 2025, 16(5), 606; https://doi.org/10.3390/genes16050606 - 20 May 2025
Abstract
Background: The Polyplacophora class, which includes all chitons, is distinguished by its unique eight-piece interlocking armor, showcasing a vast diversity in marine environments. However, the detailed evolutionary relationships within the Chitonidae family remain largely unknown. The mitochondrial genome is essential for understanding
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Background: The Polyplacophora class, which includes all chitons, is distinguished by its unique eight-piece interlocking armor, showcasing a vast diversity in marine environments. However, the detailed evolutionary relationships within the Chitonidae family remain largely unknown. The mitochondrial genome is essential for understanding these relationships, but there has been a significant lack of such genomic information, especially for the Liolophura genus. Methods: We generated the first mitogenome of Liolophura japonica by assembling Illumina reads with GetOrganelle, polishing with Pilon, annotating genes with MitoZ and MITOS2, and inferring phylogeny from 13 concatenated protein-coding genes (PCGs) using MAFFT and IQ-TREE. Results: The mitogenome is 15,209 base pairs long and includes 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The mitogenome exhibited a slight AT bias common in Chitonidae and showcased structural uniqueness with no control region found. Notably, all protein-coding genes demonstrated evidence of purifying selection, with Ka/Ks ratios below 1, highlighting evolutionary conservation. Phylogenetic analysis reveals a close relationship between L. japonica, Acanthopleura loochooana Broderip & Sowerby 1829, and Acanthopleura vaillantii Rochebrune, 1882, potentially warranting future taxonomic re-evaluation. This research emphasizes the crucial role of mitochondrial genomes in mollusk phylogeny and sets the stage for advanced genetic studies within this group. Conclusions: The significance of this study lies in its contribution to understanding the mitochondrial genome of L. japonica, a key species within the Polyplacophora class. By analyzing its mitogenome, we aim to enhance our understanding of evolutionary processes in chitons and other mollusks.
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(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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Open AccessArticle
Systems Genetics Reveals the Gene Regulatory Mechanisms of Arrb2 in the Development of Autism Spectrum Disorders
by
Junyu Xia, Akhilesh K. Bajpai, Yamei Liu, Lele Yu, Yating Dong, Feng Li, Fuxue Chen, Lu Lu and Shini Feng
Genes 2025, 16(5), 605; https://doi.org/10.3390/genes16050605 - 20 May 2025
Abstract
Background: Autism spectrum disorder (ASD) involves complex interactions between genetic and environmental factors. Recent studies suggest that dysregulation of β-arrestin2 (Arrb2) in the central nervous system is linked to ASD. However, its specific mechanisms remain unknown. Methods: This study employs a
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Background: Autism spectrum disorder (ASD) involves complex interactions between genetic and environmental factors. Recent studies suggest that dysregulation of β-arrestin2 (Arrb2) in the central nervous system is linked to ASD. However, its specific mechanisms remain unknown. Methods: This study employs a systems genetics approach to comprehensively investigate Arrb2 in multiple brain tissues, including the amygdala, cerebellum, hippocampus, and prefrontal cortex, using BXD recombinant inbred (RI) strains. In addition, genetic variance analysis, correlation analysis, expression quantitative trait loci (eQTL) mapping, and functional annotation were used to identify the key downstream targets of Arrb2, validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blotting (WB). Results: Arrb2 exhibited expression variations across the four brain regions in BXD mice. eQTL mapping revealed that Arrb2 is cis-regulated, and increased Arrb2 expression levels were significantly correlated with ASD-like symptoms, such as impaired social interactions and abnormal learning and memory. Furthermore, protein–protein interaction (PPI) network analysis, tissue correlation, functional relevance to autism, and differential expression identified eight downstream candidate genes regulated by Arrb2. The experimental results demonstrated that deletion of Arrb2 led to the downregulation of Myh9, Dnmt1, and Brd4 expression, along with protein kinase A (PKA)-induced hyperactivation of Synapsin I. These findings suggest that Arrb2 may contribute to the pathogenesis of autism by modulating the expression of these genes. Conclusions: This study highlights the role of Arrb2 in ASD pathogenesis and identifies Myh9, Dnmt1, and Brd4 as key downstream regulators. These findings provide new insights into the molecular mechanisms of ASD and pave the way for novel therapeutic targets.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Multimorbidity Through the Lens of the Eye: Pathogenic Variants for Multiple Systemic Disorders Found in an Autosomal Dominant Congenital Cataract Cohort
by
Vanita Berry, Manav B. Ponnekanti, Nancy Aychoua, Alex Ionides, Chrysanthi Tsika, Roy A. Quinlan and Michel Michaelides
Genes 2025, 16(5), 604; https://doi.org/10.3390/genes16050604 - 20 May 2025
Abstract
Background: This paper will identify the potential genetic causes of multimorbidity associated with autosomal dominant congenital cataract (ADCC). Methods: Whole exome sequencing (WES) was performed on 13 individuals affected with ADCC. Subsequent bioinformatic analyses identified variants with deleterious pathogenicity scores. Results: Disease-causing variants
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Background: This paper will identify the potential genetic causes of multimorbidity associated with autosomal dominant congenital cataract (ADCC). Methods: Whole exome sequencing (WES) was performed on 13 individuals affected with ADCC. Subsequent bioinformatic analyses identified variants with deleterious pathogenicity scores. Results: Disease-causing variants were identified in 8 genes already linked to cataract (CHMP4B, CRYAA, CRYBA1, CRYGD, CYP21A2, GJA8, OPA1, and POMGNT1), but variants previously associated with systemic disorders were also found in a further 11 genes (ACTL9, ALDH18A1, CBS, COL4A3, GALT, LRP5, NOD2, PCK2, POMT2, RSPH4A, and SMO). All variants were identified via pipeline data analysis, prioritising rare coding variants using Kaviar and the Genome Aggregation Database. The following ADCC-associated non-ocular phenotypes were identified in four patients in the cohort: (i) Horner’s pupils, vaso-vagal syncope, and paroxysmal orthostatic tachycardia syndrome; (ii) reduced kidney function and high cholesterol; (iii) hypertension, high cholesterol, and kidney stones; and (iv) grade 1 spondylolysis. Conclusions: We report 11 novel genes identified in an ADCC patient cohort associated with systemic disorders found, along with 8 known cataract-causing genes. Our findings broaden the spectrum of potentially cataract-associated genes and their related lens phenotypes, as well as evidence multimorbidities in four patients, highlighting the importance of careful multisystem phenotyping following genetic analysis.
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(This article belongs to the Special Issue Advances in Medical Genetics)
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Case Study: Genetic and In Silico Analysis of Familial Pancreatitis
by
Yash Sharma and Deborah J. Good
Genes 2025, 16(5), 603; https://doi.org/10.3390/genes16050603 - 20 May 2025
Abstract
Background/Objectives: Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes
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Background/Objectives: Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes that break down macromolecules. When these digestive enzymes do not function properly, maldigestion, malabsorption, and malnutrition may result. Presented here is a case study of an individual newly diagnosed with chronic pancreatitis, along with a genetic analysis of his son and an in-silico analysis of two of the variant proteins. Methods: This study was conducted using human subjects, namely, the proband (father) and his son. Medical genetic testing of the proband (father) identified the presence of two variants in the cystic fibrosis transmembrane receptor gene (CFTR): variant rs213950, resulting in a single amino acid change (p. Val470Met), and variant rs74767530, a nonsense variant (Arg1162Ter) with known pathogenicity for cystic fibrosis. Medical testing also revealed an additional missense variant, rs515726209 (Ala73Thr), in the CTRC gene. Cheek cell DNA was collected from both the proband and his son to determine the inheritance pattern and identify any additional variants. A variant in the human leukocyte antigen (rs7454108), which results in the HLA-DQ8 haplotype, was examined in both the proband and his son due to its known association with autoimmune disease, a condition also linked to chronic pancreatitis. In silico tools were subsequently used to examine the impact of the identified variants on protein function. Results: Heterozygosity for all variants originally identified through medical genetic testing was confirmed in the proband and was absent in the son. Both the proband and his son were found to have the DRB1*0301 (common) haplotype for the HLA locus. However, the proband was also found to carry a linked noncoding variant, rs2647088, which was absent in the son. In silico analysis of variant rs213950 (Val470Met) in CFTR and rs515726209 (Ala73Thr) in CTRC revealed distinct changes in predicted ligand binding for both proteins, which may affect protein function and contribute to the development of CP. Conclusions: This case study of a proband and his son provides additional evidence for a polygenic inheritance pattern in CP. The results also highlight new information on the role of the variants on protein function, suggesting additional testing of ligand binding for these variants should be done to confirm the functional impairments.
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(This article belongs to the Special Issue Molecular Discoveries, Clinical Diagnostics, and Personalized Treatments for Human Genetic Diseases)
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Open AccessArticle
Unraveling the Transcriptomic Profiles of Large and Small Donkey Follicles
by
Yanping Wang, Zihao Gao, Qiang Zhang, Xuchuan Guo, Wei Xia, Xinli Gu and Weibin Zeng
Genes 2025, 16(5), 602; https://doi.org/10.3390/genes16050602 - 20 May 2025
Abstract
Background: The diameter of mature follicles in donkeys is several times larger than in cattle and sheep, but the key genes responsible for maintaining follicular development and preventing apoptosis remain unclear. Methods: This study observed the process of donkey follicular development using ultrasound
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Background: The diameter of mature follicles in donkeys is several times larger than in cattle and sheep, but the key genes responsible for maintaining follicular development and preventing apoptosis remain unclear. Methods: This study observed the process of donkey follicular development using ultrasound and analyzed the changes in common reproductive hormones in serum. Granulosa cells (GCs) were collected from large (mature follicles, diameter ≥ 37 mm) and small (atretic follicles, diameter 10–25 mm) follicles for sequencing to screen differentially expressed genes (DEGs) and signaling pathways influencing the development of mature follicles. The roles of selected genes were further validated in in vitro cultured GCs. Results: Donkey follicles exhibited rapid growth 5–7 days before ovulation, reaching maturity at a diameter of 37 mm. The maximum diameter of ovulatory follicles was approximately 40.7 mm, while non-ovulatory follicles began to undergo atresia when reaching about 25 mm. Serum reproductive hormone levels aligned with follicular developmental status. RNA sequencing identified 3291 DEGs between large and small follicles, with KEGG analysis highlighting enrichment in the PI3K-Akt signaling pathway, focal adhesion, amoebiasis, and cancer pathways. Lentiviral overexpression and interference assays targeting the DEGs EMCN and SYT12 revealed that EMCN positively regulates FOXO3, a key gene in the PI3K-Akt pathway. Conclusions: The EMCN gene in mature donkey follicles regulates FOXO3 in the PI3K-Akt signaling pathway, potentially inhibiting apoptosis in follicular granulosa cells and sustaining follicular development until ovulation. This study provides insights into the mechanisms underlying follicular development in donkeys.
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(This article belongs to the Section Animal Genetics and Genomics)
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