Genes最新文献

{"title":"Whole-Genome Selective Scans Detect Genes Associated with Cashmere Traits and Climatic Adaptation in Cashmere Goats (<i>Capra hircus</i>) in China.","authors":"Hongying Dan, Hai'an Zhong, Zhanerke Akhatayeva, Kejian Lin, Songsong Xu","doi":"10.3390/genes16030292","DOIUrl":"10.3390/genes16030292","url":null,"abstract":"<p><p><b>Background:</b> Cashmere, valued for its exceptional softness and warmth, is a major focus in goat breeding due to its high economic importance. However, the molecular mechanisms underlying cashmere production remain largely unknown, hindering efforts to optimize yield and quality. Additionally, domestic goats exhibit remarkable adaptability to diverse climates, ranging from arid northern regions to humid southern areas, yet the genetic basis for these adaptations is poorly understood. Exploring the genetic factors driving cashmere production and climatic adaptation could provide crucial insights into trait evolution and support the development of breeding strategies for improved productivity and resilience. <b>Methods</b>: We utilized whole-genome resequencing data from 157 samples representing 14 goat populations to analyze the genetic diversity between cashmere and non-cashmere breeds. Additionally, we conducted the tests of selective sweeps (i.e., pairwise <i>F_ST</i>, <i>θ</i>π and XP-EHH) for cashmere traits and genome-environment association analysis (i.e., XtX statistic), respectively. <b>Results</b>: We identified strong selective signatures in previous reports (e.g., <i>AKT3</i>, <i>FOXP1</i>, <i>FGF5</i>, <i>TGFBR3</i>) and novel genes (e.g., <i>ZEB1</i>, <i>ZNRF3</i>, <i>MAPK8IP3</i>, <i>MAPK8IP2</i>, <i>AXIN1</i>) associated with cashmere traits. Further gene annotation and KEGG analyses showed that these genes were identified to be the most probable genes accounting for the cashmere traits. Also, we detected some genes such as <i>PDGFRB</i>, <i>PRDM8</i>, <i>SLC26A2</i>, <i>SCAMP1</i>, <i>EPHX1</i>, <i>CDC25A</i>, and <i>POLK</i> that played critical roles in the adaptation of goats to local climate variation. <b>Conclusions</b>: Collectively, our results provide novel insights into the genetic mechanisms underlying the cashmere traits and climatic adaptation, and also identified new genetic markers for genetic improvement in goats.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic Characterization of the <i>Maerua crassifolia</i> Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.","authors":"Sumayah M Alharbi, Nadiah Al-Sulami, Hadba Al-Amrah, Yasir Anwar, Ola A Gadah, Lina Ahmed Bahamdain, Mohammed Al-Matary, Amnah M Alamri, Ahmed Bahieldin","doi":"10.3390/genes16030285","DOIUrl":"10.3390/genes16030285","url":null,"abstract":"<p><p><b>Background/Objectives:</b><i>Maerua crassifolia</i>, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in <i>M. crassifolia's</i> rhizosphere remain underexplored. <b>Methods:</b> Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of <i>M. crassifolia</i>. <b>Results:</b> The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically <i>Rhizophagus clarus</i>, <i>Rhizophagus irregularis</i> and <i>Funneliformis geosporum</i>, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as <i>Sphingomonas</i> spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. <b>Conclusions:</b> Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of <i>M. crassifolia</i>, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DRFormer: A Benchmark Model for RNA Sequence Downstream Tasks.","authors":"Jianqi Fu, Haohao Li, Yanlei Kang, Hancan Zhu, Tiren Huang, Zhong Li","doi":"10.3390/genes16030284","DOIUrl":"10.3390/genes16030284","url":null,"abstract":"<p><p><b>Background/Objectives:</b> RNA research is critical for understanding gene regulation, disease mechanisms, and therapeutic development. Constructing effective RNA benchmark models for accurate downstream analysis has become a significant research challenge. The objective of this study is to propose a robust benchmark model, DRFormer, for RNA sequence downstream tasks. <b>Methods:</b> The DRFormer model utilizes RNA sequences to construct novel vision features based on secondary structure and sequence distance. These features are pre-trained using the SWIN model to develop a SWIN-RNA submodel. This submodel is then integrated with an RNA sequence model to construct a multimodal model for downstream analysis. <b>Results</b>: We conducted experiments on various RNA downstream tasks. In the sequence classification task, the MCC reached 94.4%, surpassing the state-of-the-art RNAErnie model by 1.2%. In the protein-RNA interaction prediction, DRFormer achieved an MCC of 0.492, outperforming advanced models like BERT-RBP and PrismNet. In RNA secondary structure prediction, the F1 score was 0.690, exceeding the widely used SPOT-RNA model by 1%. Additionally, generalization experiments on DNA tasks yielded satisfactory results. <b>Conclusions:</b> DRFormer is the first RNA sequence downstream analysis model that leverages structural features to construct a vision model and integrates sequence and vision models in a multimodal manner. This approach yields excellent prediction and analysis results, making it a valuable contribution to RNA research.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Status of SOX2 Expression in Gastric Cancers with Induction of CDX2 Defines Groups with Different Genomic Landscapes.","authors":"Ioannis A Voutsadakis","doi":"10.3390/genes16030279","DOIUrl":"10.3390/genes16030279","url":null,"abstract":"<p><strong>Background: </strong>Gastric adenocarcinoma is a highly lethal neoplasm with a short survival especially when metastatic. Few effective treatments are available for the control of the disease and palliation of patients with metastatic gastric cancer. Although progress has been made in the elucidation of molecular pathways invoked in gastric carcinogenesis, this knowledge has not yet led to major breakthroughs, in contrast to several other types of cancer. The role of stem cell transcription factors SOX2 and CDX2 is of particular interest in the pathogenesis of gastric cancer.</p><p><strong>Methods: </strong>The cohort of gastric adenocarcinomas from The Cancer Genome Atlas (TCGA) was interrogated and two groups of gastric cancers, with CDX2 induction and SOX2 suppression on the one hand and with CDX2 induction and SOX2 maintained expression on the other hand were retained. The induction of expression of the two transcription factors was defined as a mRNA expression z score compared with normal samples above zero. The two groups were compared for clinical-pathologic and genomic differences.</p><p><strong>Results: </strong>Among gastric cancers with up-regulated CDX2 mRNA, cancers with suppressed SOX2 mRNA were slightly more numerous (55.9%) than those with a maintained SOX2 expression. The SOX2 suppressed group had a higher prevalence of MSI high cancers (30.9% versus 10%) and of cases with high tumor mutation burden (35% versus 12.4%) than cancers with a SOX2 maintained expression, which presented more frequently high Chromosomal Instability (CIN). The group with SOX2 suppression had higher rates of mutations in many gastric cancer-associated genes such as epigenetic modifiers <i>ARID1A</i>, <i>KMT2D</i>, <i>KMT2C</i>, and <i>KMT2B</i>, as well as higher rates of mutations in genes encoding for receptor tyrosine kinases <i>ERBB4</i> and <i>FGFR1</i>. On the other hand, <i>TP53</i> mutations and amplifications in <i>MYC</i>, <i>ERBB2</i>, and <i>CCNE1</i> were more common in the group with a maintained expression of SOX2, approaching significance for <i>MYC</i>.</p><p><strong>Conclusions: </strong>Notable differences are present in the genomic landscape of CDX2-induced gastric cancer depending on the level of expression of SOX2 mRNA. Despite this, SOX2 mRNA expression levels were not prognostic.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First Description of Intergenic Sequences in Corydoradinae and Introducing the Complete Mitogenome of <i>Hoplisoma concolor</i> (Siluriformes: Callichthyidae).","authors":"Seong Duk Do, Jae-Sung Rhee","doi":"10.3390/genes16030282","DOIUrl":"10.3390/genes16030282","url":null,"abstract":"<p><p><b>Background/Objectives</b>: In this study, we report the complete mitochondrial genome sequence of <i>Hoplisoma concolor</i> Weitzman, 1961 (Siluriformes: Callichthyidae), a callichthyid catfish. <b>Methods</b>: DNA sequencing was performed to obtain its complete mitogenome using the HiSeq platform. To assess the phylogenetic relationships, maximum-likelihood and Bayesian inference phylogenetic trees were constructed using two ribosomal RNA (rRNA) genes and all protein-coding sequences (PCGs) concatenated from the <i>H. concolor</i> mitogenome, along with 31 other Siluriformes mitogenomes. <b>Results</b>: The complete mitogenome of <i>H. concolor</i> is 16,579 base pairs in length, with a nucleotide composition of 32.2% A, 26.0% T, 15.3% G, and 26.5% C. It contains 13 PCGs, 22 transfer RNA genes, and 2 rRNA genes. Phylogenetic analysis based on all PCGs and two rRNAs of the complete mitogenome confirms <i>H. concolor</i> as a sister species of <i>H. panda</i> within the subfamily Corydoradinae. In addition, intergenic sequences between <i>atp6</i> and <i>cox3</i> of 21 species of Corydoradinae provide further support for their phylogenetic relationship. <b>Conclusions</b>: Given the lack of detailed descriptions regarding the length and nucleotide composition of these intergenic sequences, our study contributes valuable insights into the genetic diversity and evolutionary complexity of Callichthyidae.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insight into the Characterization of Two Female Suppressor Gene Families: <i>SOFF</i> and <i>SyGI</i> in Plants.","authors":"Yanrui Zhu, Zeeshan Ahmad, Youjun Lv, Yongshan Zhang, Guodong Chen","doi":"10.3390/genes16030280","DOIUrl":"10.3390/genes16030280","url":null,"abstract":"<p><strong>Background/objectives: </strong>The Suppressor of Female Function (<i>SOFF</i>) and Shy Girl (<i>SyGI</i>) gene families play vital roles in sex determination in dioecious plants. However, their evolutionary dynamics and functional characteristics remain largely unexplored.</p><p><strong>Methods: </strong>Through this study, a systematic bioinformatics analysis of <i>SOFF</i> and <i>SyGI</i> families was performed in plants to explore their evolutionary relationships, gene structures, motif synteny and functional predictions.</p><p><strong>Results: </strong>Phylogenetic analysis showed that the <i>SOFF</i> family expanded over time and was divided into two subfamilies and seven groups, while <i>SyGI</i> was a smaller family made of compact molecules with three groups. Synteny analysis revealed that 125 duplicated gene pairs were identified in Kiwifruit where WGD/segmental duplication played a major role in duplicating these events. Structural analysis predicted that <i>SOFF</i> genes have a DUF 247 domain with a transmembrane region, while <i>SyGI</i> sequences have an REC-like conserved domain, with a \"barrel-shaped\" structure consisting of five α-helices and five β-strands. Promoter region analysis highlighted their probable regulatory roles in plant development, hormone signaling and stress responses. Protein interaction analysis exhibited only four <i>SOFF</i> genes with a close interaction with other genes, while <i>SyGI</i> genes had extensive interactions, particularly with cytokinin signal transduction pathways.</p><p><strong>Conclusions: </strong>The current study offers a crucial understanding of the molecular evolution and functional characteristics of <i>SOFF</i> and <i>SyGI</i> gene families, providing a foundation for future functional validation and genetic studies on developmental regulation and sex determination in dioecious plants. Also, this research enhances our insight into plant reproductive biology and offers possible targets for breeding and genetic engineering approaches.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential Role of <i>ABCF2</i> Gene in Pudendal Nerve Neuropathy and Interstitial Cystitis.","authors":"Antonino Musumeci, Mirella Vinci, Simone Treccarichi, Alda Ragalmuto, Giuseppe Bruno, Giordana Tinniriello, Jessica Farina, Concetta Federico, Salvatore Saccone, Francesco Calì, Daniele Porru","doi":"10.3390/genes16030281","DOIUrl":"10.3390/genes16030281","url":null,"abstract":"<p><strong>Background/objectives: </strong>Symptoms of pudendal nerve neuropathy may overlap with various symptoms of interstitial cystitis (IC). As documented, there is a well-established correlation between the genes involved in ATP metabolism, neuropathy, and IC. ATP-binding cassette (ABC) transporters genes, in fact, are vital for ATP signaling. This study aims to associate the <i>ABCF2</i> gene with a suspected pudendal nerve neuropathy and IC.</p><p><strong>Methods: </strong>Histological analysis was conducted for diagnosing IC while the genetic variant was identified by whole exome sequencing (WES) Trio and confirmed through Sanger.</p><p><strong>Results: </strong>We report a patient with IC, confirmed by histological examination, presenting with a suspected bladder and pudendal nerve neuropathy, though not analytically confirmed. Histological analysis revealed urothelial detachment caused by a dense subepithelial lymphocytic infiltrate, predominantly composed of mast cells, which serve as key diagnostic markers for interstitial cystitis (IC). WES analysis identified the heterozygous genetic variant c.1253T>G p.Phe418Cys within <i>ABCF2</i> gene, precisely in its functional domain which actively operates in the hydrolysis of ATP energizing various biological systems. As reported, this gene displays high expression patterns in bladder tissue. The variant, absent in the healthy brother, was inherited from the father which presents mosaicism. The in silico prediction analyses classified this variant as pathogenic, identifying potential alterations in the protein structure.</p><p><strong>Conclusions: </strong>Although the precise role of <i>ABCF2</i> should be supported by further studies, we hypothesize that its disruption might impair ATP metabolism, likely altering the nociceptive response and leading to the patient's neuropathy. Further analyses are imperative to validate this research, for laying the groundwork for a specific therapy targeting the genetic dysregulation involved in this condition.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of Smad2/3 Nuclear Exclusion by Follicle-Stimulating Hormone (FSH) in Chicken Follicular Granulosa Cells and Its Effect on FOXO3/4.","authors":"Yuhan Sun, Simushi Liswaniso, Hengsong Wu, Xue Sun, Chunchi Yan, Ning Qin, Rifu Xu","doi":"10.3390/genes16030283","DOIUrl":"10.3390/genes16030283","url":null,"abstract":"<p><strong>Background: </strong>This study aims to investigate the regulation of small mothers against decapentaplegic 2 and 3 (Smad2/3) protein phosphorylation and nuclear exclusion in follicular granulosa cells (GCs) by chicken follicle-stimulating hormone (FSH) through the phosphatidylinositol 3-kinase (PI3K) signaling pathway, as well as the effect of Smad2/3 proteins on forkhead box O 3 and 4 (FoxO3/4). This lays the foundation for exploring the regulatory functions of signaling pathways closely related to follicular growth and development, as well as the molecular mechanisms of subcellular localization and nuclear exclusion of various effector factors (including transcription factors).</p><p><strong>Methods: </strong>In this study, we used granulosa cells from 6-8 mm prehierachical follicles of chickens and performed immunofluorescence, quantitative real-time PCR (RT-qPCR), and Western blotting analysis to detect the phosphorylation and nuclear exclusion of Smad2/3 induced by FSH, as well as the regulatory effect of Smad2/3 on FOXO3/4 proteins.</p><p><strong>Results: </strong>The results showed that 10 ng/mL FSH and 50 μg/mL PI3K activator significantly reduced the phosphorylation level of Smad2/3 (<i>p</i> < 0.05), while no nuclear exclusion was observed. On the other hand, 16 nM/mL PI3K inhibitor and 50 μg/mL alkaline phosphatase significantly increased the phosphorylation level of Smad2/3 (<i>p</i> < 0.05). Overexpression of Smad2/3 increased the phosphorylation level of FOXO3/4 (<i>p</i> < 0.05); Smad2/3 interference resulted in a decrease in FOXO3/4 phosphorylation levels (<i>p</i> < 0.05).</p><p><strong>Conclusions: </strong>FSH can inhibit Smad2/3 phosphorylation and retain it in the nucleus through the PI3K signaling pathway. Smad2/3 and FOXO3/4 act as downstream effectors of the PI3K signaling pathway, and Smad2/3 can promote the phosphorylation of FOXO3/4.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11942245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNAs in the Mitochondria-Telomere Axis: Novel Insights into Cancer Development and Potential Therapeutic Targets.","authors":"José Alfonso Cruz-Ramos, Emmanuel de la Mora-Jiménez, Beatriz Alejandra Llanes-Cervantes, Miguel Ángel Damián-Mejía","doi":"10.3390/genes16030268","DOIUrl":"10.3390/genes16030268","url":null,"abstract":"<p><p>The mitochondria-telomere axis is recognized as an important factor in the processes of metabolism, aging and oncogenesis. <i>MicroRNAs</i> (<i>miRNAs</i>) play an essential function in this complex interaction, having an impact on aspects such as cellular homeostasis, oxidative responses and apoptosis. In recent years, <i>miRNAs</i> have been found to be crucial for telomeric stability, as well as for mitochondrial behavior, factors that influence cell proliferation and viability. Furthermore, mitochondrial <i>miRNAs</i> (<i>mitomiRs</i>) are associated with gene expression and the activity of the cGAS/STING pathway activity, linking mitochondrial <i>DNA</i> recognition to immune system responses. Hence, <i>miRNAs</i> maintain a link to mitochondrial biogenesis, metabolic changes in cancer and cellular organelles. This review focuses on the roles of a variety of <i>miRNAs</i> in cancer progression and their potential application as biomarkers or therapeutic agents.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An RB1CC1 Missense Variant in Nova Scotia Duck Tolling Retrievers with Degenerative Encephalopathy.","authors":"Juyuan Guo, Garrett Bullock, Dennis P O'Brien, Gary S Johnson, Martin L Katz","doi":"10.3390/genes16030269","DOIUrl":"10.3390/genes16030269","url":null,"abstract":"<p><strong>Background/objectives: </strong>A slowly progressive hereditary neurological disorder classified as degenerative encephalopathy (DE) occurs in Nova Scotia Duck Tolling Retrievers. The disease is characterized by frequent episodes of pronounced involuntary movements during sleep, cognitive impairment, anxiety, heightened sensitivity to sensory stimuli, and compulsive behaviors. The clinical signs are accompanied by the degeneration of several brain regions. A study was undertaken to identify the molecular genetic basis of this disorder.</p><p><strong>Methods: </strong>Whole genome sequences (WGSs) from the DNA of affected and unaffected Nova Scotia Duck Tolling Retrievers were aligned to the Dog10K_Boxer_Tasha reference genome assembly and to the WGSs of 334 additional control dogs generated by this laboratory.</p><p><strong>Results: </strong>A missense C>T variant was identified in <i>RB1CC1</i> exon 22 chromosome 29:4891014 that was uniquely homozygous in the affected dog. This variant predicts a p.G1503R change in the amino acid sequence of RB1CC1. Genotyping of 2950 Nova Scotia Duck Tolling Retrievers at the variant locus found complete concordance between the disease phenotype and <i>RB1CC1</i> genotype.</p><p><strong>Conclusions: </strong>RBCC1 is an essential component of a protein complex that mediates the initiation of autophagosome formation. Therefore, it appears likely that the disease results, at least in part, from impaired autophagy. Consistent with this possibility, brain neurons of an affected dog were found to contain abnormal lysosomal storage body-like inclusions. This disorder could serve as a valuable model to elucidate the mechanisms underlying human diseases associated with impaired autophagy. Identification of the disease-causing DNA sequence variant will enable owners of Nova Scotia Duck Tolling Retrievers to screen their dogs for the <i>RB1CC1</i> risk variant.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"16 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11941761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}