Mammalian Genome最新文献

{"title":"Complement in brain and eye disease: shared mechanisms, convergent pathologies, and common therapeutic opportunities.","authors":"Jacqui Nimmo, Matthew Bright, Zhizhong Yang, Laura Elisabeth Nicholls, Bryan Paul Morgan, Nikoleta Daskoulidou, Wioleta Milena Zelek","doi":"10.1007/s00335-026-10199-3","DOIUrl":"10.1007/s00335-026-10199-3","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"33"},"PeriodicalIF":2.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12868058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"m5c-modified LINC01094 participates in epithelial-mesenchymal transition and metastasis of cervical cancer cells via the ZNF582-SIRT1/p53 axis.","authors":"Xia Lu, Lili Yao, Xu Xu, Mayinuer Guli Rexiti, Xiaoli He, Yanyan Yang","doi":"10.1007/s00335-026-10200-z","DOIUrl":"10.1007/s00335-026-10200-z","url":null,"abstract":"<p><p>Cervical cancer (CC) remains a significant global health burden despite advances in prevention and screening. Emerging evidence highlights the critical role of long non-coding RNAs (lncRNAs) and RNA modifications in tumorigenesis. Here, we identified LINC01094 as a highly expressed lncRNA in CC through TCGA analysis and clinical specimens. Functional studies, including CCK-8 method, flow cytometry, Transwell and Western blot assays, demonstrated that LINC01094 knockdown suppressed cell proliferation, migration, and epithelial-mesenchymal transition while promoting apoptosis in CC cells (Caski and SiHa). Mechanistically, NSUN2-mediated 5-methylcytosine methylation stabilized LINC01094, enhancing its expression in CC. Furthermore, LINC01094 facilitated ZNF582-dependent transcriptional activation of SIRT1, promoted the deacetylation and degradation of p53. Rescue experiments confirmed that ectopic expression of either LINC01094 or SIRT1 reversed the tumor-suppressive effects of NSUN2 or LINC01094 knockdown, respectively. Collectively, NSUN2-mediated stabilization of LINC01094 upregulated SIRT1 expression, thereby suppressing the p53 pathway and accelerating CC progression. These findings uncover a novel NSUN2/LINC01094/SIRT1 axis as an epigenetic-transcriptional driver of CC, offering potential therapeutic targets.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"32"},"PeriodicalIF":2.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide in-silico identification and characterization of LTR retrotransposons in domestic goat (Capra hircus).","authors":"Beenish Ishtiaq, Fiaz Khan, Faisal Nouroz, Shumaila Noreen","doi":"10.1007/s00335-025-10175-3","DOIUrl":"https://doi.org/10.1007/s00335-025-10175-3","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"31"},"PeriodicalIF":2.7,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Candidate genes related to growth and milk production in three Anatolian goats revealed by GWAS.","authors":"Eymen Demir, Umit Bilginer, Huriye Doğru, Burak Karacaören, Hasan Meydan, Zeynep Çiftçi, Serdar Yağci, Sarp Kaya, Taki Karsli","doi":"10.1007/s00335-026-10203-w","DOIUrl":"10.1007/s00335-026-10203-w","url":null,"abstract":"<p><p>This study aimed to identify candidate genes related to birth weight (BW), live weight at 90th day (90-LW), and lactation milk yield (LMY) in Hair (HAI), Honamlı (HNM), and Kabakulak (KBK) goats, providing a genome-wide basis for further selection strategies. The genome-wide efficient mixed model association approach was assessed with 309.342 bi-allelic single nucleotide polymorphisms (SNPs) across 481 animals to detect significant variants and their corresponding genomic regions. False discovery rate (FDR) correction and suggestive significance threshold were applied to identify SNPs having direct and potential effects on traits of interest, respectively. A total of 138 outlier SNPs (20 in HNM, 47 in HAI, and 71 in KBK) exceeded suggestive significance, of which 12 SNPs were identified to meet Benjamini-Hochberg's FDR criterion, suggesting that the overlapped protein-coding genes directly influence the phenotypic traits of interest. This approach revealed that the ID4 and CXCR4 genes directly affect BW and LMY traits in HNM goats, whereas no significant associations were observed regarding these traits in HAI and KBK goats. Additionally, a total of 8 protein-coding genes were identified to directly influence the 90-LW trait in HAI (MFSD1, CHMP4C, and MAP1B) and KBK (IGSF21, RALY, ZNF507, SLC38A10, and PGBD5) goats. The remaining 126 suggestive SNPs, on the other hand, either overlapped or were located near 103 protein-coding genes, indicating their potential effects on growth and milk yield. Both direct and potential protein-coding genes identified in this study seem promising for designing comprehensive selection strategies to improve growth and milk traits in Anatolian goats.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"30"},"PeriodicalIF":2.7,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12864215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.","authors":"J Saalom King, Marykutty Thomas, Jinty Sukumaran, P M Rojan, M R Akhila, T X Seena, K A Bindu","doi":"10.1007/s00335-026-10197-5","DOIUrl":"https://doi.org/10.1007/s00335-026-10197-5","url":null,"abstract":"<p><p>Beetal goats, the second largest indigenous goat breed in India, are known for their superior growth and production traits. In this study, we performed a comprehensive genome-wide characterization of insertion-deletion (indel) variants in the Beetal goat genome using pooled whole-genome resequencing. Following stringent filtering criteria, a total of 373,084 high-confidence indels were identified in the Beetal goat genome. Chromosome-wise distribution revealed the highest number of variants on Capra hircus chromosome (CHI) 1 (26,590), while CHI 25 showed the lowest (4303). Insertion variants (57.82%) outnumbered deletion variants (42.12%), yielding a deletion-to-insertion ratio of 0.73:1, a pattern distinct from most other mammalian genomes. The identified indel variants were distributed across intergenic (63.07%) and genic (36.93%) regions of the genome. Functional annotation classified 99.88% of the variants as MODIFIER and 0.05% as HIGH-impact, which included frameshift (144), splice site (31), donor disruptions (8) and start codon (1) mutations. Notably, high-impact indel variants were identified in key genes associated with growth and body conformation-LEPR, LCORL and PLAG1-underscoring their potential as candidate markers for larger body size. Functional enrichment analysis of high-impact indel variants using DAVID revealed significant overrepresentation (p ≤ 0.05) of biological processes related to G protein-coupled receptor signalling, immune regulation and innate immunity; molecular functions such as olfactory receptor activity and metal ion binding and KEGG pathways including olfactory transduction and extracellular matrix (ECM)-receptor interaction. These findings provide valuable insights into the functional relevance of indel variants and establish a foundational resource for future genomic selection strategies in Beetal goats.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"29"},"PeriodicalIF":2.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147839894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fifteen years of the Diversity Outbred mouse model: a review.","authors":"Zachary Tatom, Michael F Miles, Abraham A Palmer","doi":"10.1007/s00335-026-10196-6","DOIUrl":"10.1007/s00335-026-10196-6","url":null,"abstract":"<p><p>Mouse models have played a critical role in complementing human genetics research due to their genetic similarity to humans and well-annotated and tractable genome. For over 15 years, the Diversity Outbred (DO) mice have existed as a powerful tool for mapping complex traits. With eight founder strains contributing to high levels of genetic diversity, heterozygosity, and large numbers of recombination events, DO mice allow for high-resolution genetic mapping. DO mice have been used to dissect the genetic architecture of physiological traits like blood lipids, behavioral traits such as cocaine self-administration, and molecular phenotypes such as gene expression across various tissues. Here we aim to exhaustively catalog DO mouse studies over the last 15 years, including both mapping and non-mapping studies, as well as to provide an overview of software tools and online resources related to the model.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"28"},"PeriodicalIF":2.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12852284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of selection signatures in indigenous African cattle reveals genomic footprints of adaptation, production and temperament traits.","authors":"Rodney Okwasiimire, Donald R Kugonza, Junxin Gao, Melak Weldenegodguad, Mahlako L Makgahlela, Nasser Ghanem, Catarina Ginja, Richard P M A Crooijmans, Juha Kantanen, Pekka Uimari, Kisun Pokharel","doi":"10.1007/s00335-026-10193-9","DOIUrl":"10.1007/s00335-026-10193-9","url":null,"abstract":"<p><p>Indigenous cattle account for approximately 80% of Uganda's cattle population. These animals are well adapted to the country's ten agroecological zones and are mainly kept under pastoral and agropastoral systems. Unlike commercial breeds, they thrive on low-quality feeds, while tolerating major tropical diseases and parasites including tsetse flies, ticks, and vector-borne infections. Whole-genome sequence (WGS) analysis offers opportunities to uncover genomic regions underlying these adaptations and to trace the genetic footprints of long-term breeding decisions taken by cattle keepers. In this study, WGS data from 95 animals representing six indigenous cattle populations (Ankole, Karamojong, Nganda10, Nganda17, Nkedi, and Ntuku) were analyzed to identify genomic regions under putative selection. Two complementary approaches were applied: enumeration of the µ-statistic in RAiSD and runs of homozygosity (ROH) analysis. RAiSD identified population-level signals, while conserved ROH regions were defined using breed-specific SNP-incidence thresholds. The two methods identified 803 and 49 candidate genes respectively. The top genes identified included SLC37A1 (BTA1), CHCHD3 (BTA4), and RAB3GAP1 (BTA2) detected by RAiSD, and IL26 (BTA5), FBXL7 (BTA20), and HSPA9 (BTA7) contained in ROH. Furthermore, the regions harbored 107 novel genes (92 detected by RAiSD and 15 by ROH), corresponding to 255 quantitative trait loci. The identified genes under putative selection are associated with economically important traits including adaptation to tropical environments, resistance to parasites and diseases, and other farmer-preferred characteristics. These findings provide insights into the genetic basis of adaptation, selection and production in Ugandan indigenous cattle, supporting conservation and breeding strategies to enhance resilience and productivity.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"27"},"PeriodicalIF":2.7,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12852251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the molecular function of LYPD3 from pan-cancer to lung cancer: based on bioinformatics and cellular experiments.","authors":"Yuan-Xiang Shi, Jian-Hua Yan, Peng-Hui Dai","doi":"10.1007/s00335-026-10198-4","DOIUrl":"10.1007/s00335-026-10198-4","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"26"},"PeriodicalIF":2.7,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12816081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145998617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics Mendelian randomization and machine learning identify candidate therapeutic targets for Alzheimer's and Parkinson's diseases.","authors":"Xun Li, Lei Zhang, Jinyan Xia, Meiling Zheng, Zhipeng Zhou, Jing Cai","doi":"10.1007/s00335-025-10191-3","DOIUrl":"10.1007/s00335-025-10191-3","url":null,"abstract":"<p><p>Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD) and Parkinson's disease (PD), are major public health challenges lacking effective therapies. To identify potential drug targets, we integrated large-scale genome-wide association studies with expression, methylation, protein, and splicing QTL datasets using Mendelian Randomization (MR) and summary-data-based MR (SMR). Colocalization analysis and machine learning were applied to prioritize candidate genes, followed by in silico druggability evaluation through molecular docking and molecular dynamics (MD) simulations. In animal models, candidate genes identified by transcriptomic analysis were further validated using integrative molecular and functional experiments. We identified several genes with potential causal links to AD (e.g., IQCE, HDHD2, ALPP) and PD (e.g., IL15, STK3, CHRNB1). Transcriptomic analyses indicated a consistent downregulation of IL-15 in PD model mice, corroborated by subsequent Western blot and immunohistochemical validation. Among predicted compounds, Prednisolone (ALPP), Sirolimus (IL15), and CHEMBL379975 (STK3) showed favorable binding affinities and stable MD trajectories, suggesting promising therapeutic relevance. Collectively, these findings highlight 12 QTL-regulated genes as promising molecular targets for further investigation in the context of NDDs. While the computational results provide a useful basis for hypothesis generation, experimental validation will be essential to determine the biological relevance and therapeutic potential of these candidate genes and compounds.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"24"},"PeriodicalIF":2.7,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and validation of PANX1 as an inflammasome-related biomarker in gestational diabetes mellitus: insights from machine learning and experimental approaches.","authors":"Padmanaban M Abirami, K L Milan, M Anuradha, Kunka Mohanram Ramkumar","doi":"10.1007/s00335-026-10195-7","DOIUrl":"10.1007/s00335-026-10195-7","url":null,"abstract":"<p><p>Gestational diabetes mellitus (GDM) is characterized by glucose intolerance during pregnancy, resulting from insulin resistance, and is associated with increased maternal and neonatal risks. Inflammasomes play a critical role in GDM pathophysiology by driving immune dysregulation and chronic inflammation. This study aimed to identify inflammasome-related genes, which may serve as potential diagnostic markers and contribute to GDM pathogenesis. RNA sequencing datasets from the GEO were merged and analysed to identify differentially expressed genes (DEGs). The key genes identified by LASSO logistic regression, random forest, Boruta, and SVM-RFE algorithms were superimposed with genes related to inflammasomes. In addition, the CIBERSORT algorithm was used to analyse the immune characteristics of GDM. The expression of inflammasome-related genes was validated in the clinical samples by qPCR and correlated with clinical parameters. PANX1 was identified as a key inflammasome-associated gene, with its diagnostic potential confirmed by ROC curve analysis with an AUC of 93.75%. CIBERSORT and correlation analyses confirmed a significant association between PANX1 expression and immune cell infiltration. qPCR validation using placental samples from GDM and control subjects revealed elevated PANX1 expression in GDM. Furthermore, a significant correlation was observed between PANX1 expression and levels of glucose, HbA1c, and HOMA-IR, suggesting that elevated PANX1 may be associated with metabolic dysregulation in GDM. This study highlights PANX1 as a novel diagnostic biomarker and a therapeutic target in GDM pathophysiology.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"25"},"PeriodicalIF":2.7,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145989484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}