Mammalian Genome最新文献

{"title":"Impact of scale parameter for marker variance prior in some Bayesian whole-genome regression methods.","authors":"Özge Kozakli, Ayhan Ceyhan","doi":"10.1007/s00335-026-10233-4","DOIUrl":"https://doi.org/10.1007/s00335-026-10233-4","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775554","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":"PI3KCD gene expression and its role in diabetic intervertebral disc degeneration running title: PI3KCD gene crucial for diabetic IDH.","authors":"Peng Wang, Feng Zhou","doi":"10.1007/s00335-026-10234-3","DOIUrl":"https://doi.org/10.1007/s00335-026-10234-3","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775624","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":"Oncogenic role of LncRNA DLEU2 in thyroid cancer through a NAT10/USP39 regulatory axis.","authors":"Jiwen Yang, Cheng Li, Weili Yin, Fang Fang, Zhiyong Zhao","doi":"10.1007/s00335-026-10225-4","DOIUrl":"https://doi.org/10.1007/s00335-026-10225-4","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775581","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":"Genomic-microbial coevolution in human development: chromosome 2 fusion, and human accelerated regions.","authors":"Siddharth Singh, Md Shahadab, Kumar Sachin, Rajan Kumar Pandey, Pankaj Trivedi, Amit Kumar Mishra, Hem Chandra Jha","doi":"10.1007/s00335-026-10228-1","DOIUrl":"https://doi.org/10.1007/s00335-026-10228-1","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775567","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":"Are we fully exploiting genetic discoveries to understand and treat Alzheimer's disease?","authors":"Julie Williams","doi":"10.1007/s00335-026-10227-2","DOIUrl":"https://doi.org/10.1007/s00335-026-10227-2","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13099805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775597","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":"Cell-type-specific causal effects of CEBPD in CD8 + S100B + Tcells and ZFP36 in monocytes modulate the protective and risk phenotypes in psoriasis.","authors":"Luofei Huang, Jian Shi","doi":"10.1007/s00335-026-10230-7","DOIUrl":"10.1007/s00335-026-10230-7","url":null,"abstract":"<p><p>Psoriasis is a chronic immune-mediated inflammatory skin disease characterized by dysregulated keratinocyte proliferation, immune cell infiltration, and systemic comorbidities. Despite the identification of numerous genetic susceptibility loci for psoriasis through genome-wide association studies (GWAS), their functional roles and underlying causal contributions to psoriasis pathogenesis remain largely unclear. Integrating multi-omics data with causal inference approaches, such as Mendelian randomization (MR), represents a promising strategy for addressing this gap and identifying key regulatory genes. We integrated transcriptome data from the Gene Expression Omnibus database (GEO) database (GSE14905 and GSE30999) and performed weighted gene co-expression network analysis and differential expression analysis to identify psoriasis-related genes. Protein-protein interaction networks and four centrality algorithms (Maximal Clique Centrality (MCC), Maximum Neighborhood Component (MNC), Edge Percolated Component (EPC), and Degree centrality) were applied to identify hub genes, and machine learning methods (least absolute shrinkage and selection operator regression, Random Forest, and artificial neural network) were used to screen diagnostic biomarkers. Immune infiltration analysis was performed using CIBERSORT, and the causal association of signature genes with psoriasis was examined using two-sample MR with single-cell expression quantitative trait locus data from the OneK1K cohort and GWAS summary statistics from FinnGen. Module genes that were significantly associated with psoriasis were identified in our study, among which 19 hub genes were screened. Using machine learning approaches, we further refined these findings to seven signature genes. The diagnostic model based on these seven genes achieved an area under the curve of 0.980. Immune infiltration analysis revealed strong associations between CCAAT/enhancer-binding protein delta (CEBPD) and activated CD4 + memory T cells and follicular helper T cells, and between zinc finger protein 36 (ZFP36) and M1 macrophages. MR analysis demonstrated that higher CEBPD expression in CD8 + S100B + T cells was protective (odds ratio [OR] = 0.795, P = 0.015), whereas higher expression of the ZFP36 gene in monocytes was a risk factor (OR = 1.214, P = 0.043) for psoriasis. Our study identified a robust seven-gene signature with high diagnostic accuracy for psoriasis and provided genetic evidence for the cell type-specific causal role of CEBPD and ZFP36. These findings enhance our understanding of psoriasis pathogenesis and suggest potential targets for developing cell-selective immunomodulatory therapies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147698989","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 investigations of the lipid accumulation product index pinpoints polygenic determinants underlying pancreatitis susceptibility.","authors":"Chia-Fu Chien, Zhengwei Qi, Zhengye Liu, Hanze Du, Ziqi Wan, Haotian Chen, Xiaoyin Bai, Jiarui Mi","doi":"10.1007/s00335-026-10215-6","DOIUrl":"10.1007/s00335-026-10215-6","url":null,"abstract":"<p><p>The lipid accumulation product index (LAP) is a robust marker of lipid burden. However, its genetic architecture and causal relevance to pancreatitis remain poorly characterized. We performed a genome-wide association study (GWAS) of LAP in 388,213 European from UK Biobank, followed by colocalization, transcriptome-wide association studies (TWAS), LD score regression and Mendelian randomization for causal relationships. Polygenic risk scores (PRS) were constructed and tested against chronic pancreatitis (CP), hypertriglyceridemic acute pancreatitis (HTG-AP), and acute pancreatitis (AP) using regression models. Gene-environment interactions were evaluated for dietary and lifestyle factors. The GWAS identified 235 independent loci associated with LAP; 18 and 26 genes showed significant colocalization with hepatic and visceral-adipose eQTLs, respectively. TWAS revealed 292 (PrediXcan) and 417 (JTI) genes in visceral fat, and 164 (PrediXcan) and 281 (JTI) in liver, whose expression associated with LAP. Positive genetic correlations were observed between LAP and CP (rg = 0.252) and AP (rg = 0.219). Mendelian randomization supported a causal effect of LAP on CP (β = 6.86 × 10^-3, P = 0.030) and AP (β = 1.68 × 10^-3, P = 0.045). Each 1-SD increase in LAP-PRS conferred higher risk of HTG-AP (OR = 1.11, 95% CI 1.02-1.20) and CP (OR = 1.07, 95% CI 1.00-1.14), but not AP. Furthermore, a healthier dietary pattern can attenuate the HTG-AP risk genetically driven by LAP PRS. This study delineates the polygenic basis of LAP and establishes its causal role in CP and HTG-AP susceptibility, offering a genetically informed indicator for risk assessment of pancreatitis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147690994","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":"AFAP1-AS1 regulates oral squamous cell carcinoma development through the miR-93-3p/CCND1 signaling pathway.","authors":"Kuangzheng Li, Chengwei Li, Qian He, Xiaosheng Fan, Lili Xu, Yixia Jiang","doi":"10.1007/s00335-026-10223-6","DOIUrl":"10.1007/s00335-026-10223-6","url":null,"abstract":"<p><p>Actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) has been found to be closely associated with the initiation and progression of various tumors; however, its role in oral squamous cell carcinoma (OSCC) remains unclear. AFAP1-AS1 expression in OSCC cells was detected using qRT-PCR. The regulatory effects of AFAP1-AS1 on tumor cell proliferation, migration, and invasive capabilities were systematically evaluated through CCK-8 proliferation, colony formation, wound healing, and Transwell invasion assays. Flow cytometry was employed to quantitatively analyze its impact on cell cycle progression and apoptotic. Based on bioinformatics predictions, a dual-luciferase reporter system was utilized to validate the targeting interactions among AFAP1-AS1, miR-93-3p, and CCND1. Functional rescue experiments were conducted to elucidate the functional regulatory network among them. Furthermore, a xenograft tumor model in nude mice was employed to verify in vivo the promoting effect of AFAP1-AS1 on tumor growth. AFAP1-AS1 was significantly upregulated in OSCC cells. AFAP1-AS1 knockdown inhibited the malignant phenotypes of OSCC cells. Mechanistic studies revealed that AFAP1-AS1 could target miR-93-3p and regulate CCND1 expression, thereby influencing OSCC progression. Subcutaneous tumor model in mice further confirmed the in vivo relevance of the AFAP1-AS1/miR-93-3p/CCND1 axis. AFAP1-AS1 downregulation inhibited OSCC progression through the miR-93-3p/CCND1 axis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147645512","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":"Mapping genomic adaptation to environmental heterogeneity in Indian native goat populations through landscape genomics.","authors":"Pallavi Rathi, Nidhi Sukhija, Indrajit Ganguly, S P Dixit, Sanjeev Singh, Chandana Sree Chinnareddyvari, C A Dharaamshaw","doi":"10.1007/s00335-026-10214-7","DOIUrl":"10.1007/s00335-026-10214-7","url":null,"abstract":"<p><p>India harbours a diverse range of indigenous goat breeds that have adapted to varied climatic zones over centuries. This study investigated the genomic basis of local adaptation in these populations (n= 11) divided into seven agro-climatic zones using genome-wide SNP data and century-scale environmental variables. A total of 2,295,833 SNPs and 15 non-collinear bioclimatic predictors were analyzed using the landscape genomics tool R SamBada for genotype-environment association. Models were selected based on G-score and q-value thresholds (q < 0.01). Several loci showed strong signatures of selection, with associated genes enriched in key adaptive pathways, including HIF-1 signalling, insulin signalling, and toll-like receptor pathways. Many key genes and pathways were identified with both direct and indirect roles in adaptation to specific agro-climatic zone. Only 9 SNP variants showed SIFT score < 0.05 (deleterious) out of which, only 2 variants each harbouring gene PTPRC and PLCB1 were predicted to be deleterious with high confidence. Further downstream technical validation for functionality was done using PTPRC and PLCB1 present in coding region and exhibited significant environmental associations. Missense mutations in these genes were further characterized using I-Mutant, ConSurf, and Phyre2. The PTPRC variant was predicted to reduce protein stability within a moderately conserved immune domain, and structural modelling indicated altered folding in mutant proteins. These adaptive variants likely contribute to resilience against heat, humidity, and pathogen-driven stress. This integrative landscape genomics approach reveals how natural selection and environmental pressures have shaped the adaptive genome of Indian indigenous goats and provides a foundation for marker-assisted selection to enhance climate resilience in future breeding programs. This study represents the first landscape genomics analysis in indigenous goat populations of India.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628152","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 characterization of HSP70 and HSP90 subfamilies in Yak (Bos grunniens): expression patterns under cold and chemical hypoxia conditions.","authors":"Yufei Zan, Caiwei Ma, Ziqiang Ding, Yi Liu, Fengcheng Song, Yixuan Tang, Jia Li, Liang Du, Xian Guo, Zhengrong Yuan, Yi Ma","doi":"10.1007/s00335-026-10221-8","DOIUrl":"https://doi.org/10.1007/s00335-026-10221-8","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628096","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}