Mammalian Genome最新文献

{"title":"Exploration of shared gene signatures and molecular mechanisms between psoriasis and COVID-19: evidence from transcriptome data.","authors":"Rong-Jing Dong, Lu-Hui Yang, Yu-Ye Li, You-Wang Lu","doi":"10.1007/s00335-026-10194-8","DOIUrl":"10.1007/s00335-026-10194-8","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"23"},"PeriodicalIF":2.7,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12799721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145966475","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":"MiR-324-5p mitigates experimental acute pancreatitis by suppressing Rock2 expression.","authors":"Qian Chen, Zhao Shen, Qingmei Wang, Ru Jiao, Yehong Liu, Tingting Meng, Yunhui Fei, Caixia Liu","doi":"10.1007/s00335-025-10190-4","DOIUrl":"10.1007/s00335-025-10190-4","url":null,"abstract":"<p><p>Acute pancreatitis (AP) is a lethal pancreatic disease with limited therapeutic options. MicroRNA-324-5p (miR-324-5p) has shown dual roles across diseases, but its specific role and molecular targets in AP remain unclear. Plasma miR-324-5p levels were measured in 80 AP patients and 40 healthy controls using RT-qPCR. An in vivo AP mouse model was induced by caerulein, and agomir miR-324-5p was administered to assess its therapeutic effect. In vitro, MPC-83 pancreatic acinar cells were treated with caerulein and transfected with miR-324-5p mimics or co-transfected with Rock2 overexpression plasmids. Apoptosis and inflammation were evaluated using qPCR, Western blot, ELISA, and histology. Potential targets of miR-324-5p were predicted using StarBase, microT, miRmap, and PITA databases. Rock2 targeting was experimentally confirmed using dual-luciferase reporter assay, RNA pull-down, and RIP assays. MiR-324-5p was significantly downregulated in AP patient plasma and AP mouse pancreas. Experimental agomir-mediated overexpression of miR-324-5p alleviated pancreatic injury alleviated pancreatic injury, reduced serum amylase/lipase, MPO levels, and suppressed cytokines expression in vivo. In vitro, miR-324-5p restored cell viability, inhibited apoptosis, and suppressed inflammatory cytokines in caerulein-treated MPC-83 cells. Bioinformatic and experimental assays identified Rock2 as a direct target of miR-324-5p. Rock2 overexpression reversed the protective effects of miR-324-5p on apoptosis and inflammation in both cell and animal models. MiR-324-5p plays a protective role in AP by directly targeting Rock2 and suppressing inflammatory and apoptotic responses.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"21"},"PeriodicalIF":2.7,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145959580","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":"Genetic heritage of war: exploring transgenerational inheritance of PTSD and its molecular background.","authors":"Nerma Džaferović, Adna Ašić","doi":"10.1007/s00335-025-10192-2","DOIUrl":"10.1007/s00335-025-10192-2","url":null,"abstract":"<p><p>This review article summarizes the available data about the potential link between war-related trauma and post-traumatic stress disorder (PTSD) and epigenetic alterations that could manifest in future generations. DNA methylation variations in stress-related genes such FKBP5, NR3C1, NR3C2, BDNF, and SLC6A4 have been seen in parents and/or their offspring in populations exposed to genocide, conflict, or combat. Certain results point to timing-dependent or parent-specific patterns, especially when maternal stress occurs during pregnancy. Results, however, are not consistent; some studies have found no significant differences in methylation, and the effects that are seen vary depending on the tissues, methods, and populations. Conclusions about causality or genuine inheritance are limited by the majority of existing studies' small sample sizes, cross-sectional designs, and inadequate control of environmental and psychosocial variables. Overall, existing research suggests potential links between epigenetic variation and war-related trauma, but clear evidence for transgenerational inheritance is still unconclusive, underscoring the need for more thorough and longitudinal studies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"22"},"PeriodicalIF":2.7,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145959587","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":"Alantolactone curbs the malignant progression of bladder cancer partly via the HSP90AB1/LRP5/β-catenin axis.","authors":"Lijun Zhi, Lin Yuan","doi":"10.1007/s00335-025-10182-4","DOIUrl":"10.1007/s00335-025-10182-4","url":null,"abstract":"<p><p>Bladder cancer (BCa) represents a global health problem. Traditional Chinese medicine has a long history of treating cancers. This study has been conducted to illustrate the anti-cancer effects of alantolactone (ALT) in BCa and to explore the potential mechanism. The effects of ALT on the malignant behavior of T24 and TCCSUP cells were investigated. Bioinformatic methods were utilized to predict potential targets of ALT. Cells were infected with lentiviral overexpression vectors for heat shock protein HSP 90-beta (HSP90AB1) or treated with the β-catenin signaling inhibitor MSAB to explore their effects on BCa cell behaviors. The effects on tumorigenesis were also analyzed in a xenograft tumor model. ALT markedly reduced the proliferation, migration, and invasion of BCa cells and induced apoptosis. ALT treatment was associated with decreased HSP90AB1 levels in BCa cells and increased low-density lipoprotein receptor-related protein 5 (LRP5) ubiquitination, thereby impairing β-catenin activation. HSP90AB1 overexpression attenuated the anti-cancer effects of ALT, while MSAB repressed the malignant progression of BCa cells promoted by HSP90AB1 overexpression. Forced overexpression of HSP90AB1 enhanced BCa development in vivo, which was mitigated by MSAB. In conclusion, our findings suggest that ALT exerts anti-cancer activity in BCa, potentially through modulation of HSP90AB1 and β-catenin signaling pathways.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"20"},"PeriodicalIF":2.7,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145819985","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 structure and selection history across Angus populations worldwide: insights from ROH, selection mapping, and functional analyses.","authors":"Henrique A Mulim, Gabriel S Campos, Fernando F Cardoso, Victor Breno Pedrosa, Kajal Latimer, Lindsay R Upperman, A J Knowles, Andre Garcia, Kelli Retallick, Steve Miller, Hinayah Rojas de Oliveira","doi":"10.1007/s00335-025-10188-y","DOIUrl":"10.1007/s00335-025-10188-y","url":null,"abstract":"<p><p>Angus cattle, originally from Scotland, have been selectively bred for over 400 years, making them one of the most prominent beef breeds globally. Known for their adaptability, natural polled traits, and high-quality beef, Angus cattle have been intensively selected for growth, body size, and feed efficiency. This study investigates the genetic diversity, selection history, and key genomic regions across five Angus populations from the USA, Canada, Australia, Brazil, and Red Angus of America. Genomic data from 71,283 animals born between 1961 and 2024 were analyzed using Principal Component Analysis (PCA), phylogenetic tree construction, and Runs of Homozygosity (ROH), with the Generation Proxy Selection Mapping (GPSM) approach used to assess selection history. Functional annotation identified candidate genes and pathways related to selection. Our analysis revealed both similarities and differences across populations. The PCA and FST metrics showed minimal differentiation between the American, Canadian, Australian, and Brazilian populations, with greater differentiation observed in the Red Angus population. The ROH analysis revealed that the Brazilian population had the highest number of ROHs. The ROH islands identified on BTA8 and BTA13 in the American and Australian populations were linked to traits like body weight, marbling, and tenderness. The GPSM identified significant markers associated with body weight and growth in all populations, reflecting ongoing selection pressures. This study highlights the potential of genomics to improve our understanding of Angus cattle's genetic architecture and selection history. It underscores the feasibility of integrating global populations for more accurate genomic evaluations, enhancing genetic predictions, and supporting sustainable beef production worldwide.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"19"},"PeriodicalIF":2.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12722264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145810499","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":"Genome-wide SNP evidence for the genetic uniqueness of indigenous cattle population.","authors":"Kiyevi G Chishi, Sanjeev Singh, Rangasai Chandra Goli, K K Kanaka, Indrajit Ganguly, S V Kuralkar, Sat Pal Dixit","doi":"10.1007/s00335-025-10186-0","DOIUrl":"https://doi.org/10.1007/s00335-025-10186-0","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"18"},"PeriodicalIF":2.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804906","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":"Long-read whole-genome sequencing of SHR rat substrains with distinct substance use phenotypes.","authors":"Adil Abdurahaman, Paige M Lemen, Kathleen M Kantak, Britahny M Baskin, Camron D Bryant, Hao Chen","doi":"10.1007/s00335-025-10187-z","DOIUrl":"10.1007/s00335-025-10187-z","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"17"},"PeriodicalIF":2.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12722307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804868","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":"Rare and common variants in ERAP1 and ERAP2 selected for in response to Yersinia pestis infection contribute to autoimmune disease including inflammatory bowel disease.","authors":"Lynn K Win, Guo Cheng, James J Ashton, Alex Z Kadhim, Zachary Green, R Mark Beattie, Sarah Ennis","doi":"10.1007/s00335-025-10183-3","DOIUrl":"10.1007/s00335-025-10183-3","url":null,"abstract":"<p><p>Endoplasmic reticulum aminopeptidases (ERAP) facilitate antigen presentation. Variation in ERAP1 and ERAP2 genes underwent selection during the Black Death and impact autoimmune disease susceptibility. We assess the burden of functionally impactful variants present in ERAP1 and ERAP2 in 2 cohorts of patients diagnosed with inflammatory bowel disease (IBD; Crohn's disease (CD) or ulcerative colitis (UC)). We analysed the Southampton Genetics of IBD cohort comprising patients diagnosed with IBD, with exome and clinical data on autoimmune comorbidities (n_CD = 661, n_UC = 330); and a subset of UK Biobank IBD patients and selected controls (n_CD = 891, n_UC = 1409, n_control = 60,075). Common single variants (minor-allele-frequency > 0.05) underwent Fisher's exact test with permutations (n = 1000), comparing UC versus CD patients in the Southampton cohort. A gene-burden based test of functionally impactful variants (GenePy) was used to examine rare and common variants in both cohorts. Predicted haplotypes were assessed in each cohort and compared with known haplotypes of ERAP1 and ERAP2. In the Southampton cohort, variant-level analysis identified 6 common variants that were nominally significant when testing between UC versus CD (p < 0.05; empirical permuted p-value). Gene-level analysis using Mann-Whitney-U identified an altered burden of functionally impactful variants for ERAP1 in UC versus CD patients (p = 0.0073), but not for ERAP2. Patients with an isolated diagnosis of UC (p = 0.037,θ = 0.457) vs patients with a concurrent diagnosis of UC and any autoimmune diagnoses had an altered burden of functionally impactful variants in ERAP2. For the UK Biobank cohort, participants diagnosed with UC versus controls had a significantly altered burden of functionally impactful variants in ERAP1 (p = 0.0004) and ERAP2 (p = 0.0006). Both variant and gene-level analysis indicate a role for ERAP1 and ERAP2 in predisposing individuals to developing UC or UC with concurrent autoimmune diagnosis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"16"},"PeriodicalIF":2.7,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12722269/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145804889","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":"Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination.","authors":"Jeffrey M Kidd","doi":"10.1007/s00335-025-10178-0","DOIUrl":"10.1007/s00335-025-10178-0","url":null,"abstract":"<p><p>Genetic maps are a key resource for the analysis of genetic variation. Prior maps in dogs were based on the canFam3.1 genome assembly, which contains thousands of sequence gaps that include functional elements. Although long-read technologies have enabled the generation of updated reference assemblies, updated maps are required to take full advantage of these new resources. We inferred fine-scale recombination maps that consider population demographic history for four populations of village dogs sequenced by the Dog10K consortium. The newly inferred maps are broadly consistent with previous studies of recombination in dogs. At small scales, stronger correlations are observed among maps inferred using linkage disequilibrium than with a pedigree-based map. The position of recombination hotspots showed significant overlap among inferred maps and were enriched for sequences that were gaps in a previous canine genome assembly. When using the Dog10K samples as a reference panel, a phase error rate of approximately 2% was found with the choice of genetic map having little effect. We describe genetic maps based on the canFam4 assembly which will be useful for future studies of genetic variation that rely on updated dog genome references.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"12"},"PeriodicalIF":2.7,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12701031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743288","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":"Genome-wide detection of copy number variations in indigenous Red Sindhi cattle using ddRAD sequencing.","authors":"Sonali Sonejita Nayak, Shikha Mittal, Surya Kant Verma, Triveni Dutt, Manjit Panigrahi","doi":"10.1007/s00335-025-10184-2","DOIUrl":"10.1007/s00335-025-10184-2","url":null,"abstract":"<p><p>In livestock, copy number variations (CNVs) are important structural differences that affect phenotypic variety and adaptation. The genome-wide CNVs in 72 Red Sindhi cattle, an indigenous breed prized for its disease resistance and heat tolerance, were characterised in this study using double-digest restriction-site associated DNA sequencing (ddRAD-seq). The Illumina Novaseq platform was used to sequence the genomic DNA, and CNVs were identified using CNVnator with a 1000 bp bin size. PANTHER and Animal QTLdb were then utilized for functional annotation. A total of 3,269 high-confidence CNVs were found, mostly on autosomes. The highest number of CNVs (205) was detected on chromosome 1. Duplications mainly occurred in larger size classes (100 kb-1 Mb), while deletions were frequent in the 10-100 kb range. All regions contained 253 CNV regions (CNVRs), and 46% of individuals had a significant duplication on chromosome 18 (1-4.43 Mb). These CNVs overlapped with 2,593 genes associated with 112 quantitative trait loci (QTLs) that affected environmental adaptability, immunology, milk production, and reproduction. Znrf1, Snca, and Bola loci are important genes that have been linked to immune response and stress tolerance, underscoring their importance in the robustness of the breed. This study presents the first comprehensive CNV map for Red Sindhi cattle, highlighting the affordability of ddRAD-seq as a native breed genomic research tool. These findings support the use of marker-assisted selection and conservation techniques to produce climate-smart tropical animals.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"37 1","pages":"13"},"PeriodicalIF":2.7,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743305","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}