Mammalian Genome最新文献_第2页

Comprehensive analysis of breast cancer oxidative stress related gene signature: a combination of bulk and single-cell RNA sequencing analysis. 乳腺癌氧化应激相关基因特征的综合分析：整体和单细胞RNA测序分析的结合。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-24 DOI: 10.1007/s00335-025-10130-2

Yuheng Shao, Yumeng Zhang, Jie Chen, Liang Yang, Meihong Wu, Zhiyuan Fan, Zhigang Zhuang

{"title":"Comprehensive analysis of breast cancer oxidative stress related gene signature: a combination of bulk and single-cell RNA sequencing analysis.","authors":"Yuheng Shao, Yumeng Zhang, Jie Chen, Liang Yang, Meihong Wu, Zhiyuan Fan, Zhigang Zhuang","doi":"10.1007/s00335-025-10130-2","DOIUrl":"https://doi.org/10.1007/s00335-025-10130-2","url":null,"abstract":"Oxidative stress influences the tumor microenvironment, driving breast cancer progression and drug resistance. This study aimed to develop a prognostic gene signature based on oxidative stress-related genes (OSRGs) to assess patient outcomes and immune status. UCSC Xena ( http://xena.ucsc.edu/ ) and GEO ( https://www.ncbi.nlm.nih.gov/geo/ ) databases were used to obtain RNA-seq data and corresponding clinical information. The classification of OSRG subtypes was performed using consensus cluster. The oxidative stress related scoring (OSRS) model was established combining Lasso regression and multivariable Cox regression. The analysis of tumor mutation burden (TMB) and somatic mutation were carried out using the R package 'maftools'. Python package 'pySCENIC' was used to construct and analyze the transcription factor network. Additionally, immune infiltration was analyzed using R packages 'CIBERSORT' and 'ESTIMATE'. Three OSRG subgroups were identified and the Differentially Expressed Genes (DEGs) among them were enriched in humoral immunity, cytokine communication and drug metabolism pathways. OSRS model was established based on the DEGs and revealed association with patients' overall survival, somatic mutations, immune statuses, and drug resistance. Finally, transcription factor TFAP2B was identified as a key regulatory factor in high OSRS cells, and associated with a negative prognostic outcome in Basal-like breast cancer patients.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011415","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}

引用次数: 0

Advancing precision ear medicine: leveraging animal models for disease insights and therapeutic innovations. 推进精准耳医学：利用动物模型进行疾病洞察和治疗创新。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-22 DOI: 10.1007/s00335-025-10126-y

Sandrine Vitry, Clara Mendia, Audrey Maudoux, Aziz El-Amraoui

{"title":"Advancing precision ear medicine: leveraging animal models for disease insights and therapeutic innovations.","authors":"Sandrine Vitry, Clara Mendia, Audrey Maudoux, Aziz El-Amraoui","doi":"10.1007/s00335-025-10126-y","DOIUrl":"https://doi.org/10.1007/s00335-025-10126-y","url":null,"abstract":"Gene therapy offers significant promise for treating inner ear disorders, but its clinical translation requires robust preclinical validation, often reliant on animal models. This review examines the role of these models in advancing gene therapeutics for inherited inner ear disorders, focusing on successes, challenges, and treatment solutions. By providing a precise understanding of disease mechanisms, these models offer a versatile preclinical platform that is essential for assessing and validating therapies. Successful gene supplementation and editing have shown potential in restoring hearing and balance functions and preventing their decline. However, challenges such as limitations in gene delivery methods, surgical access, immune responses, and discrepancies in disease manifestation between animal models and humans hinder clinical translation. Current efforts are dedicated to developing innovative strategies aimed at enhancing the efficiency of gene delivery, overcoming physical barriers such as the blood-labyrinth barrier, improving target specificity, and maximizing therapeutic efficacy while minimizing adverse immune responses. Diverse gene supplementation and editing strategies, along with evolving technologies, hold promise for maximizing therapeutic outcomes using disease relevant models. The future of inner ear gene therapeutics will hinge on personalized therapies and team science fueling interdisciplinary collaborations among researchers, clinicians, companies, and regulatory agencies to expedite the translation from bench to bedside and unlock the immense potential of precision medicine in the inner ear.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006948","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}

引用次数: 0

TCR CDR3 chemical complementarity to HPV epitopes is associated with a better outcome for cervical cancer. TCR CDR3与HPV表位的化学互补与宫颈癌更好的预后相关。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-11 DOI: 10.1007/s00335-025-10127-x

Deo Rei L Agnila, Rahul Jain, Michael J Diaz, Tabitha R Hudlock, Rachel A Eakins, Andrea Chobrutskiy, Boris I Chobrutskiy, George Blanck

{"title":"TCR CDR3 chemical complementarity to HPV epitopes is associated with a better outcome for cervical cancer.","authors":"Deo Rei L Agnila, Rahul Jain, Michael J Diaz, Tabitha R Hudlock, Rachel A Eakins, Andrea Chobrutskiy, Boris I Chobrutskiy, George Blanck","doi":"10.1007/s00335-025-10127-x","DOIUrl":"https://doi.org/10.1007/s00335-025-10127-x","url":null,"abstract":"Despite the fact that HPV vaccines are likely to lead to a significant reduction in cervical cancer occurrence, there remains cervical cancer incidence independent of the vaccine and cervical cancer arising in the absence of vaccination. Thus, continued efforts are needed to address the potential parameters of cervical cancer that could impact therapy and could lead to additional ways of reducing cervical cancer death rates. Adaptive immune receptor recombinations were obtained from the cancer genome atlas (TCGA) cervical cancer database through tumor exome and RNAseq files as well as from the independent Cancer Genome Characterization Initiative (CGCI) cervical cancer dataset. T-cell receptor (TCR) complementarity determining region-3's (CDR3s) were then assessed, based on chemical complementarity to human papillomavirus (HPV) T-cell epitopes. Results indicated increased overall survival probabilities consistently across the three TCR datasets with TCR CDR3 chemical complementarity to the same HPV epitopes, specifically immune epitope database (IEDB) designations: IEDB-1625373, IEDB-174148, and IEDB-110943. Among other potential applications of these results, the results may indicate HPV epitopes that could be useful targets for immunotherapy.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001233","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}

引用次数: 0

Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds. Nelore， Gir和Red Sindhi牛品种的选择特征检测。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-02 DOI: 10.1007/s00335-025-10125-z

Maria Victória Henrique Genuíno, Ayrton Fernandes de Oliveira Bessa, Roney Teixeira da Silva, Giovanna Maria Dos Santos Câmara, João Cláudio do Carmo Panetto, Marco Antônio Machado, Sabrina Luzia Caetano, Salvador Boccaletti Ramos, Danísio Prado Munari, Tad Sonstegard, Marcos Vinícius Gualberto Barbosa da Silva, Marcos Eli Buzanskas

{"title":"Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.","authors":"Maria Victória Henrique Genuíno, Ayrton Fernandes de Oliveira Bessa, Roney Teixeira da Silva, Giovanna Maria Dos Santos Câmara, João Cláudio do Carmo Panetto, Marco Antônio Machado, Sabrina Luzia Caetano, Salvador Boccaletti Ramos, Danísio Prado Munari, Tad Sonstegard, Marcos Vinícius Gualberto Barbosa da Silva, Marcos Eli Buzanskas","doi":"10.1007/s00335-025-10125-z","DOIUrl":"https://doi.org/10.1007/s00335-025-10125-z","url":null,"abstract":"Technological advances in genomics and bioinformatics made it possible to study the genetic structure of breeds and understand genome changes caused by selection over generations. Our objective was to evaluate selection signatures (SS) in Nelore, Gir, and Red Sindhi cattle from Brazil and the Asian continent to identify divergent variants due to the history of formation and selection of populations, with a focus on the SS of animals from Brazil. Extended haplotype homozygosities between populations (XP-EHH), the ratio of site-specific extended haplotype homozygosity between populations (Rsb), and the allelic fixation index (Fst) were used to detect SS. Considering a window size of 50-kb, a non-sliding window approach was used to define SS regions. A total of 62, 57, and 72 genes were co-located within SS regions for Nelore, Gir, and Red Sindhi, respectively, and used to perform functional analyses per breed. Most genes were associated with productive and reproductive traits, while others were related to thermotolerance, the immune system, temperament, and coat color. The identified SS demonstrate how animal breeding programs shape the genetic makeup of these breeds to meet production system requirements, given that animals from Brazil and the Asian continent have undergone different selection processes. The identification of genes related to thermotolerance, temperament, and the immune system suggests specific alleles have enabled animals to adapt to environmental conditions and selection criteria in Brazil. Understanding SS can support breeding strategies for Nelore, Gir, and Red Sindhi cattle, contributing to enhanced resistance, adaptation, and productivity to meet food production demands.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772465","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}

引用次数: 0

Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India. 编目拷贝数变异区域和相关的多样性在整个印度山羊品种。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-04-02 DOI: 10.1007/s00335-025-10122-2

Nidhi Sukhija, K K Kanaka, Indrajit Ganguly, Satpal Dixit, Sanjeev Singh, Rangasai Chandra Goli, Pallavi Rathi, P B Nandini, Subrata Koloi

{"title":"Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India.","authors":"Nidhi Sukhija, K K Kanaka, Indrajit Ganguly, Satpal Dixit, Sanjeev Singh, Rangasai Chandra Goli, Pallavi Rathi, P B Nandini, Subrata Koloi","doi":"10.1007/s00335-025-10122-2","DOIUrl":"https://doi.org/10.1007/s00335-025-10122-2","url":null,"abstract":"Huge genetic diversity is evident among the diverse goat breeds in terms of production, reproduction, adaptability, growth, disease resistance and thermo-tolerance. This diversity is an outcome of both natural and artificial selection acting on the caprine genome over the years. A fine characterization of whole genome variation is now possible by employing Next Generation Sequencing (NGS) technologies. To explore underlying genetics, genome-wide analysis of genetic markers is the best resolution. The study strived to capture variation in terms of CNV/CNVRs among 11 Indian goat breeds. In this study, the first ever resequencing-based CNV/CNVR distribution of Indigenous goat breeds was delineated, providing a sizable addition to the prior caprine CNVRs reported. Different diversity metrics were analyzed using identified CNVR. Principal component analysis (PCA) showed separate clustering of Kanniadu (KAN) and Jharkhand Black (JB) from other breeds under the study, indicating their unique genetic profile as the former breeds were sampled from institutional farms. The admixture analysis and introgression revealed by f3 statistics suggested distinct genetic structuring of JB, KAN and TEL(Tellicherry) as compared to the rest of the studied populations. Apart from this, we also identified 32 selection signatures through VST (Variance-stabilizing transformation) method and key genes such as ZBTB7C, BHLHE22, AGT were found elucidating the genetic architecture of hot and cold adaptation in Indian goats. Information generated hereby in the form of 32,711 autosomal CNVRs and the custom scripts ( https://github.com/kkokay07/Climate-Variables-Analysis.git , https://github.com/chau-mau/SelectCNVR.git and https://github.com/chau-mau/CNVrecaller.git ) will be of relevance in further studies on copy number based genetics.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772349","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}

引用次数: 0

Identification and validation of mitochondrial endoplasmic reticulum membrane-related genes in atherosclerosis. 动脉粥样硬化中线粒体内质网膜相关基因的鉴定和验证。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-28 DOI: 10.1007/s00335-025-10124-0

Li-Rong Wang, Chun-Xi Zhang, Lv-Bo Tian, Jie Huang, Li-Jun Jia, Hao Tao, Neng-Wei Yu, Bing-Hu Li

引用次数: 0

The mouse resource at National Resource Center for Mutant Mice of China. 中国国家突变小鼠资源中心的小鼠资源。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-27 DOI: 10.1007/s00335-025-10118-y

Bingzhou Han, Dongshen Chen, Zhong Chen, Ting Wang, Kaiyuan Zi, Rui Feng, Xiaoliu Yang, Ling'en Li, Juan Liang, Xiang Gao

引用次数: 0

The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas. RSPO2基因与吉娃娃双侧前amelia相关。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-25 DOI: 10.1007/s00335-025-10123-1

Lucie Chevallier, Marin Green, Julia Vo, Karen Vernau, Denis J Marcellin-Little, Vidhya Jagannathan, Tosso Leeb, Danika Bannasch

{"title":"The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas.","authors":"Lucie Chevallier, Marin Green, Julia Vo, Karen Vernau, Denis J Marcellin-Little, Vidhya Jagannathan, Tosso Leeb, Danika Bannasch","doi":"10.1007/s00335-025-10123-1","DOIUrl":"https://doi.org/10.1007/s00335-025-10123-1","url":null,"abstract":"Bilateral anterior amelia (BAA) is the congenital absence of thoracic limbs and has been reported in the Chihuahua as an autosomal recessive disorder. In some cases, the digits of the pelvic limbs can be variably affected, but otherwise, the pelvic limbs are generally spared. A GWAS performed with nine BAA affected Chihuahuas identified a significant association on chromosome 13, and homozygosity mapping delineated a 2.1 Mb chromosomal region containing the RSPO2 gene. Loss of function variants of RSPO2 in humans and cattle has been associated with the absence of all limbs. Six affected Chihuahuas were whole genome sequenced (WGS) and aligned to the CanFam4 assembly. SNVs, small indels, and structural variants within the critical interval that fitted a recessive model were investigated. Three SNVs (NC_049234.1:g.8891861C > T; NC_049234.1:g.8974204C > T and NC_049234.1:g.9789424G > A) were homozygous in five cases and absent from 3,418 genetically diverse control genome sequences, except for one Small Poodle that was heterozygous. One SNV resided in RSPO2's second intron, while the two others were intergenic. The three candidate variants were genotyped in 7 additional cases and 100 control Chihuahuas. Twelve of 13 cases were homozygous for the mutant allele, and one case was heterozygous. Controls were either homozygous for the reference allele (97%) or heterozygous (3%). Our data should facilitate genetic testing of Chihuahuas to prevent the unintentional production of BAA affected dogs. Moreover, the identification of these variants enhances understanding of RSPO2 gene function in limb development.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710595","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}

引用次数: 0

Identification of NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis. 利用RNA测序和单细胞分析鉴定nets相关基因作为缺血性脑卒中的诊断生物标志物。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-19 DOI: 10.1007/s00335-025-10117-z

Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen

{"title":"Identification of NETs-related genes as diagnostic biomarkers in ischemic stroke using RNA sequencing and single-cell analysis.","authors":"Rongxing Qin, Wei Xu, Qingchun Qin, Xiaojun Liang, Xinyu Lai, Minshan Xie, Li Chen","doi":"10.1007/s00335-025-10117-z","DOIUrl":"https://doi.org/10.1007/s00335-025-10117-z","url":null,"abstract":"Neutrophil extracellular traps (NETs) are increasingly recognized for their involvement in ischemic stroke (IS), yet their precise contribution to IS outcomes is not fully understood. This study aims to elucidate the role of NETs in IS progression and identify potential biomarkers and therapeutic targets. In this study, mice were subjected to middle cerebral artery occlusion (MCAO). RNA sequencing was conducted on brain tissue samples to identify differentially expressed genes (DEGs) using the \"limma\" package. The diagnostic potential of these biomarkers was assessed using receiver operating characteristic (ROC) curve analysis. Additionally, single-cell RNA sequencing data were analyzed with the Seurat package to further investigate the cellular dynamics. We identified DEGs, and NETs-related genes associated with IS progression. Specifically, Ceacam3, Tnf, Selp, and Fcgr4 were found to be upregulated in MCAO samples, exhibiting diagnostic value as biomarkers for IS. Immune infiltration analysis indicated associations between these genes and various immune cell types. Gene Set Enrichment Analysis (GSEA) revealed their involvement in IS-related pathways, including ferroptosis, IL-17 signaling, leukocyte transendothelial migration, necroptosis, and NETs formation. Single-cell data confirmed the expression of Tnf, Selp, and Fcgr4 in neutrophils. CellChat analysis uncovered key cell-cell interactions in IS, emphasizing the role of neutrophils in communicating with microglia and T cells via the JAM pathway, with Thbs1 and Cd47 as key mediators. The findings provide insights into the cellular and molecular mechanisms underlying IS and may pave the way for novel therapeutic strategies targeting NETs in IS patients.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663921","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}

引用次数: 0

Rat models of musculoskeletal lysosomal storage disorders and their role in pre-clinical evaluation of gene therapy approaches. 肌肉骨骼溶酶体贮积症大鼠模型及其在基因治疗方法临床前评估中的作用。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2025-03-18 DOI: 10.1007/s00335-025-10121-3

Sara Marcó, Sergio Muñoz, Fatima Bosch, Veronica Jimenez

{"title":"Rat models of musculoskeletal lysosomal storage disorders and their role in pre-clinical evaluation of gene therapy approaches.","authors":"Sara Marcó, Sergio Muñoz, Fatima Bosch, Veronica Jimenez","doi":"10.1007/s00335-025-10121-3","DOIUrl":"https://doi.org/10.1007/s00335-025-10121-3","url":null,"abstract":"Mice have been a cornerstone of biomedical research for decades for studying a wide range of biological processes, disease mechanisms, and the assessment of therapies. Moreover, mice present several practical advantages such as small size, low cost and ease of genetic manipulation. While mice offer numerous benefits, for certain disease areas, rat models provide a closer representation of human disease progression, offering better insights for translational research and therapeutic development. This closer resemblance is particularly important for research focusing on diseases involving the cardiovascular and musculoskeletal system. In rats, the pathophysiology of these diseases mirrors the clinical alterations observed in humans. This review focuses on the key phenotypic differences between mouse and rat models of lysosomal storage disorders that specifically manifest with cardiac, skeletal muscle, and bone and joint involvement (Pompe and Danon diseases, and Maroteaux-Lamy and Morquio A syndromes). Furthermore, we discuss the therapeutic potential of various adeno-associated viral vector-mediated gene therapies that have been evaluated in these rat models, highlighting their contributions to advancing treatment options for these debilitating conditions.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657668","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}

引用次数: 0