Genomics, proteomics & bioinformatics最新文献_第2页

Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes. 基于差分基因整合的时间序列动态网络识别白血病相关基因。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-29 DOI: 10.1093/gpbjnl/qzaf037

Jin A, Ju Xiang, Xiangmao Meng, Yue Sheng, Hongling Peng, Min Li

{"title":"Identifying Leukemia-related Genes based on Time-series Dynamical Network by Integrating Differential Genes.","authors":"Jin A, Ju Xiang, Xiangmao Meng, Yue Sheng, Hongling Peng, Min Li","doi":"10.1093/gpbjnl/qzaf037","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf037","url":null,"abstract":"Leukemia is a malignant disease of progressive accumulation characterized by high morbidity and mortality rates, and investigating its disease genes is crucial for understanding its etiology and pathogenesis. Network propagation methods have emerged and been widely employed in disease gene prediction, but most of them focus on static biological networks, which hinders their applicability and effectiveness in the study of progressive diseases. Moreover, there is currently a lack of special algorithms for the identification of leukemia disease genes. Here, we proposed DyNDG, a novel dynamic network-based model, which integrates differentially expressed genes to identify leukemia-related genes. Initially, we constructed a time-series dynamic network to model the development trajectory of leukemia. Then, we built a background-temporal multilayer network by integrating both the dynamic network and the static background network, which was initialized with differentially expressed genes at each stage. To quantify the associations between genes and leukemia, we extended a random walk process to the background-temporal multilayer network. The experimental results demonstrate that DyNDG achieves superior accuracy compared to several state-of-the-art methods. Moreover, after excluding housekeeping genes, DyNDG yields a set of promising candidate genes associated with leukemia progression or potential biomarkers, indicating the value of dynamic network information in identifying leukemia-related genes. The implementation of DyNDG is available at both https://ngdc.cncb.ac.cn/biocode/tool/BT7617 and https://github.com/CSUBioGroup/D yNDG.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144046297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes. 主动脉瘤和夹层的全基因组关联荟萃分析鉴定出五个新基因。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-29 DOI: 10.1093/gpbjnl/qzaf039

Yifan Du, Yunlong Guan, Zhonghe Shao, Minghui Jiang, Minghan Qu, Yifan Kong, Hongji Wu, Da Luo, Shu Peng, Si Li, Xi Cao, Jing Chen, Ping Ye, Jiahong Xia, Xingjie Hao

{"title":"Integrative Genome-wide Association Meta-analysis of Aortic Aneurysm and Dissection Identifies Five Novel Genes.","authors":"Yifan Du, Yunlong Guan, Zhonghe Shao, Minghui Jiang, Minghan Qu, Yifan Kong, Hongji Wu, Da Luo, Shu Peng, Si Li, Xi Cao, Jing Chen, Ping Ye, Jiahong Xia, Xingjie Hao","doi":"10.1093/gpbjnl/qzaf039","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf039","url":null,"abstract":"Aortic aneurysm and dissection (AAD) is a multifaceted condition characterized by significant genetic predisposition and a considerable contribution to cardiovascular-related mortality. Previous studies have suggested that AAD subtypes share similar genetic mechanisms, however, these studies investigated the subtypes separately. Here, we performed a large genome-wide association study (GWAS) meta-analysis for AAD by combining its subtypes, including 11,148 cases and 708,468 controls of European ancestry. We identified 24 susceptibility loci, including four novel loci at 1p21.2 (PALMD), 2p22.2 (CRIM1), 6q22.1 (FRK), and 12q14.3 (HMGA2), which were partially validated in both internal and external populations. Cell type-specific analysis highlighted the artery as the most relevant tissue where the susceptibility variants may exert their effects in a tissue-specific manner. By using four approaches, we prioritized 53 genes, reinforcing the importance of elastic fiber formation and transforming growth factor-beta (TGF-β) signaling in the formation of AAD, and suggested potential target drugs for the treatment. Additionally, various cardiovascular diseases were genetically correlated with AAD, and several cardiovascular risk factors [e.g., body mass index (BMI), lipid levels, and pulse pressure] showed causal associations with AAD, underscoring their shared genetic structures and mechanisms underlying the comorbidity. Moreover, five prioritized genes (PALMD, CRIM1, FRK, HMGA2, and NT5DC1) at the novel loci were supported as regulators of smooth muscle and endothelial cell functions through ex vivo and in vitro experiments. Together, these findings enhance our understanding of the genetic architecture of AAD and provide novel insights into future biological mechanism studies and therapeutic strategies.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP. UNISOM：统一的躯体呼叫和基于机器学习的分类增强了对CHIP的发现。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-29 DOI: 10.1093/gpbjnl/qzaf040

Shulan Tian, Garrett Jenkinson, Alejandro Ferrer, Huihuang Yan, Joel A Morales-Rosado, Kevin L Wang, Terra L Lasho, Benjamin B Yan, Saurabh Baheti, Janet E Olson, Linda B Baughn, Wei Ding, Susan L Slager, Mrinal S Patnaik, Konstantinos N Lazaridis, Eric W Klee

{"title":"UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP.","authors":"Shulan Tian, Garrett Jenkinson, Alejandro Ferrer, Huihuang Yan, Joel A Morales-Rosado, Kevin L Wang, Terra L Lasho, Benjamin B Yan, Saurabh Baheti, Janet E Olson, Linda B Baughn, Wei Ding, Susan L Slager, Mrinal S Patnaik, Konstantinos N Lazaridis, Eric W Klee","doi":"10.1093/gpbjnl/qzaf040","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf040","url":null,"abstract":"Clonal hematopoiesis (CH) of indeterminate potential (CHIP), driven by somatic mutations in leukemia-associated genes, confers increased risk of hematologic malignancies, cardiovascular disease, and all-cause mortality. In blood of healthy individuals, small CH clones can expand over time to reach 2% variant allele frequency (VAF), the current threshold for CHIP. Nevertheless, reliable detection of low-VAF CHIP mutations is challenging, often relying on deep targeted sequencing. Here, we present UNISOM, a streamlined workflow for enhancing CHIP detection from whole-genome and whole-exome sequencing data that are underpowered, especially for low VAFs. UNISOM utilizes a meta-caller for variant detection, in couple with machine learning models which classify variants into CHIP, germline, and artifact. In whole-exome data, UNISOM recovered nearly 80% of the CHIP mutations identified via deep targeted sequencing in the same cohort. Applied to whole-genome sequencing data from Mayo Clinic Biobank, it recapitulated the patterns previously established in much larger cohorts, including the most frequently mutated CHIP genes, predominant mutation types and signatures, as well as strong associations of CHIP with age and smoking status. Notably, 30% of the identified CHIP mutations had < 5% VAFs, demonstrating its high sensitivity toward small mutant clones. This workflow is applicable to CHIP screening in population genomic studies. The UNISOM pipeline is freely available at https://github.com/shulanmayo/UNISOM and https://ngdc.cncb.ac.cn/biocode/tool/7816.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Computational and Functional Screening Identify G9a Inhibitors for SETD2-Mutant Leukemia. 综合计算和功能筛选确定setd2突变白血病的G9a抑制剂。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-29 DOI: 10.1093/gpbjnl/qzaf035

Ya Zhang, Mengfang Xia, Zhenyi Yi, Pinpin Sui, Xudong He, Liping Wang, Qiyi Chen, Hong-Hu Zhu, Gang Huang, Qian-Fei Wang

{"title":"Integrated Computational and Functional Screening Identify G9a Inhibitors for SETD2-Mutant Leukemia.","authors":"Ya Zhang, Mengfang Xia, Zhenyi Yi, Pinpin Sui, Xudong He, Liping Wang, Qiyi Chen, Hong-Hu Zhu, Gang Huang, Qian-Fei Wang","doi":"10.1093/gpbjnl/qzaf035","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf035","url":null,"abstract":"SETD2, a frequently mutated epigenetic tumor suppressor in acute leukemia, is associated with chemotherapy resistance and poor patient outcomes. To explore potential therapeutics for SETD2-mutant leukemia, we employed an integrated approach combining computational prediction with epigenetic compound library screening. This approach identified G9a inhibitors as promising candidates, capable of reversing gene expression signatures associated with Setd2 deficiency and selectively inhibiting SETD2-deficient cells. RNA-sequencing analysis revealed that G9a inhibitor significantly downregulated Myc and Myc-regulated genes involved in translation, DNA replication, and G1/S transition in Setd2-mutant cells. Further chromatin immunoprecipitation sequencing analysis showed that G9a inhibition reduced H3K9me2 levels at the long non-coding RNA Mir100hg locus, coinciding with specific upregulation of the embedded microRNA let-7a-2 in Setd2-mutant cells. Given the established role of let-7a in MYC suppression, these findings suggest a potential mechanism by which G9a inhibitors induce MYC downregulation in SETD2-mutant leukemia. Additionally, correlation analysis between computational prediction and phenotypic outcomes highlighted the MYC signature as a key predictor of drug efficacy. Collectively, our study identifies G9a inhibitors as a promising therapeutic avenue for SETD2-mutant leukemia and provides novel insights into refining drug prediction strategies.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Pathogen Adaptation of HLA Alleles and the Correlation with Autoimmune Diseases in the Han Chinese. 汉族HLA等位基因的病原适应性及其与自身免疫性疾病的相关性

Genomics, proteomics & bioinformatics Pub Date : 2025-04-29 DOI: 10.1093/gpbjnl/qzaf038

Shuai Liu, Yanyan Li, Tingrui Song, Jingjing Zhang, Peng Zhang, Huaxia Luo, Sijia Zhang, Yiwei Niu, Tao Xu, Shunmin He

{"title":"The Pathogen Adaptation of HLA Alleles and the Correlation with Autoimmune Diseases in the Han Chinese.","authors":"Shuai Liu, Yanyan Li, Tingrui Song, Jingjing Zhang, Peng Zhang, Huaxia Luo, Sijia Zhang, Yiwei Niu, Tao Xu, Shunmin He","doi":"10.1093/gpbjnl/qzaf038","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf038","url":null,"abstract":"Human leukocyte antigen (HLA) genes play a crucial role in the adaptation of human populations to the dynamic pathogenic environment. Despite their significance, investigating the pathogen-driven evolution of HLAs and the implications for autoimmune diseases presents considerable challenges. Here, we genotyped over twenty HLA genes at 3-field resolution in 8278 individuals from diverse ethnic backgrounds, including 4013 unrelated Han Chinese. We focused on the adaptation of HLAs in the Han Chinese by analyzing their binding affinity for various pathogens, and explored the potential correlations between pathogen adaptation and autoimmune diseases. Our findings reveal that specific HLA alleles like HLA-DRB1*07:01 and HLA-DQB1*06:01 confer strong pathogen adaptability at the sequence level, notably for Corynebacterium diphtheriae and Bordetella pertussis. Additionally, alleles like HLA-C*03:02 demonstrate adaptive selection against pathogens like Mycobacterium tuberculosis and coronavirus at the gene expression level. Simultaneously, the aforementioned HLA alleles are closely related to some autoimmune diseases such as multiple sclerosis (MS). These exploratory discoveries shed light on the intricate coevolutionary relationships between pathogen adaptation and autoimmune diseases in the human population. These efforts led to an HLA database at http://bigdata.ibp.ac.cn/HLAtyping, aiding searches for HLA allele frequencies across populations.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR Technology and Its Emerging Applications. CRISPR技术及其新兴应用。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-23 DOI: 10.1093/gpbjnl/qzaf034

Xuejing Zhang, Dongyuan Ma, Feng Liu

引用次数: 0

TRAIT: A Comprehensive Database for T-cell Receptor-Antigen Interactions. TRAIT: t细胞受体-抗原相互作用的综合数据库。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-21 DOI: 10.1093/gpbjnl/qzaf033

Mengmeng Wei, Jingcheng Wu, Shengzuo Bai, Yuxuan Zhou, Yichang Chen, Xue Zhang, Wenyi Zhao, Ying Chi, Gang Pan, Feng Zhu, Shuqing Chen, Zhan Zhou

{"title":"TRAIT: A Comprehensive Database for T-cell Receptor-Antigen Interactions.","authors":"Mengmeng Wei, Jingcheng Wu, Shengzuo Bai, Yuxuan Zhou, Yichang Chen, Xue Zhang, Wenyi Zhao, Ying Chi, Gang Pan, Feng Zhu, Shuqing Chen, Zhan Zhou","doi":"10.1093/gpbjnl/qzaf033","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf033","url":null,"abstract":"Comprehensive and integrated resources on interactions between T-cell receptors (TCRs) and antigens are still lacking for adoptive T-cell-based immunotherapies, highlighting a significant gap that must be addressed to fully comprehend the mechanisms of antigen recognition by T-cells. In this study, we present the T-cell receptor-antigen interaction database (TRAIT), a comprehensive database that profiles the interactions between TCRs and antigens. TRAIT stands out due to its comprehensive description of TCR-antigen interactions by integrating sequences, structures, and affinities. It provides millions of experimentally validated TCR-antigen pairs, resulting in an exhaustive landscape of antigen-specific TCRs. Notably, TRAIT emphasizes single-cell omics as a major reliable data source for TCR-antigen interactions and includes millions of reliable non-interactive TCRs. Additionally, it thoroughly demonstrates the interactions between mutations of TCRs and antigens, thereby benefiting affinity maturation of engineered TCRs as well as vaccine design. TCRs on clinical trials were innovatively provided. With the significant efforts made towards elucidating the complex interactions between TCRs and antigens, TRAIT is expected to ultimately contribute superior algorithms and substantial advancements in the field of T-cell-based immunotherapies. TRAIT is freely accessible at https://pgx.zju.edu.cn/traitdb.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes. GCRP：来自11,951只鸡基因组的综合全球鸡参考面板。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-15 DOI: 10.1093/gpbjnl/qzaf032

Di Zhu, Yuzhan Wang, Hao Qu, Chugang Feng, Hui Zhang, Zheya Sheng, Yunliang Jiang, Qinghua Nie, Suqiao Chu, Dingming Shu, Ziqin Jiang, Dexiang Zhang, Lingzhao Fang, Hui Li, Zhenqiang Xu, Yiqiang Zhao, Yuzhe Wang, Xiaoxiang Hu

{"title":"GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.","authors":"Di Zhu, Yuzhan Wang, Hao Qu, Chugang Feng, Hui Zhang, Zheya Sheng, Yunliang Jiang, Qinghua Nie, Suqiao Chu, Dingming Shu, Ziqin Jiang, Dexiang Zhang, Lingzhao Fang, Hui Li, Zhenqiang Xu, Yiqiang Zhao, Yuzhe Wang, Xiaoxiang Hu","doi":"10.1093/gpbjnl/qzaf032","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf032","url":null,"abstract":"Chickens are a crucial source of protein for humans and a popular model animal for bird research. Despite the emergence of imputation as a reliable genotyping strategy for large populations, the lack of a high-quality chicken reference panel has hindered progress in chicken genome research. To address this, here we introduce the first phase of the 100K Global Chicken Reference Panel (100K GCRP). Currently, two panels are available: a comprehensive mix panel (CMP) for domestication diversity research and a commercial breed panel (CBP) for breeding broilers specifically. Evaluation of genotype imputation quality showed that CMP had the highest imputation accuracy compared to imputation using existing chicken panels in Animal-SNPAtlas and Animal Genotype Imputation Database (AGIDB), whereas CBP performed stably in the imputation of commercial populations. Additionally, we found that genome-wide association studies using GCRP-imputed data, whether on simulated or real phenotypes, exhibited greater statistical power. In conclusion, our study indicates that the GCRP effectively fills the gap in high-quality reference panels for chickens, providing an effective imputation platform for future genetic and breeding research. The project includes 11,951 samples and provides services for various applications on its website at http://farmrefpanel.com/GCRP/#/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights. PlateletBase：血小板研究和疾病洞察的综合知识库。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-12 DOI: 10.1093/gpbjnl/qzaf031

Huaichao Luo, Changchun Wu, Sisi Yu, Hanxiao Ren, Xing Yin, Ruiling Zu, Lubei Rao, Peiying Zhang, Xingmei Zhang, Ruohao Wu, Ping Leng, Kaijiong Zhang, Qi Peng, Bangrong Cao, Rui Qin, Hulin Wei, Jianlin Qiao, Shanling Xu, Qun Yi, Yang Zhang, Jian Huang, Dongsheng Wang

{"title":"PlateletBase: A Comprehensive Knowledgebase for Platelet Research and Disease Insights.","authors":"Huaichao Luo, Changchun Wu, Sisi Yu, Hanxiao Ren, Xing Yin, Ruiling Zu, Lubei Rao, Peiying Zhang, Xingmei Zhang, Ruohao Wu, Ping Leng, Kaijiong Zhang, Qi Peng, Bangrong Cao, Rui Qin, Hulin Wei, Jianlin Qiao, Shanling Xu, Qun Yi, Yang Zhang, Jian Huang, Dongsheng Wang","doi":"10.1093/gpbjnl/qzaf031","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf031","url":null,"abstract":"Platelets are vital in many pathophysiological processes, yet there is a lack of a comprehensive resource dedicated specifically to platelet research. To fill this gap, we have developed PlateletBase, a knowledge base aimed at enhancing the understanding and study of platelets and related diseases. Our team retrieved information from various public databases, specifically extracting and analyzing RNA sequencing (RNA-seq) data from 3711 samples across 41 different conditions available on the National Center of Biotechnology Information (NCBI). PlateletBase offers six analytical and visualization tools, enabling users to perform gene similarity analysis, pair correlation, multi-correlation, expression ranking, clinical information association, and gene annotation for platelets. The current version of PlateletBase includes 10,278 genomic entries, 31,758 transcriptomic entries, 4869 proteomic entries, 2614 omics knowledge entries, 1833 drugs, 97 platelet resources, 438 diseases/traits, and six analysis modules. Each entry has been carefully curated and supported by experimental evidence. Additionally, PlateletBase features a user-friendly interface designed for efficient querying, manipulation, browsing, visualization, and analysis of detailed platelet protein and gene information. The case studies on gray platelet syndrome and angina pectoris demonstrate that PlateletBase is a suitable tool for identifying diagnostic biomarkers and exploring disease mechanisms, thereby advancing research in platelet functionality. PlateletBase is accessible at http://plateletbase.clinlabomics.org.cn/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plasma Proteomic Profiling Reveals ITGA2B as A Key Regulator of Heart Health in High-altitude Settlers. 血浆蛋白质组学分析显示ITGA2B是高海拔移民心脏健康的关键调节因子

Genomics, proteomics & bioinformatics Pub Date : 2025-04-08 DOI: 10.1093/gpbjnl/qzaf030

Yihao Wang, Pan Shen, Zhenhui Wu, Bodan Tu, Cheng Zhang, Yongqiang Zhou, Yisi Liu, Guibin Wang, Zhijie Bai, Xianglin Tang, Chengcai Lai, Haitao Lu, Wei Zhou, Yue Gao

{"title":"Plasma Proteomic Profiling Reveals ITGA2B as A Key Regulator of Heart Health in High-altitude Settlers.","authors":"Yihao Wang, Pan Shen, Zhenhui Wu, Bodan Tu, Cheng Zhang, Yongqiang Zhou, Yisi Liu, Guibin Wang, Zhijie Bai, Xianglin Tang, Chengcai Lai, Haitao Lu, Wei Zhou, Yue Gao","doi":"10.1093/gpbjnl/qzaf030","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf030","url":null,"abstract":"Myocardial injury is a common disease in the plateau, especially in the lowlanders who have migrated to the plateau, in which the pathogenesis is not well understood. Here, we established a cohort of lowlanders comprising individuals from both low-altitude and high-altitude areas and conducted plasma proteome profiling. Proteomic data showed that there was a significant shift in energy metabolism and inflammatory response in individuals with myocardial abnormalities at high altitude. Notably, integrin ITGA2B emerged as a potential key player in this context. Functional studies demonstrated that ITGA2B upregulated the transcription and secretion of interleukin-6 (IL-6) through integrin-linked kinase (ILK) and nuclear factor-κB (NF-κB) signaling axis under hypoxic conditions. Moreover, ITGA2B disrupted mitochondrial structure and function, increased glycolytic capacity, and aggravated energy reprogramming from oxidative phosphorylation to glycolysis. Leveraging the therapeutic potential of traditional Chinese medicine in cardiac diseases, we discovered that tanshinone ⅡA (TanⅡA) effectively alleviated the high-altitude myocardial injury caused by the abnormally elevated expression of ITGA2B, thus providing a novel candidate therapeutic strategy for the prevention and treatment of high-altitude myocardial injury.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0