Genomics, proteomics & bioinformatics最新文献_第4页

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

Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-lineage Acute Lymphoblastic Leukemia. 糖酵解通过组蛋白乳酸化诱导t系急性淋巴细胞白血病的异常转录。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-07 DOI: 10.1093/gpbjnl/qzaf029

Wenyan Wu, Jingyi Zhang, Huiying Sun, Xiaoyu Wu, Han Wang, Bowen Cui, Shuang Zhao, Kefei Wu, Yanjun Pan, Rongrong Fan, Ying Zhong, Xiang Wang, Ying Wang, Xiaoxiao Chen, Jianan Rao, Ronghua Wang, Kai Luo, Xinrong Liu, Liang Zheng, Shuhong Shen, Meng Yin, Yangyang Xie, Yu Liu

{"title":"Glycolysis Induces Abnormal Transcription Through Histone Lactylation in T-lineage Acute Lymphoblastic Leukemia.","authors":"Wenyan Wu, Jingyi Zhang, Huiying Sun, Xiaoyu Wu, Han Wang, Bowen Cui, Shuang Zhao, Kefei Wu, Yanjun Pan, Rongrong Fan, Ying Zhong, Xiang Wang, Ying Wang, Xiaoxiao Chen, Jianan Rao, Ronghua Wang, Kai Luo, Xinrong Liu, Liang Zheng, Shuhong Shen, Meng Yin, Yangyang Xie, Yu Liu","doi":"10.1093/gpbjnl/qzaf029","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf029","url":null,"abstract":"The Warburg effect, which excessively produce lactate, and transcriptional dysregulation are two hallmarks of tumors. However, the precise influence of lactate on epigenetic modifications at a genome-wide level and its impact on gene transcription in tumor cells remain unclear. We conducted an analysis of genome-wide histone H3 lysine 18 lactylation (H3K18la) modifications in T-cell acute lymphoblastic leukemia (T-ALL). We found an increased level of lactate and H3K18la in T-ALL tumor cells compared to normal T cells and the H3K18la modification is associated with cell proliferation. Accordingly, we observed a significant shift in genome-wide H3K18la modification from T cell immunity in normal T cells to leukemogenesis in T-ALL, which correlated with altered gene transcription profiles. We showed that H3K18la is primarily involved in actively regulating gene transcription and observed clusters of H3K18la modifications exhibiting patterns reminiscent of super-enhancers. Disrupting H3K18la modification revealed both synergistic and divergent changes between H3K18la and histone H3 lysine 27 acetylation (H3K27ac) modifications. Finally, we found that the high transcription of H3K18la target genes, IGFBP2 and IARS, is associated with inferior prognosis of T-ALL. These findings enhance our understanding of how metabolic disruptions contribute to transcription dysregulation through epigenetic changes in T-ALL, underscoring the interplay of histone modifications in maintaining oncogenic epigenetic stability.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805197","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

Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response. 无细胞DNA片段组学检测鉴别乳腺结节恶性肿瘤及评价治疗效果。

Genomics, proteomics & bioinformatics Pub Date : 2025-04-04 DOI: 10.1093/gpbjnl/qzaf028

Jiaqi Liu, Yalun Li, Wanxiangfu Tang, Tianyi Qian, Lijun Dai, Ziqi Jia, Heng Cao, Chenghao Li, Yuchen Liu, Yansong Huang, Jiang Wu, Dongxu Ma, Guangdong Qiao, Hua Bao, Shuang Chang, Dongqin Zhu, Shanshan Yang, Xuxiaochen Wu, Xue Wu, Hengyi Xu, Hongyan Chen, Yang Shao, Xiang Wang, Zhihua Liu, Jianzhong Su

{"title":"Cell-free DNA Fragmentomics Assay to Discriminate the Malignancy of Breast Nodules and Evaluate Treatment Response.","authors":"Jiaqi Liu, Yalun Li, Wanxiangfu Tang, Tianyi Qian, Lijun Dai, Ziqi Jia, Heng Cao, Chenghao Li, Yuchen Liu, Yansong Huang, Jiang Wu, Dongxu Ma, Guangdong Qiao, Hua Bao, Shuang Chang, Dongqin Zhu, Shanshan Yang, Xuxiaochen Wu, Xue Wu, Hengyi Xu, Hongyan Chen, Yang Shao, Xiang Wang, Zhihua Liu, Jianzhong Su","doi":"10.1093/gpbjnl/qzaf028","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf028","url":null,"abstract":"The fragmentomics-based cell-free DNA (cfDNA) assays have recently illustrated prominent abilities to identify various cancers from non-conditional healthy controls, while their accuracy for identifying early-stage cancers from benign lesions with inconclusive imaging results remains uncertain. Especially for breast cancer, current imaging-based screening methods suffer from high false positive rates for women with breast nodules, leading to unnecessary biopsies, which add to discomfort and healthcare burden. Here, we enrolled 613 female participants in this multi-center study and demonstrated that cfDNA fragmentomics (cfFrag) is a robust non-invasive biomarker for breast cancer using whole-genome sequencing. Among the multimodal cfFrag profiles, the fragment size ratio (FSR), fragment size distribution (FSD), and copy number variation (CNV) show more distinguishing ability than Griffin, motif breakpoint (MBP), and neomer. The cfFrag model using the optimal three fragmentomics features discriminated early-stage breast cancers from benign nodules, even at a low sequencing depth (3×). Notably, it demonstrated a specificity of 94.1% in asymptomatic healthy women at a 90% sensitivity for breast cancers. Moreover, we comprehensively showcased the clinical utilities of the cfFrag model in predicting patient responses to neoadjuvant chemotherapy (NAC) and in combining with multimodal features, including radiological results and cfDNA methylation features [with area under the curve (AUC) values of 0.93-0.94 and 0.96, respectively].","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143784657","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

Clonal Hematopoietic Mutations in Plasma Cell Disorders: Clinical Subgroups and Shared Pathogenesis. 浆细胞疾病的克隆造血突变：临床亚群和共同发病机制。

Genomics, proteomics & bioinformatics Pub Date : 2025-03-27 DOI: 10.1093/gpbjnl/qzaf027

Xuezhu Wang, Liping Zuo, Yanying Yu, Xinyi Xiong, Jian Xu, Bing Qiao, Jia Chen, Hao Cai, Qi Yan, Hongxiao Han, Xin-Xin Cao, Jun Deng, Chunyan Sun, Jian Li

{"title":"Clonal Hematopoietic Mutations in Plasma Cell Disorders: Clinical Subgroups and Shared Pathogenesis.","authors":"Xuezhu Wang, Liping Zuo, Yanying Yu, Xinyi Xiong, Jian Xu, Bing Qiao, Jia Chen, Hao Cai, Qi Yan, Hongxiao Han, Xin-Xin Cao, Jun Deng, Chunyan Sun, Jian Li","doi":"10.1093/gpbjnl/qzaf027","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf027","url":null,"abstract":"Plasma cell disorders (PCDs) are marked by the clonal proliferation of abnormal plasma cells and bone marrow plasma cells (BMPCs), causing various clinical complications. These PCDs include subtypes with distinct clinical features. Multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS) are more common and relatively well-studied. In contrast, primary light-chain amyloidosis (AL) and POEMS syndrome (POEMS) are rare and remain less understood. To investigate the role of clonal hematopoietic (CH) mutations and potential interconnections in these diseases, we sequenced CH mutations in lymphoid and myeloid lineages, and myeloma driver gene mutations, in BMPCs from affected patients. Recurrent lymphoid CH mutations (in FAT1, KMT2D, MGA, and SYNE1) and myeloma driver gene mutations (in ZFHX3 and DIS3) were found in the dominant clonal and subclonal plasma cell populations. These moderately aging-associated lymphoid CH mutations had a higher burden in MM than in AL or POEMS. Binary matrix factorization of these mutations revealed the subgroups associated with progression-free survival (PFS) (observed in MM, AL, and POEMS), age at diagnosis (in AL and POEMS), serum differences in free light chain (dFLC) levels, and plasma cell burden (in AL), and serum vascular endothelial growth factor (VEGF) levels (in POEMS). Also, the poor PFS associated with MGA or SYNE1 mutations was confirmed across MM, AL, and POEMS. CH mutations partially explained the shared pathogenesis of MM, AL, POEMS, and MGUS, and helped identify patient subgroups with specific clinical features.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733745","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

HemAtlas: A Multi-omics Hematopoiesis Database. HemAtlas：一个多组学造血数据库。

Genomics, proteomics & bioinformatics Pub Date : 2025-03-19 DOI: 10.1093/gpbjnl/qzaf026

Zhixin Kang, Tongtong Zhu, Dong Zou, Mengyao Liu, Yifan Zhang, Lu Wang, Zhang Zhang, Feng Liu

{"title":"HemAtlas: A Multi-omics Hematopoiesis Database.","authors":"Zhixin Kang, Tongtong Zhu, Dong Zou, Mengyao Liu, Yifan Zhang, Lu Wang, Zhang Zhang, Feng Liu","doi":"10.1093/gpbjnl/qzaf026","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf026","url":null,"abstract":"Advancements in high-throughput omics technologies have facilitated a systematic exploration of crucial hematopoietic organs across diverse species. A thorough understanding of hematopoiesis in vivo and facilitation of generating functional hematopoietic stem and progenitor cells (HSPCs) in vitro necessitate a comprehensive hematopoietic cross-stage developmental landscape across species. To address this need, we developed HemAtlas, a platform designed for the systematic mapping of hematopoiesis both in vivo and in vitro. HemAtlas features detailed analyses of multi-omics datasets from humans, mice, zebrafish, and HSPC in vitro culture systems. Utilizing literature curation and data normalization, HemAtlas integrates various functional modules, allowing interactive exploration and visualization of any collected omics data based on user-specific interests. Moreover, by applying a systematic and uniform integration method, we constructed organ-wide hematopoietic references for each species with manually curated cell annotations, enabling a comprehensive decoding of cross-stage developmental hematopoiesis at the organ level. Of particular significance are three distinctive functions-single-cell cross-stage, cross-species, and cross-model analysis-that HemAtlas employs to elucidate the hematopoietic development in zebrafish, mice, and humans, and to offer guidance on the generation of HSPCs in vitro. Simultaneously, HemAtlas incorporates a comprehensive map of HSPC cross-stage development to reveal HSPC stage-specific properties. Taken together, HemAtlas serves as a crucial resource to advance our understanding of hematopoiesis and is available at https://ngdc.cncb.ac.cn/hematlas/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665771","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