Genomics, proteomics & bioinformatics最新文献

Plasma Proteomic Profiling Reveals ITGA2B as A Key Regulator of Heart Health in High-altitude Settlers.

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.

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.

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.

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.

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

Harnessing the Foundation Model for Exploration of Single-cell Expression Atlases in Plants.

Genomics, proteomics & bioinformatics Pub Date : 2025-03-17 DOI: 10.1093/gpbjnl/qzaf024

Guangshuo Cao, Haoyu Chao, Wenqi Zheng, Yangming Lan, Kaiyan Lu, Yueyi Wang, Ming Chen, He Zhang, Dijun Chen

{"title":"Harnessing the Foundation Model for Exploration of Single-cell Expression Atlases in Plants.","authors":"Guangshuo Cao, Haoyu Chao, Wenqi Zheng, Yangming Lan, Kaiyan Lu, Yueyi Wang, Ming Chen, He Zhang, Dijun Chen","doi":"10.1093/gpbjnl/qzaf024","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf024","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into plant cellular diversity by enabling high-resolution analyses of gene expression at the single-cell level. However, the complexity of scRNA-seq data, including challenges in batch integration, cell type annotation, and gene regulatory network (GRN) inference, demands advanced computational approaches. To address these challenges, we developed scPlantLLM, a Transformer model trained on millions of plant single-cell data points. Using a sequential pretraining strategy incorporating masked language modeling and cell type annotation tasks, scPlantLLM generates robust and interpretable single-cell data embeddings. When applied to Arabidopsis thaliana datasets, scPlantLLM excels in clustering, cell type annotation, and batch integration, achieving an accuracy of up to 0.91 in zero-shot learning scenarios. Furthermore, the model demonstrates an ability to identify biologically meaningful GRNs and subtle cellular subtypes, showcasing its potential to advance plant biology research. Compared to traditional methods, scPlantLLM outperforms in key metrics such as adjusted rand index (ARI), normalized mutual information (NMI) and silhouette score (SIL), highlighting its superior clustering accuracy and biological relevance. scPlantLLM represents a foundational model for exploring plant single-cell expression atlases, offering unprecedented capabilities to resolve cellular heterogeneity and regulatory dynamics across diverse plant systems. The code used in this study is available at https://github.com/compbioNJU/scPlantLLM.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652870","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

LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals.

Genomics, proteomics & bioinformatics Pub Date : 2025-03-17 DOI: 10.1093/gpbjnl/qzaf025

Fengting Bai, Yudong Cai, Min Qi, Chen Liang, Linqian Pan, Yayi Liu, Yanshuai Feng, Xuesha Cao, Qimeng Yang, Gang Ren, Shaohua Jiao, Siqi Gao, Meixuan Lu, Xihong Wang, Rasmus Heller, Johannes A Lenstra, Yu Jiang

{"title":"LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals.","authors":"Fengting Bai, Yudong Cai, Min Qi, Chen Liang, Linqian Pan, Yayi Liu, Yanshuai Feng, Xuesha Cao, Qimeng Yang, Gang Ren, Shaohua Jiao, Siqi Gao, Meixuan Lu, Xihong Wang, Rasmus Heller, Johannes A Lenstra, Yu Jiang","doi":"10.1093/gpbjnl/qzaf025","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf025","url":null,"abstract":"Natural variants can significantly improve growth traits in livestock and serve as safe targets for gene editing, thus being applied in animal molecular designed breeding. However, such safe and large-effect mutations are severely lacking. Using ancestral recombination graphs, we investigated recent selection signatures in beef cattle breeds, pinpointing sweep-driving variants in the LCORL and STC2 loci with notable effects on body size and growth rate. The ACT-to-A frameshift mutation in LCORL occurs mainly in central-European cattle, and stimulates growth. Remarkably, convergent truncating mutations were also found in commercial breeds of sheep, goats, pigs, horses, dogs, rabbits, and chickens. In STC2 gene, we identified a missense mutation (A60P) located within the conserved region across vertebrates. We validated the two natural mutations in gene-edited mouse models, where both variants in homozygous carriers significantly increase the average weight by 11%. Our findings provide insights into a seemingly recurring gene target of body size enhancing truncating mutations across domesticated species, and offer valuable targets for gene editing-based breeding in animals.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652871","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 High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans. PD-1的高表达定义了对COVID-19疫苗有反应的Tfh细胞亚群。

Genomics, proteomics & bioinformatics Pub Date : 2025-03-13 DOI: 10.1093/gpbjnl/qzaf019

Jingxin Guo, Zhangfan Fu, Yi Zhang, Mengyuan Xu, Jinhang He, Haocheng Zhang, Qiran Zhang, Jieyu Song, Ke Lin, Mingxiang Fan, Zhangyufan He, Guanmin Yuan, Ning Jiang, Huang Huang, Chao Qiu, Jingwen Ai, Wenhong Zhang

{"title":"The High Expression of PD-1 Defines A Subpopulation of Tfh Cells Responding to COVID-19 Vaccine in Humans.","authors":"Jingxin Guo, Zhangfan Fu, Yi Zhang, Mengyuan Xu, Jinhang He, Haocheng Zhang, Qiran Zhang, Jieyu Song, Ke Lin, Mingxiang Fan, Zhangyufan He, Guanmin Yuan, Ning Jiang, Huang Huang, Chao Qiu, Jingwen Ai, Wenhong Zhang","doi":"10.1093/gpbjnl/qzaf019","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf019","url":null,"abstract":"Inactivated coronavirus disease 2019 (COVID-19) vaccines and receptor binding domain subunit (RBD-subunit) booster vaccination can induce effective humoral immune response. CD4+ T helper cells are essential in helping B cells and antibody response. However, the response of CD4+ T cells to booster vaccination, especially the virus-induced T follicular helper (Tfh) cells, needs to be better characterized. In this study, it was investigated using tools of single-cell sequencing and flow cytometry. Additionally, a customized analysis algorithm was applied to identify virus-induced T cell receptor (VI-TCR) which is useful to explore the activation and persistence of virus-induced CD4+ T cell response. We identified a subset of classic Tfh (cTfh) cells with high expression of PD-1 and IFN-γ. They were notably activated following booster vaccination, and their proportion was correlated with the antibody titer level. We used trajectory analysis to analyze the dynamic changes of activated and found that a subset of virus-induced cTfh cells might maintain immune responses beyond 90 days post-vaccination. In summary, we found a group of PD-1high cTfh cells in COVID-19 vaccination, which can enhance the humoral response and show the persistence of immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We also provided a method for single-cell immune data analysis to understand the virus-induced responses. Understanding how cTfh cells help antibody production will provide essential insights into the rational design of new vaccine strategies to optimize long-term immunity.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627250","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

Haplotype-based Pangenomics: A Blueprint for Climate Adaptation in Plants.

Genomics, proteomics & bioinformatics Pub Date : 2025-03-10 DOI: 10.1093/gpbjnl/qzaf023

Wanfei Liu, Peng Cui

引用次数: 0

High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.

Genomics, proteomics & bioinformatics Pub Date : 2025-03-10 DOI: 10.1093/gpbjnl/qzaf022

Qingxin Yang, Yuntao Sun, Shuhan Duan, Shengjie Nie, Chao Liu, Hong Deng, Mengge Wang, Guanglin He

{"title":"High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.","authors":"Qingxin Yang, Yuntao Sun, Shuhan Duan, Shengjie Nie, Chao Liu, Hong Deng, Mengge Wang, Guanglin He","doi":"10.1093/gpbjnl/qzaf022","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf022","url":null,"abstract":"Large-scale international and regional human genomic and pangenomic resources derived from population-scale biobanks and ancient DNA sequences have provided significant insights into human evolution and the genetic determinants of complex diseases and traits. Despite these advances, challenges persist in optimizing the integration of phasing tools, merging haplotype reference panels (HRPs), developing imputation algorithms, and fully exploiting the diverse applications of post-imputation data. This review comprehensively summarizes the advancements, applications, limitations, and future directions of HRPs in human genomics research. Recent progress in the reconstruction of HRPs, based on over 830,000 human whole-genome sequences, has been synthesized, highlighting the broad spectrum of human genetic diversity captured. Additionally, we recapitulate advancements in fifty-six HRPs for global and regional populations. The evaluation of imputation accuracy indicated that Beagle and GLIMPSE are the most effective tools for phasing and imputing data from genotyping arrays and low-coverage sequencing, respectively. A critical strategy for selecting an appropriate HRP involves matching the population background of target groups with HRP reference populations and considering multi-ancestry or homogeneous genetic structures. The necessity of a single, integrative, high-quality HRP that captures haplotype structures and genetic diversity across various genetic variation types from globally representative populations is emphasized to support both modern and ancient genomic research and advance human precision medicine.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588971","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