iMeta最新文献

{"title":"TCellSI: A novel method for T cell state assessment and its applications in immune environment prediction","authors":"Jing-Min Yang,&nbsp;Nan Zhang,&nbsp;Tao Luo,&nbsp;Mei Yang,&nbsp;Wen-Kang Shen,&nbsp;Zhen-Lin Tan,&nbsp;Yun Xia,&nbsp;Libin Zhang,&nbsp;Xiaobo Zhou,&nbsp;Qian Lei,&nbsp;An-Yuan Guo","doi":"10.1002/imt2.231","DOIUrl":"https://doi.org/10.1002/imt2.231","url":null,"abstract":"<p>T cell is an indispensable component of the immune system and its multifaceted functions are shaped by the distinct T cell types and their various states. Although multiple computational models exist for predicting the abundance of diverse T cell types, tools for assessing their states to characterize their degree of resting, activation, and suppression are lacking. To address this gap, a robust and nuanced scoring tool called T cell state identifier (TCellSI) leveraging Mann–Whitney <i>U</i> statistics is established. The TCellSI methodology enables the evaluation of eight distinct T cell states—Quiescence, Regulating, Proliferation, Helper, Cytotoxicity, Progenitor exhaustion, Terminal exhaustion, and Senescence—from transcriptome data, providing T cell state scores (TCSS) for samples through specific marker gene sets and a compiled reference spectrum. Validated against sizeable pseudo-bulk and actual bulk RNA-seq data across a range of T cell types, TCellSI not only accurately characterizes T cell states but also surpasses existing well-discovered signatures in reflecting the nature of T cells. Significantly, the tool demonstrates predictive value in the immune environment, correlating T cell states with patient prognosis and responses to immunotherapy. For better utilization, the TCellSI is readily accessible through user-friendly R package and web server (https://guolab.wchscu.cn/TCellSI/). By offering insights into personalized cancer therapies, TCellSI has the potential to improve treatment outcomes and efficacy.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142449234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of respiratory system microbiota in development of lung cancer and clinical application","authors":"Bowen Li,&nbsp;Daoyun Wang,&nbsp;Chengye Zhang,&nbsp;Yadong Wang,&nbsp;Zhicheng Huang,&nbsp;Libing Yang,&nbsp;Huaxia Yang,&nbsp;Naixin Liang,&nbsp;Shanqing Li,&nbsp;Zhihua Liu","doi":"10.1002/imt2.232","DOIUrl":"https://doi.org/10.1002/imt2.232","url":null,"abstract":"<p>Microbes play a significant role in human tumor development and profoundly impact treatment efficacy, particularly in immunotherapy. The respiratory tract extensively interacts with the external environment and possesses a mucosal immune system. This prompts consideration of the relationship between respiratory microbiota and lung cancer. Advancements in culture-independent techniques have revealed unique communities within the lower respiratory tract. Here, we provide an overview of the respiratory microbiota composition, dysbiosis characteristics in lung cancer patients, and microbiota profiles within lung cancer. We delve into how the lung microbiota contributes to lung cancer onset and progression through direct functions, sustained immune activation, and immunosuppressive mechanisms. Furthermore, we emphasize the clinical utility of respiratory microbiota in prognosis and treatment optimization for lung cancer.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary therapies interlinking with gut microbes toward human health: Past, present, and future","authors":"Jiali Chen,&nbsp;Jiaqiang Luo,&nbsp;Sjaak Pouwels,&nbsp;Beijinni Li,&nbsp;Bian Wu,&nbsp;Tamer N. Abdelbaki,&nbsp;Jayashree Arcot,&nbsp;Wah Yang","doi":"10.1002/imt2.230","DOIUrl":"https://doi.org/10.1002/imt2.230","url":null,"abstract":"<p>Overview of personalized dietary therapies. This flow chart exhibits the future prospect for integrating human microbiome and bio-medical research to revolutionize the precise personalized dietary therapies. With the development of artificial intelligence (AI), incorporating database may achieve personalized dietary therapies with high precision.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.230","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"tigeR: Tumor immunotherapy gene expression data analysis R package","authors":"Yihao Chen,&nbsp;Li-Na He,&nbsp;Yuanzhe Zhang,&nbsp;Jingru Gong,&nbsp;Shuangbin Xu,&nbsp;Yuelong Shu,&nbsp;Di Zhang,&nbsp;Guangchuang Yu,&nbsp;Zhixiang Zuo","doi":"10.1002/imt2.229","DOIUrl":"https://doi.org/10.1002/imt2.229","url":null,"abstract":"<p>Immunotherapy shows great promise for treating advanced cancers, but its effectiveness varies widely among different patients and cancer types. Identifying biomarkers and developing robust predictive models to discern which patients are most likely to benefit from immunotherapy is of great importance. In this context, we have developed the tumor immunotherapy gene expression R package (tigeR 1.0) to address the increasing need for effective tools to explore biomarkers and construct predictive models. tigeR encompasses four distinct yet closely interconnected modules. The Biomarker Evaluation module enables researchers to evaluate whether the biomarkers of interest are associated with immunotherapy response via built-in or custom immunotherapy gene expression data. The Tumor Microenvironment Deconvolution module integrates 10 open-source algorithms to obtain the proportions of different cell types within the tumor microenvironment, facilitating the investigation of the association between immune cell populations and immunotherapy response. The Prediction Model Construction module equips users with the ability to construct sophisticated prediction models using a range of built-in machine-learning algorithms. The Response Prediction module predicts the immunotherapy response for the patients from gene expression data using our pretrained machine learning models or public gene expression signatures. By providing these diverse functionalities, tigeR aims to simplify the process of analyzing immunotherapy gene expression data, thus making it accessible to researchers without advanced programming skills. The source code and example for the tigeR project can be accessed at http://github.com/YuLab-SMU/tigeR.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.229","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OmicShare tools: A zero-code interactive online platform for biological data analysis and visualization","authors":"Hongyan Mu,&nbsp;Jianzhou Chen,&nbsp;Wenjie Huang,&nbsp;Gui Huang,&nbsp;Meiying Deng,&nbsp;Shimiao Hong,&nbsp;Peng Ai,&nbsp;Chuan Gao,&nbsp;Huangkai Zhou","doi":"10.1002/imt2.228","DOIUrl":"https://doi.org/10.1002/imt2.228","url":null,"abstract":"<p>The OmicShare tools platform is a user-friendly online resource for data analysis and visualization, encompassing 161 bioinformatic tools. Users can easily track the progress of projects in real-time through an overview interface. The platform has a powerful interactive graphics engine that allows for the custom-tailored modification of charts generated from analyses. The visually appealing charts produced by OmicShare improve data interpretability and meet the requirements for publication. It has been acknowledged in over 4000 publications and is available in https://www.omicshare.com/tools/.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.228","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142449033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell landscape revealed immune characteristics associated with disease phases in brucellosis patients","authors":"Yi Wang,&nbsp;Siyuan Yang,&nbsp;Bing Han,&nbsp;Xiufang Du,&nbsp;Huali Sun,&nbsp;Yufeng Du,&nbsp;Yinli Liu,&nbsp;Panpan Lu,&nbsp;Jinyu Di,&nbsp;Laurence Don Wai Luu,&nbsp;Xiao Lv,&nbsp;Songnian Hu,&nbsp;Linghang Wang,&nbsp;Rongmeng Jiang","doi":"10.1002/imt2.226","DOIUrl":"10.1002/imt2.226","url":null,"abstract":"<p>A comprehensive immune landscape for <i>Brucella</i> infection is crucial for developing new treatments for brucellosis. Here, we utilized single-cell RNA sequencing (scRNA-seq) of 290,369 cells from 35 individuals, including 29 brucellosis patients from acute (<i>n</i> = 10), sub-acute (<i>n</i> = 9), and chronic (<i>n</i> = 10) phases as well as six healthy donors. Enzyme-linked immunosorbent assays were applied for validation within this cohort. <i>Brucella</i> infection caused a significant change in the composition of peripheral immune cells and inflammation was a key feature of brucellosis. Acute patients are characterized by potential cytokine storms resulting from systemic upregulation of <i>S100A8</i>/<i>A9</i>, primarily due to classical monocytes. Cytokine storm may be mediated by activating S100A8/A9-TLR4-MyD88 signaling pathway. Moreover, monocytic myeloid-derived suppressor cells were the probable contributors to immune paralysis in acute patients. Chronic patients are characterized by a dysregulated Th1 response, marked by reduced expression of IFN-γ and Th1 signatures as well as a high exhausted state. Additionally, <i>Brucella</i> infection can suppress apoptosis in myeloid cells (e.g., mDCs, classical monocytes), inhibit antigen presentation in professional antigen-presenting cells (APCs; e.g., mDC) and nonprofessional APCs (e.g., monocytes), and induce exhaustion in CD8⁺ T/NK cells, potentially resulting in the establishment of chronic infection. Overall, our study systemically deciphered the coordinated immune responses of <i>Brucella</i> at different phases of the infection, which facilitated a full understanding of the immunopathogenesis of brucellosis and may aid the development of new effective therapeutic strategies, especially for those with chronic infection.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.226","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141812274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C","authors":"Yu-Xi Lu,&nbsp;Jin-Bao Yang,&nbsp;Chen-Ying Li,&nbsp;Yun-Han Tian,&nbsp;Rong-Rong Chang,&nbsp;Da-Shuai Kong,&nbsp;Shu-Lin Yang,&nbsp;Yan-Fang Wang,&nbsp;Yu-Bo Zhang,&nbsp;Xiu-Sheng Zhu,&nbsp;Wei-Hua Pan,&nbsp;Si-Yuan Kong","doi":"10.1002/imt2.227","DOIUrl":"10.1002/imt2.227","url":null,"abstract":"<p>Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 5","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.227","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141815430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intestinal microbiota by angiotensin receptor blocker therapy exerts protective effects against hypertensive damages","authors":"Jing Li,&nbsp;Si-Yuan Wang,&nbsp;Kai-Xin Yan,&nbsp;Pan Wang,&nbsp;Jie Jiao,&nbsp;Yi-Dan Wang,&nbsp;Mu-Lei Chen,&nbsp;Ying Dong,&nbsp;Jiu-Chang Zhong","doi":"10.1002/imt2.222","DOIUrl":"10.1002/imt2.222","url":null,"abstract":"<p>Dysbiosis of the gut microbiota has been implicated in hypertension, and drug–host–microbiome interactions have drawn considerable attention. However, the influence of angiotensin receptor blocker (ARB)-shaped gut microbiota on the host is not fully understood. In this work, we assessed the alterations of blood pressure (BP), vasculatures, and intestines following ARB-modified gut microbiome treatment and evaluated the changes in the intestinal transcriptome and serum metabolome in hypertensive rats. Hypertensive patients with well-controlled BP under ARB therapy were recruited as human donors, spontaneously hypertensive rats (SHRs) receiving normal saline or valsartan were considered animal donors, and SHRs were regarded as recipients. Histological and immunofluorescence staining was used to assess the aorta and small intestine, and 16S rRNA amplicon sequencing was performed to examine gut bacteria. Transcriptome and metabonomic analyses were conducted to determine the intestinal transcriptome and serum metabolome, respectively. Notably, ARB-modified fecal microbiota transplantation (FMT), results in marked decreases in systolic BP levels, collagen deposition and reactive oxygen species accumulation in the vasculature, and alleviated intestinal structure impairments in SHRs. These changes were linked with the reconstruction of the gut microbiota in SHR recipients post-FMT, especially with a decreased abundance of <i>Lactobacillus</i>, <i>Aggregatibacter</i>, and <i>Desulfovibrio</i>. Moreover, ARB-treated microbes contributed to increased intestinal <i>Ciart</i>, <i>Per1</i>, <i>Per2</i>, <i>Per3</i>, and <i>Cipc</i> gene levels and decreased <i>Nfil3</i> and <i>Arntl</i> expression were detected in response to ARB-treated microbes. More importantly, circulating metabolites were dramatically reduced in ARB-FMT rats, including 6beta-Hydroxytestosterone and Thromboxane B2. In conclusion, ARB-modified gut microbiota exerts protective roles in vascular remodeling and injury, metabolic abnormality and intestinal dysfunctions, suggesting a pivotal role in mitigating hypertension and providing insights into the cross-talk between antihypertensive medicines and the gut microbiome.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.222","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141825005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits","authors":"Ming-Yuan Xue,&nbsp;Yun-Yi Xie,&nbsp;Xin-Wei Zang,&nbsp;Yi-Fan Zhong,&nbsp;Xiao-Jiao Ma,&nbsp;Hui-Zeng Sun,&nbsp;Jian-Xin Liu","doi":"10.1002/imt2.225","DOIUrl":"10.1002/imt2.225","url":null,"abstract":"<p>Over the years, microbiome research has achieved tremendous advancements driven by culture-independent meta-omics approaches. Despite extensive research, our understanding of the functional roles and causal effects of the microbiome on phenotypes remains limited. In this study, we focused on the rumen metaproteome, combining it with metatranscriptome and metabolome data to accurately identify the active functional distributions of rumen microorganisms and specific functional groups that influence feed efficiency. By integrating host genetics data, we established the potentially causal relationships between microbes-proteins/metabolites-phenotype, and identified specific patterns in which functional groups of rumen microorganisms influence host feed efficiency. We found a causal link between <i>Selenomonas bovis</i> and rumen carbohydrate metabolism, potentially mediated by bacterial chemotaxis and a two-component regulatory system, impacting feed utilization efficiency of dairy cows. Our study on the nutrient utilization functional groups in the rumen of high-feed-efficiency dairy cows, along with the identification of key microbiota functional proteins and their potentially causal relationships, will help move from correlation to causation in rumen microbiome research. This will ultimately enable precise regulation of the rumen microbiota for optimized ruminant production.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141647117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases","authors":"Dacheng Wang,&nbsp;Yingqiao Wan,&nbsp;Dekun Liu,&nbsp;Ning Wang,&nbsp;Jingni Wu,&nbsp;Qin Gu,&nbsp;Huijun Wu,&nbsp;Xuewen Gao,&nbsp;Yiming Wang","doi":"10.1002/imt2.223","DOIUrl":"10.1002/imt2.223","url":null,"abstract":"<p>Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.223","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141833129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}