iMeta最新文献

{"title":"Cell-type-specific expression analysis of liver transcriptomics with clinical parameters to decipher the cause of intrahepatic inflammation in chronic hepatitis B","authors":"Jun Wang,&nbsp;Qian Li,&nbsp;Yuanwang Qiu,&nbsp;Simo Kitanovski,&nbsp;Chen Wang,&nbsp;Chenxia Zhang,&nbsp;Fahong Li,&nbsp;Xiaoguang Li,&nbsp;Zhenfeng Zhang,&nbsp;Lihua Huang,&nbsp;Jiming Zhang,&nbsp;Daniel Hoffmann,&nbsp;Mengji Lu,&nbsp;Hongzhou Lu","doi":"10.1002/imt2.221","DOIUrl":"10.1002/imt2.221","url":null,"abstract":"<p>Functional cure for chronic hepatitis B (CHB) remains challenging due to the lack of direct intervention methods for hepatic inflammation. Multi-omics research offers a promising approach to understand hepatic inflammation mechanisms in CHB. A Bayesian linear model linked gene expression with clinical parameters, and population-specific expression analysis (PSEA) refined bulk gene expression into specific cell types across different clinical phases. These models were integrated into our analysis of key factors like inflammatory cells, immune activation, T cell exhaustion, chemokines, receptors, and interferon-stimulated genes (ISGs). Validation through multi-immune staining in liver specimens from CHB patients bolstered our findings. In CHB patients, increased gene expression related to immune cell activation and migration was noted. Marker genes of macrophages, T cells, immune-negative regulators, chemokines, and ISGs showed a positive correlation with serum alanine aminotransferase (ALT) levels but not hepatitis B virus DNA levels. The PSEA model confirmed T cells as the source of exhausted regulators, while macrophages primarily contributed to chemokine expression. Upregulated ISGs (<i>ISG20, IFI16, TAP2, GBP1, PSMB9</i>) in the hepatitis phase were associated with T cell and macrophage infiltration and positively correlated with ALT levels. Conversely, another set of ISGs (<i>IFI44, ISG15, IFI44L, IFI6, MX1</i>) mainly expressed by hepatocytes and B cells showed no correlation with ALT levels. Our study presents a multi-omics analysis integrating bulk transcriptomic, single-cell sequencing data, and clinical data from CHB patients to decipher the cause of intrahepatic inflammation in CHB. The findings confirm that macrophages secrete chemokines like CCL20, recruiting exhausted T cells into liver tissue; concurrently, hepatocyte innate immunity is suppressed, hindering the antiviral effects of ISGs.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141677555","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":"Prophylactic supplementation with Bifidobacterium infantis or its metabolite inosine attenuates cardiac ischemia/reperfusion injury","authors":"Hao Zhang,&nbsp;Jiawan Wang,&nbsp;Jianghua Shen,&nbsp;Siqi Chen,&nbsp;Hailong Yuan,&nbsp;Xuan Zhang,&nbsp;Xu Liu,&nbsp;Ying Yu,&nbsp;Xinran Li,&nbsp;Zeyu Gao,&nbsp;Yaohui Wang,&nbsp;Jun Wang,&nbsp;Moshi Song","doi":"10.1002/imt2.220","DOIUrl":"10.1002/imt2.220","url":null,"abstract":"<p>Emerging evidence has demonstrated the profound impact of the gut microbiome on cardiovascular diseases through the production of diverse metabolites. Using an animal model of myocardial ischemia–reperfusion (I/R) injury, we found that the prophylactic administration of a well-known probiotic, <i>Bifidobacterium infantis</i> (<i>B. infantis</i>), exhibited cardioprotective effects in terms of preserving cardiac contractile function and preventing adverse cardiac remodeling following I/R and that these cardioprotective effects were recapitulated by its metabolite inosine. Transcriptomic analysis further revealed that inosine mitigated I/R-induced cardiac inflammation and cell death. Mechanistic investigations elucidated that inosine suppressed the production of pro-inflammatory cytokines and reduced the numbers of dendritic cells and natural killer cells, achieved through the activation of the adenosine A2A receptor (A2AR) that when inhibited abrogated the cardioprotective effects of inosine. Additionally, in vitro studies using C2C12 myoblasts revealed that inosine attenuated cell death by serving as an alternative carbon source for adenosine triphosphate (ATP) generation through the purine salvage pathway when subjected to oxygen-glucose deprivation/reoxygenation that simulated myocardial I/R injury. Likewise, inosine reversed the I/R-induced decrease in ATP levels in mouse hearts. Taken together, our findings indicate that <i>B. infantis</i> or its metabolite inosine exerts cardioprotective effects against I/R by suppressing cardiac inflammation and attenuating cardiac cell death, suggesting prophylactic therapeutic options for acute ischemic cardiac injury.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141685597","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":"MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility","authors":"Xin Wei,&nbsp;Li Guo,&nbsp;Hongliu Cai,&nbsp;Silan Gu,&nbsp;Lingling Tang,&nbsp;Yuxin Leng,&nbsp;Minghui Cheng,&nbsp;Guojun He,&nbsp;Yijiao Han,&nbsp;Xindie Ren,&nbsp;Baoyue Lin,&nbsp;Longxian Lv,&nbsp;Huanzhang Shao,&nbsp;Mingqiang Wang,&nbsp;Hongyu Wang,&nbsp;Dan Dang,&nbsp;Shengfeng Wang,&nbsp;Nan Wang,&nbsp;Peng Shen,&nbsp;Qianqian Wang,&nbsp;Yinghe Xu,&nbsp;Yongpo Jiang,&nbsp;Ning Zhang,&nbsp;Xuwei He,&nbsp;Xuntao Deng,&nbsp;Muhua Dai,&nbsp;Lin Zhong,&nbsp;Yonghui Xiong,&nbsp;Yujie Pan,&nbsp;Kankai Tang,&nbsp;Fengqi Liu,&nbsp;Bin Yang,&nbsp;Lili Ren,&nbsp;Jianwei Wang,&nbsp;Chao Jiang,&nbsp;Lingtong Huang","doi":"10.1002/imt2.218","DOIUrl":"https://doi.org/10.1002/imt2.218","url":null,"abstract":"<p>The MASS cohort comprises 2000 ICU patients with severe pneumonia, covering community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, sourced from 19 hospitals across 10 cities in three provinces. A wide array of samples including bronchoalveolar lavage fluid, sputum, feces, and whole blood are longitudinally collected throughout patients' ICU stays. The cohort study seeks to uncover the dynamics of lung and gut microbiomes and their associations with severe pneumonia and host susceptibility, integrating deep metagenomics and transcriptomics with detailed clinical data.\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":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.218","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967097","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":"Majorbio Cloud 2024: Update single-cell and multiomics workflows","authors":"Chang Han,&nbsp;Caiping Shi,&nbsp;Linmeng Liu,&nbsp;Jichen Han,&nbsp;Qianqian Yang,&nbsp;Yan Wang,&nbsp;Xiaodan Li,&nbsp;Wenyao Fu,&nbsp;Hao Gao,&nbsp;Huasheng Huang,&nbsp;Xianglin Zhang,&nbsp;Kegang Yu","doi":"10.1002/imt2.217","DOIUrl":"https://doi.org/10.1002/imt2.217","url":null,"abstract":"<p>Majorbio Cloud (https://cloud.majorbio.com/) is a one-stop online analytic platform aiming at promoting the development of bioinformatics services, narrowing the gap between wet and dry experiments, and accelerating the discoveries for the life sciences community. In 2024, three single-omics workflows, two multiomics workflows, and extensions were newly released to facilitate omics data mining and interpretation.\u0000\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":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.217","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967098","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":"Smaller microorganisms outcompete larger ones in resistance and functional effects under disturbed agricultural ecosystems","authors":"Chunling Liang,&nbsp;Jiejun Qi,&nbsp;Wenyuan Wu,&nbsp;Xingyu Chen,&nbsp;Mingyu Li,&nbsp;Yu Liu,&nbsp;Ziheng Peng,&nbsp;Shi Chen,&nbsp;Haibo Pan,&nbsp;Beibei Chen,&nbsp;Jiai Liu,&nbsp;Yihe Wang,&nbsp;Sanfeng Chen,&nbsp;Sen Du,&nbsp;Gehong Wei,&nbsp;Shuo Jiao","doi":"10.1002/imt2.219","DOIUrl":"https://doi.org/10.1002/imt2.219","url":null,"abstract":"<p>Body size is a key ecological trait of soil microorganisms related to their adaptation to environmental changes. In this study, we reveal that the smaller microorganisms show stronger community resistance than larger organisms in both maize and rice soil. Compared with larger organisms, smaller microorganisms have higher diversity and broader niche breadth to deploy survival strategies, because of which they are less affected by environmental selection and thus survive in complex and various kinds of environments. In addition, the strong correlation between smaller microorganisms and ecosystem functions reflects their greater metabolic flexibility and illustrates their significant roles in adaptation to continuously changing environments. This research highlights the importance of body size in maintaining stability of the soil microbiome and forecasting agroecosystem dynamics under environmental disturbances.\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":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968086","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":"Genetic manipulations of nonmodel gut microbes","authors":"Wen-Bing Jin,&nbsp;Chun-Jun Guo","doi":"10.1002/imt2.216","DOIUrl":"https://doi.org/10.1002/imt2.216","url":null,"abstract":"<p>Hundreds of microbiota gene expressions are significantly different between healthy and diseased humans. The “bottleneck” preventing a mechanistic dissection of how they affect host biology/disease is that many genes are encoded by nonmodel gut commensals and not genetically manipulatable. Approaches to efficiently identify their gene transfer methodologies and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. This paper will introduce a step-by-step protocol to identify gene transfer conditions and build the gene manipulation tools for nonmodel gut microbes, focusing on Gram-negative <i>Bacteroidia</i> and Gram-positive <i>Clostridia</i> organisms. This protocol enables us to identify gene transfer methods and develop gene manipulation tools without prior knowledge of their genome sequences, by targeting bacterial 16s ribosomal RNAs or expanding their compatible replication origins combined with clustered regularly interspaced short palindromic repeats machinery. Such an efficient and generalizable approach will facilitate functional studies that causally connect gut microbiota genes to host diseases.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.216","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968084","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":"BioLadder: A bioinformatic platform primarily focused on proteomic data analysis","authors":"Yupeng Zhang,&nbsp;Chunyuan Yang,&nbsp;Jinhao Wang,&nbsp;Lixin Wang,&nbsp;Yan Zhao,&nbsp;Longqing Sun,&nbsp;Wei Sun,&nbsp;Yunping Zhu,&nbsp;Jingli Li,&nbsp;Songfeng Wu","doi":"10.1002/imt2.215","DOIUrl":"https://doi.org/10.1002/imt2.215","url":null,"abstract":"<p>BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes three classes of experimental data analysis modules and four classes of common data analysis modules. It allows for a variety of proteomics analyses to be conducted easily and efficiently. Additionally, most modules can also be utilized for the analysis of other omics data. To facilitate user experience, we have carefully designed four different kinds of functions for customers to quickly and accurately utilize the relevant analysis modules.\u0000\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":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.215","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967021","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":"Deep learning enhancing guide RNA design for CRISPR/Cas12a-based diagnostics","authors":"Baicheng Huang,&nbsp;Ling Guo,&nbsp;Hang Yin,&nbsp;Yue Wu,&nbsp;Zihan Zeng,&nbsp;Sujie Xu,&nbsp;Yufeng Lou,&nbsp;Zhimin Ai,&nbsp;Weiqiang Zhang,&nbsp;Xingchi Kan,&nbsp;Qian Yu,&nbsp;Shimin Du,&nbsp;Chao Li,&nbsp;Lina Wu,&nbsp;Xingxu Huang,&nbsp;Shengqi Wang,&nbsp;Xinjie Wang","doi":"10.1002/imt2.214","DOIUrl":"10.1002/imt2.214","url":null,"abstract":"<p>Rapid and accurate diagnostic tests are fundamental for improving patient outcomes and combating infectious diseases. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas12a-based detection system has emerged as a promising solution for on-site nucleic acid testing. Nonetheless, the effective design of CRISPR RNA (crRNA) for Cas12a-based detection remains challenging and time-consuming. In this study, we propose an enhanced crRNA design system with deep learning for Cas12a-mediated diagnostics, referred to as EasyDesign. This system employs an optimized convolutional neural network (CNN) prediction model, trained on a comprehensive data set comprising 11,496 experimentally validated Cas12a-based detection cases, encompassing a wide spectrum of prevalent pathogens, achieving Spearman's <i>ρ</i> = 0.812. We further assessed the model performance in crRNA design for four pathogens not included in the training data: Monkeypox Virus, Enterovirus 71, Coxsackievirus A16, and <i>Listeria monocytogenes</i>. The results demonstrated superior prediction performance compared to the traditional experiment screening. Furthermore, we have developed an interactive web server (https://crispr.zhejianglab.com/) that integrates EasyDesign with recombinase polymerase amplification (RPA) primer design, enhancing user accessibility. Through this web-based platform, we successfully designed optimal Cas12a crRNAs for six human papillomavirus (HPV) subtypes. Remarkably, all the top five predicted crRNAs for each HPV subtype exhibited robust fluorescent signals in CRISPR assays, thereby suggesting that the platform could effectively facilitate clinical sample testing. In conclusion, EasyDesign offers a rapid and reliable solution for crRNA design in Cas12a-based detection, which could serve as a valuable tool for clinical diagnostics and research applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141336521","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":"A universal oral microbiome-based signature for periodontitis","authors":"Mingyan Geng,&nbsp;Min Li,&nbsp;Yun Li,&nbsp;Jiaying Zhu,&nbsp;Chuqing Sun,&nbsp;Yan Wang,&nbsp;Wei-Hua Chen","doi":"10.1002/imt2.212","DOIUrl":"10.1002/imt2.212","url":null,"abstract":"<p>We analyzed eight oral microbiota shotgun metagenomic sequencing cohorts from five countries and three continents, identifying 54 species biomarkers and 26 metabolic biomarkers consistently altered in health and disease states across three or more cohorts. Additionally, machine learning models based on taxonomic profiles achieved high accuracy in distinguishing periodontitis patients from controls (internal and external areas under the receiver operating characteristic curves of 0.86 and 0.85, respectively). These results support metagenome-based diagnosis of periodontitis and provide a foundation for further research and effective treatment strategies.\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":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141352263","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":"JCVI: A versatile toolkit for comparative genomics analysis","authors":"Haibao Tang,&nbsp;Vivek Krishnakumar,&nbsp;Xiaofei Zeng,&nbsp;Zhougeng Xu,&nbsp;Adam Taranto,&nbsp;Johnathan S. Lomas,&nbsp;Yixing Zhang,&nbsp;Yumin Huang,&nbsp;Yibin Wang,&nbsp;Won Cheol Yim,&nbsp;Jisen Zhang,&nbsp;Xingtan Zhang","doi":"10.1002/imt2.211","DOIUrl":"10.1002/imt2.211","url":null,"abstract":"<p>The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python-based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high-level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication-ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141354097","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}