Applying Bioinformatics to Research in Immune, Muscle, and Bone Diseases

将生物信息学应用于免疫、肌肉和骨骼疾病的研究

基本信息

批准号：
10926592
负责人：
Hong-Wei Sun
金额：
$ 241.88万
依托单位：
NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10926592
关键词：
ATAC-seq Address Adolescent Adult-Onset Still&apos s Disease Affect Affinity Architecture Area Arthritis Artificial Intelligence Asthma Autoimmune Diseases B-Cell Lymphomas B-Lymphocytes Bioinformatics Biomedical Research Blood coagulation Bone Diseases Bone necrosis CD3 Antigens CD4 Positive T Lymphocytes CRISPR screen CRISPR/Cas technology Cell Line Cells Cellular Indexing of Transcriptomes and Epitopes by Sequencing Cellular Metabolic Process Cellular biology ChIP-seq Child Chromatin Cicatrix Clinical Clone Cells Cohort Analysis Complex Computational Biology Computer Models Consultations Corneal Injury Coronavirus Custom DNA sequencing Dasatinib Data Data Analyses Data Science Data Set Dedications Development Diagnosis Disease Disease remission Enhancers Ensure Epidermis Epithelial Cells Exons Experimental Designs Exposure to Fabry Disease Family Female Fibrosis Flare Fostering G-Quartets Gene Expression Gene Expression Profiling Gene Expression Regulation Generations Genes Genetic Transcription Genome Genomics Germ-Line Mutation Helper-Inducer T-Lymphocyte Hi-C Homeostasis Human Genome Immune Immune System Diseases Infection Intramural Research Program Investigation JAK1 gene Jaw Joints Juvenile Dermatomyositis Knockout Mice Lead Liver Liver Fibrosis Lupus Lymphoma Lymphoproliferative Disorders Machine Learning Malignant Neoplasms Mammals Manuscripts Mendelian disorder Mentors Merkel cell carcinoma Metabolism Methodology Methods MicroRNAs Mining Mitomycin C Modeling Mus Mutation Mutation Analysis Myopathy Myositis National Institute of Arthritis, and Musculoskeletal, and Skin Diseases Natural History Ophthalmologic Surgical Procedures PAPA syndrome Pathway interactions Patients Peripheral Blood Mononuclear Cell Phagocytosis Pharmaceutical Preparations Pharmacotherapy Phosphotransferases Play Process Proliferating Prospective Studies Protein Tyrosine Kinase Pythons Quality Control RNA RNA Processing Regulation Relapsing polychondritis Research Research Personnel Research Project Grants Rheumatoid Arthritis Role Sampling Scientific Advances and Accomplishments Signaling Molecule Skin Somatic Mutation Specific qualifier value Spondylarthritis Stat5 protein Structure Structure of germinal center of lymph node Symptoms Syndrome Systemic Lupus Erythematosus TLR7 gene Takayasu&apos s Arteritis Techniques Technology Time Tissue-Specific Gene Expression Training Transcriptional Regulation United States National Institutes of Health Up-Regulation Vaccines Variant Vasculitis Visualization Withholding Treatment amino acid metabolism autoinflammatory autoinflammatory diseases big biomedical data bisulfite sequencing boys cancer cell cancer type chemotherapeutic agent cohort collaborative environment computerized data processing corneal epithelium coronavirus disease crosslinking and immunoprecipitation sequencing data analysis pipeline data quality data submission data wrangling database of Genotypes and Phenotypes design differential expression empowerment exome sequencing experience genome browser genome-wide genomic data global run on sequencing healing high dimensionality histone modification in vivo innovation insight kinase inhibitor large cell Diffuse non-Hodgkin&apos s lymphoma male metabolome microbiome mouse model multiple omics next generation sequencing novel plasma cell differentiation potential biomarker rapid growth rare variant response single cell analysis single-cell RNA sequencing src-Family Kinases statistics success systemic autoimmune disease systemic juvenile idiopathic arthritis therapeutic target tool transcriptome transcriptome sequencing transcriptomics wound wound healing

项目摘要

The Biodata Mining and Discovery Section projects are listed below, including major accomplishments: - Study of constitutively active Lyn kinase in autoinflammatory diseases Monogenic autoinflammatory diseases are often caused by mutations in signaling molecules. In this study, three unrelated boys were found to have mutations leading to constitutively active Lyn tyrosine kinase with small vessel vasculitis and liver fibrosis. A SRC family kinase inhibitor, dasatinib, was found to effectively reverse liver transcriptome dysregulation which led to reduction in symptoms. - Chromatin landscape governing murine epidermal differentiation Epidermal differentiation is driven by changes in transcriptome that are regulated by changes in chromatin landscape and regulatory networks. This study provides a comprehensive view of transcriptome, chromatin accessibility, chromatin architecture, histone modification and Dlx3 regulation in mouse epidermal development. - Role of Mitomycin C in corneal wound repair Mitomycin C is a chemotherapeutic agent used to treat various types of cancers. It is also known to reduce scarring and fibrosis in response to eye surgery. In this study, we show that corneal epithelial cells respond to soluble secretions from transient treatment with Mitomycin C. Among these are IL-1a and TGFb1. These lead to increased expression of phagocytosis related genes. - Role of STAT5 in transcriptional programming of T helper cell metabolism Activation of T helper cells leads to rapid changes in transcriptome related to metabolism in order to meet the energetic and biosynthetic demands required by rapid growth and proliferation. In this study, genome, transcriptome and metabolome analysis were used to determine that STAT5 is a master regulator of energy and amino acid metabolism in CD4+ T helper cells. - Gene expression studies of arthritis patients treated with different drugs Gene expression profiles from peripheral blood mononuclear cell (PBMC) samples of 101 arthritis patients treated with three distinct drugs were examined using RNA-seq. Data were collected at multiple time points, encompassing both treatment cessation and three months thereafter. The gene expression data were employed to construct computational models aimed at predicting patients' status, whether experiencing flares or remaining in remission, three months after drug treatment cessation. Additionally, these models were utilized to pinpoint potential biomarkers. This project is currently ongoing, with plans to include and analyze additional samples. - Natural history of coronavirus (COVID-19) in systemic autoimmune diseases: an observational prospective study This study aims to understand the immune drivers and the clinical consequences of autoimmune disease patients exposed to either COVID infection or COVID vaccine. We are currently processing RNA-Seq data from over 200 patients and healthy controls. Both inference statistics and machine learning will be employed for downstream data analysis. - Chromatin landscape and regulatory networks in lineage specification and differentiation Through the analysis of datasets that profiled expression dynamics (RNA-seq), chromatin accessibility (ATAC-seq), architecture (Hi-C), and histone modifications (ChIP-seq) in the epidermis, the temporospatial differentiation axis in murine epidermal cells was defined in vivo. - Exploratory analysis to identify the putative role of a novel JAK1 mutation in the onset of Lupus The onset of Lupus is typically seen in females. In this unique case, a male in his 40s was diagnosed. Sequencing found a novel JAK1 variant. scRNA-seq explored impact, including data from the patient, as well as healthy and patient (without the mutation) controls. It was found that JAK1 variant cells resembled the healthy control more than the patient control. Differentially expressed genes on a JAK1-centered PPI network showed 80% perturbation, hinting at the variant's role in disease. - Exploring cellular dynamics through scRNA-Seq in Systemic Juvenile Idiopathic Arthritis (SJIA). Systemic Juvenile Idiopathic Arthritis (SJIA) affects children. PBMCs from patients and controls were studied with scRNA-seq. Azimuth R package ensured confident cell cluster annotations. Differential gene expression analysis highlighted new pathways in SJIA samples. Patient transcriptome diversity challenged conventional analysis. Innovative pipeline identified patient-specific gene markers against controls. Enrichment analysis revealed pathways underlying the onset of SJIA. - Role of RNA G-quadruplex structures in cancer Bioinformatics analysis of the human genome sequence identified genes with high (>4) and low (<3) numbers of G-quadruplex structures. Conservation analysis across seven mammals, as obtained from the UCSC Genome Browser, revealed that genes with a high number of G-quadruplex structures are more highly conserved. Currently, we are investigating the role of these highly conserved structures in gene expression within cancer cells. - Regulation of PRMT1 gene in B cell fate in germinal center We have hypothesized that positively selected germinal center B cells determine their fate for proliferation or differentiation. Based on the observed high-level expression of PRMT1 in germinal B cells, a PRMT1-specific knockout mouse model was generated, elucidating PRMT1's necessity in expanding germinal center B cells, advancing affinity maturation, and contributing to memorial B cell formation, plasma cell differentiation, and B cell lymphoma differentiation. Analysis of the publicly available scRNA-seq data revealed the up-regulation of PRMT1 in positively selected germinal center B cells after infection. - Deciphering transcriptional regulation in diffuse large B cell lymphoma (DLBCL) using genome-wide CRISPR/Cas9 screens To better understand gene regulation in DLBCL, the most common aggressive lymphoma, 47 super-enhancer-controlled genes important for B cell biology were screened in the DLBCL cell line SU-DHL-4 using CRISPR/Cas9. Around 1500 activators and repressors were found across the genes, along with 884 dual-function regulators. This reveals complex multilayered gene regulation in DLBCL, providing insights into the disease while identifying potential therapeutic targets. One key finding is AFF2 as a regulator highly expressed in germinal center B cells. - Investigation of rare variants in NIAMS Stills disease cohort We performed WES joint variant calling in 964 NIAMS sJIA/Adult-onset Still disease patients and 2952 NIH database of Genotypes and Phenotypes controls. We also performed data Quality Control (QC) and initial analysis, providing guidance on rare variant enrichment analysis for the cohort. - Family-based mutation analysis in NIAMS Whole Exome Sequencing (WES) cohort We performed trio-based and custom-made mutation analysis in more than 30 NIAMS patients with various diseases. And we identified mutations in biologically interesting genes such as FANCM, TLR7, KMT2D and CSK. - Investigation of somatic mutations in vasculitis patients We performed somatic and germline variant calls in patients with medium vessel vasculitis, blood clots, and hypereosinophilia with a CD3-CD4+ T cell clone. And we developed a variant prioritization strategy and provided consultation on mutation analysis. - Enhancing the current RNA-seq pipeline We have enhanced the existing RNA-seq data processing and analysis pipeline by incorporating comprehensive QC checks and visualization techniques. This pipeline is powered by the SNAKEMAKE framework, offering efficient workflow management. It encompasses over 15 Python and R scripts for data parsing and visualization throughout multiple data generation and analysis stages.

Biodata采矿和发现部分项目如下列出，包括主要成就： - 研究自发疾病中的组成性活性LYN激酶单基自发性疾病通常是由信号分子突变引起的。在这项研究中，发现三个无关的男孩具有突变，导致具有小血管血管炎和肝纤维化的组成型活性Lyn酪氨酸激酶。发现SRC家族激酶抑制剂Dasatinib有效地逆转肝转录组失调，导致症状减轻。 - 染色质景观管理鼠表皮分化表皮分化是由转录组的变化驱动的，这些变化受染色质景观和调节网络的变化调节。这项研究提供了小鼠表皮发育中转录组，染色质可及性，染色质结构，组蛋白修饰和DLX3调控的全面视图。 - 丝裂霉素C在角膜伤口修复中的作用丝裂霉素C是一种用于治疗各种癌症的化学治疗剂。众所周知，可以减少疤痕和纤维化，以应对眼科手术。在这项研究中，我们表明角膜上皮细胞对丝裂霉素的短暂性治疗可溶性分泌反应。其中包括IL-1A和TGFB1。这些导致吞噬作用相关基因的表达增加。 - STAT5在T辅助细胞代谢的转录编程中的作用 T辅助细胞的激活导致与代谢相关的转录组的快速变化，以满足快速生长和增殖所需的能量和生物合成需求。在这项研究中，使用基因组，转录组和代谢组分析来确定STAT5是CD4+ T辅助细胞中能量和氨基酸代谢的主要调节剂。 - 用不同药物治疗的关节炎患者的基因表达研究使用RNA-SEQ检查了101例用三种不同药物治疗的101例关节炎患者的外周血单核细胞（PBMC）样品的基因表达谱。数据是在多个时间点收集的，包括治疗停止和此后三个月。使用基因表达数据来构建旨在预测患者状态的计算模型，无论是经历耀斑还是在缓解中，在药物治疗停止后三个月。此外，这些模型还用于查明潜在的生物标志物。该项目目前正在进行中，并计划包括和分析其他样本。 - 全身自身免疫性疾病中冠状病毒的自然史（Covid-19）：一项观察性前瞻性研究这项研究旨在了解暴露于COVID感染或共同疫苗的自身免疫性疾病患者的免疫驱动因素和临床后果。我们目前正在处理来自200多名患者和健康对照组的RNA-seq数据。推理统计和机器学习都将用于下游数据分析。 - 谱系规范和分化中的染色质景观和调节网络通过分析表达表达动力学（RNA-SEQ），染色质可及性（ATAC-SEQ），体系结构（HI-C）和组蛋白修饰（CHIP-SEQ）的数据集，在体内定义了鼠类表皮细胞中的暂时性分化轴。 - 探索性分析以确定新型JAK1突变在狼疮发作中的推定作用狼疮的发作通常在女性中看到。在这种独特的情况下，一个40多岁的男性被诊断出来。测序发现了一种新颖的JAK1变体。 Scrna-Seq探索了影响，包括患者的数据，以及健康和患者（无突变）对照。发现JAK1变体细胞比患者对照更像健康对照。在以JAK1为中心的PPI网络上差异表达的基因显示80％的扰动，暗示了该变异在疾病中的作用。 - 通过SCRNA-SEQ在全身性特发性关节炎（SJIA）中探索细胞动力学。全身少年特发性关节炎（SJIA）会影响儿童。用SCRNA-SEQ研究了来自患者和对照的PBMC。 Azimuth R软件包确保了自信的单元格群集注释。差异基因表达分析突出了SJIA样品中的新途径。患者转录组多样性挑战常规分析。创新的管道确定了针对对照的患者特异性基因标记。富集分析揭示了SJIA发作的途径。 - RNA G-四链体结构在癌症中的作用人类基因组序列的生物信息学分析鉴定出具有较高（> 4）和低（<3）数量的G-四链体结构的基因。从UCSC基因组浏览器获得的七个哺乳动物的保护分析表明，具有大量G-四链体结构的基因更加保守。目前，我们正在研究这些高度保守的结构在癌细胞中基因表达中的作用。 - 在生发中心B细胞命运中PRMT1基因的调节我们假设积极选择的生发中心B细胞决定了它们的增殖或分化的命运。基于在生发B细胞中观察到的PRMT1的高级表达，生成了PRMT1特异性小鼠模型，从而阐明了PRMT1在扩展生发中心B细胞，提高亲和力成熟的情况下的必要性，并促进纪念B细胞形成，血浆细胞分化和B细胞分化以及B细胞淋巴瘤分化。对公开可用的SCRNA-SEQ数据的分析表明，感染后，PRMT1在正面选择的生发中心B细胞中的上调。 - 使用基因组CRISPR/CAS9筛选的扩散大B细胞淋巴瘤（DLBCL）中的解密转录调节为了更好地了解DLBCL中的基因调节，使用CRISPR/CAS9在DLBCL细胞系SU-DHL-4中筛选了最常见的侵袭性淋巴瘤，47个对B细胞生物学重要的超能控制基因。在整个基因上发现了大约1500个激活剂和阻遏物，以及884个双功能调节器。这揭示了DLBCL中复杂的多层基因调节，在识别潜在的治疗靶标的同时，提供了对疾病的见解。一个关键发现是AFF2作为在生发中心B细胞中高度表达的调节剂。 - 调查NIAMS静止疾病队列中的稀有变体我们在964个NIAMS SJIA/成人静止病患者和2952 NIH基因型和表型控制数据库中进行了WES联合变体。我们还进行了数据质量控制（QC）和初始分析，为同类群体提供了稀有变体富集分析的指导。 - 基于家庭的突变分析NIAMS全外显子组测序（WES）队列我们对30多个患有各种疾病的NIAMS患者进行了基于三重奏和定制的突变分析。我们确定了诸如FANCM，TLR7，KMT2D和CSK等生物学有趣的基因中的突变。 - 研究血管炎患者的体细胞突变我们用CD3-CD4+ T细胞克隆进行了中血管炎，血凝块和嗜性粒细胞性粒细胞炎的患者进行体细胞和种系变体调用。我们制定了一种变异的优先级策略，并提供了有关突变分析的咨询。 - 增强当前的RNA-Seq管道我们通过合并全面的QC检查和可视化技术来增强现有的RNA-seq数据处理和分析管道。该管道由Snakemake框架提供动力，提供有效的工作流程管理。它包含超过15个Python和R脚本，用于整个数据生成和分析阶段的数据解析和可视化。