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

• 批准号: 10707817
• 负责人: Hong-Wei Sun
• 金额: $ 170.99万
• 依托单位: NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
• 依托单位国家: 美国
• 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/10707817
• 关键词: 3-Dimensional; ATAC-seq; Adolescent; Adult-Onset Still' s Disease; Aftercare; Alternative Splicing; Area; Arteritis; Arthritis; Asthma; Bioinformatics; Biological Process; Biomedical Research; Bone Diseases; Bone necrosis; Calcinosis; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; Cellular Metabolic Process; Ceramide glucosyltransferase; ChIP-seq; Childhood; Clustered Regularly Interspaced Short Palindromic Repeats; Cohort Analysis; Computational Biology; Computing Methodologies; Consultations; Copper; Custom; DNA sequencing; Data; Data Analyses; Data Science; Data Set; Dermatomyositis; Development; Dimensions; Disease; Disulfiram; Doxycycline; EZH2 gene; Endothelial Cells; Exhibits; Exons; Experimental Designs; Fabry Disease; Family; Gene Expression; Gene set enrichment analysis; Genes; Genetic; Genetic Transcription; Genome; Genomics; Glycosphingolipids; Goals; Graph; Helper-Inducer T-Lymphocyte; Homeostasis; Human; Immune System Diseases; Infection; Inflammatory; Interferon Type II; Interferons; Interleukin-2; Internet; Intramural Research Program; Investigation; Jaw; Joints; Kidney; Large Intestine; Learning; Lupus; Lymphoproliferative Disorders; Malignant Neoplasms; Manuscripts; Measures; Mentors; Merkel cell carcinoma; Messenger RNA; Metabolism; Methods; MicroRNAs; Mining; Mitochondria; Modality; Modeling; Modification; Mus; Muscle Cells; Muscle satellite cell; Mutation; Mutation Analysis; Myopathy; Myositis; NF-kappa B; National Institute of Arthritis, and Musculoskeletal, and Skin Diseases; Natural Killer Cells; Osteoblasts; Pathway Analysis; Pathway interactions; Patients; Play; Preparation; Process; Protein Isoforms; Quality Control; RELA gene; RNA; RNA Binding; Regulation; Relapsing polychondritis; Research; Research Personnel; Research Project Grants; Retrieval; Rheumatoid Arthritis; Role; Sampling; Short Tandem Repeat; Signal Pathway; Skeletal Muscle; Skin; Somatic Mutation; Spliced Genes; Spondylarthritis; Stat5 protein; Syndrome; System; Systemic Lupus Erythematosus; Training; Transcriptional Regulation; Tumor-Infiltrating Lymphocytes; Variant; Visualization; Whole Blood; Work; autoinflammatory; base; big biomedical data; bisulfite sequencing; cancer cell; cell type; cohort; computerized data processing; crosslinking and immunoprecipitation sequencing; data analysis pipeline; data quality; data wrangling; design; differential expression; disease-causing mutation; early onset; epigenetic regulation; exome sequencing; experimental study; extracellular; gene function; genome sequencing; genome-wide; genomic data; global run on sequencing; high dimensionality; human leukocyte antigen testing; improved; interest; keratinocyte; microbiome; multimodality; multiple omics; neutrophil; next generation sequencing; novel; oral cavity epithelium; population based; practical application; prevent; programs; rare variant; response; single-cell RNA sequencing; skin wound; stem cell function; systemic juvenile idiopathic arthritis; tool; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; treatment effect; user-friendly; whole genome; wound healing

The Biodata Mining and Discovery Section projects are listed below, including major accomplishments: - Investigation of genetic causes for severe calcinosis through whole genome sequencing Processed 56 Whole Genome Sequencing (WGS) samples from patients with sporadic or familial severe calcinosis. Performed data Quality Control (QC) and initial analysis. Provided consultations on the analysis of short-tandem repeats, mitochondria mutations, HLA typing and somatic mutations. - Investigation of genetic causes for Systemic Lupus Erythematous through whole genome sequencing Processed more than 230 new WGS samples sequenced by the NIAMS core. Implemented new sample QC tool that detects and prevents sample contamination. Performed trio-based WGS mutation analysis. - Family-based mutation analysis in the NIAMS Whole Exome Sequencing (WES) cohort Performed trio-based mutation analysis in more than 15 NIAMS patients with various diseases including Systemic Juvenile Idiopathic Arthritis (sJIA), Adult-Onset Stills Disease (AOSD), Takayasus arteritis, Relapsing Polychondritis, and Behcets-like disease. Identified a disease-causing mutation in the RELA gene. - Population-based mutation analysis in the NIAMS WES cohort Performed cohort analysis in non-trio samples for patients with Takayasus arteritis, Relapsing Polychondritis and sJIA. Performed joint variant call on more than 3000 WES Relapsing Polychondritis and control samples. Performed joint variant call on more than 3000 WES Takayasus arteritis and control samples. Provided guidance on variant enrichment analysis for the cohort. - The role of a NEMO isoform in the newly characterized autoinflammatory disease, NDAS A higher proportion of alternative splicing was identified in multiple patients with an autoinflammatory disease that are associated with an IKBKG mutation, leading to increased IFN and NF-kB responses. It was determined that patients with this mutation express a truncated NEMO isoform protein and exhibit a pediatric autoinflammatory syndrome, newly defined as NDAS. - Exploring human neutrophil subsets using single cell RNA-Seq Neutrophils are low mRNA cells that are difficult to study using typical single cell RNA-Seq workflows. Alternative computational methods were explored, and improved workflows were established, which were applied to scRNA-Seq studies of neutrophils from whole blood, leading to the identification of novel subsets of neutrophils with distinct biological functions. - Single cell RNA-Seq on whole blood of baracitinib treated Juvenile Dermatomyostis (JDM) patients to reveal disease signature and effect of treatment Single cell RNA-Seq was performed to characterize the transcriptomes of JDM patients before treatment and at 3 timepoints after treatment with baracitinib. By comparing JDM patients before treatment with healthy controls, a cell specific signature of JDM disease has been explored, along with transcriptomic changes induced by the treatment. - Role of U12 splicing genes in Lupus patients U12 splicing genes were identified and their gene expression profiles were characterized in Lupus patients. A specific single cell RNA-seq data analysis pipeline was implemented to further characterize U12 genes to identify novel cell types and their markers in Lupus patients. A scoring system has been established to measure the expression profiles of customized gene-sets. -Pathway enrichment analysis on genes correlated to UDP-glucose ceramide glucosyltransferase (UGCG) in tumor infiltrating lymphocytes (TILs) The public GEO mouse TIL samples were identified and their RNA-seq gene expression data downloaded from ARCHS4. Data were analyzed using R and Partek GS. Genes with a UGCG correlation > 0.80 were used for pathway enrichment analysis with Enrichr, assisted by several in-house developed R scripts for results retrieval, organization, and graphical data analysis. Interferon-gamma signaling pathway was identified as the most significantly enriched, supporting the hypothesis that UGCG plays a previously unrecognized important role in NK cell immunometabolism. - Effect of Stat4 deletion on differentiation of large intestine ILC1s compared to Natural Killer cells in inflamed large intestine - 3D genomic organization of Mdm1-Il22-Ifng locus - Regulation of skeletal muscle stem cell function by EZH1 - Exploration of lineage specification through epigenetic regulation of Pax7 - Functions of Psat1 in muscle stem cell activation - Development of a scRNA-seq pipeline to analyze circulating human neutrophils - Investigaton of the functions of oral epithelial transcription factor Pitx1 in cutaneous wounds repair - Spatial transcriptome analysis of inflammatory mouse kidney - Investigation of the internalization of neutrophil extracellular trap-bound RNA by endothelial cells - Transcriptional programing of helper T cell metabolism by the IL-2-STAT5 axis - Essential role of glycosphingolipid metabolism for natural killer cell development and function - Gene expression profiles of cancer cells treated with copper and disulfiram - Transcriptional regulation of jaw osteoblasts - Rare variant analysis in systemic Juvenile Idiopathic Arthritis (sJIA) - Investigation of genome-wide modifications from CRISPR editing through whole genome sequencing - Mutation analysis in patients with early onset Merkel cell carcinoma Additional major accomplishments of the BMDS this year include: -Visualization of HiC data with HiCExplorer Multiple HiCExplorer tools were applied to visualize the hiC data. The contact matrices files were converted to h5 format with hicConvertFormat, normalized with smallest model with hicNormaliz, and corrected with hicCorrectMatrix. Then, hicFindTADs was applied to the corrected normalized matrices to calculate a genome-wide TAD separation score. In the end, domains, loops, and TAD score data were plotted with hicPlotTADs over regions of interest. -CUT&Tag analysis Cut&Tag data processing and analysis pipeline originally developed in the Henicoff lab has been customized and implemented for data from wild type or doxycycline-treated mouse keratinocytes. After pre-processing, the reads are aligned to the mm10 genome with bowtie2. Both SEACR and MACS2 are used for the peak calling. Counts from bam files are collected and used as input to DESeq2 for differentially expressed genes (DEG) analysis. -Single cell multiome analysis Seurat multimodal pipeline has been customized and applied to multi-modal experiments generated with differentiated mouse muscle cells. The multi-omic dataset was realigned to mm10. First, both RNA-seq count matrix and the ATAC-seq peak matrix were cleaned. Next, the Weighted Nearest Neighbor (WNN) graph was constructed to learn the relative utility of each data modality in each cell. The R packages Seurat and Signac were used for data scaling, transformation, clustering, dimensionality reduction, differential expression analysis, and most visualizations. The R package Monocle3 was used for trajectory analysis. -Built a more robust RNA-seq data analysis pipeline This pipeline uses STAR (instead of TopHat) for mapping bulk RNA reads and DESeq2 for downstream analysis -Built an R package for pathway and gene set enrichment analysis Based on our previous work, a new R package (richPathR) has been developed for pathway and gene set enrichment analysis. Powerful yet user-friendly, it is based on the popular Enrichr pathway analysis web tool, making multiple gene lists-based analysis possible. The package offers multiple utilities for enrichment data manipulation and visualization.

Biodata采矿和发现部分项目如下列出，包括主要成就： - 通过整个基因组测序研究严重钙化的遗传原因 从零星或家族性严重钙化患者中处理了56个全基因组测序（WGS）样品。执行数据质量控制（QC）和初始分析。就短串联重复，线粒体突变，HLA打字和体细胞突变进行了咨询。 - 通过整个基因组测序研究全身性红斑狼疮的遗传原因 通过Niams Core测序了230多个新的WGS样品。实施了检测和防止样品污染的新样本QC工具。进行了三重奏的WGS突变分析。 - 基于家庭的突变分析在NIAMS整个外显子组测序（WES）队列中 在15多名NIAMS患者中进行了基于三重奏的突变分析，包括全身性少年特发性关节炎（SJIA），成人发作静止病（AOSD），Takayasus Arteritis，复发性多软管炎和类似Behcets的疾病。在Rela基因中确定了引起疾病的突变。 - NIAMS WES队列中基于人群的突变分析 在非潮流动脉炎患者，复发性多个软骨炎和SJIA的患者中进行了队列分析。进行了3000多个WES复发性多层炎和对照样品的联合变体。进行了3000多个WES takayasus动脉炎和对照样品进行的联合呼叫。提供了对队列变体富集分析的指导。 - Nemo同工型在新特征的自发性疾病NDAS中的作用 在与IKBKG突变有关的多名自自炎性疾病的患者中发现了较高比例的替代剪接，从而导致IFN和NF-KB反应增加。已经确定该突变的患者表达截短的Nemo同工型蛋白，并表现出一种儿科自身炎症综合征，新定义为NDA。 - 使用单细胞RNA-seq探索人类中性粒细胞子集 中性粒细胞是低mRNA细胞，使用典型的单细胞RNA-Seq工作流很难研究。探索了替代的计算方法，并建立了改进的工作流程，这些方法应用于全血的中性粒细胞的SCRNA-SEQ研究，从而鉴定出具有不同生物学功能的中性粒细胞的新生物集。 - 巴西替尼治疗的少年皮肤科（JDM）患者的单细胞RNA-seq，以揭示疾病特征和治疗的影响 进行单细胞RNA-seq，以表征治疗前JDM患者的转录组，并在用bar依替尼治疗后的3个时间点。通过与健康对照治疗前的JDM患者进行比较，已经探索了JDM疾病的细胞特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性特异性的转录组变化是由治疗引起的。 - U12剪接基因在狼疮患者中的作用 鉴定了U12剪接基因，并在狼疮患者中表征其基因表达谱。实施了特定的单细胞RNA-seq数据分析管道，以进一步表征U12基因，以鉴定狼疮患者中新型细胞类型及其标记。已经建立了一个评分系统来衡量定制基因组的表达谱。 - 对肿瘤浸润淋巴细胞（TILS）中与UDP-葡萄糖葡萄糖基转移酶（UGCG）相关的基因的Pathway富集分析（UGCG） 鉴定了公共地理鼠标TIL样品，并从ArchS4下载其RNA-Seq基因表达数据。使用R和Partek GS分析数据。具有UGCG相关性> 0.80的基因用于富集的途径富集分析，并在几个内部开发的R脚本的协助下用于结果检索，组织和图形数据分析。干扰素伽马信号通路被确定为最显着富集的途径，这支持了这样的假设，即UGCG在NK细胞免疫代谢中扮演先前未认识到的重要作用。 - 与发炎的大肠相比，STAT4缺失对大肠ILC1的分化的影响 -MDM1-IL22-IFNG基因座的3D基因组组织 - EZH1调节骨骼肌干细胞功能 - 通过PAX7的表观遗传调节来探索谱系规范 - PSAT1在肌肉干细胞激活中的功能 - 开发SCRNA-SEQ管道以分析循环的人类中性粒细胞 - 研究皮肤伤口修复中口服上皮转录因子PITX1的功能 - 炎症小鼠肾脏的空间转录组分析 - 研究内皮细胞中性粒细胞外陷阱结合的RNA的内在化 - IL-2-STAT5轴对辅助T细胞代谢的转录编程 - 糖磷脂代谢在天然杀伤细胞发育和功能中的基本作用 - 用铜和二硫兰治疗的癌细胞的基因表达谱 - 下颌成骨细胞的转录调节 - 全身少年特发性关节炎（SJIA）的罕见变体分析 - 研究从CRISPR编辑到整个基因组测序的全基因组修饰的研究 - 早期发作默克尔细胞癌患者的突变分析 BMD今年的其他重大成就包括： - 使用HICEXPLORER的HIC数据访问 应用多个Hicexplorer工具可视化HIC数据。接触矩阵文件用HicConvertFormat转换为H5格式，并使用Hicnormaliz最小的模型归一化，并用HiccorRectMatrix校正。然后，将hicfindtads应用于校正的归一化矩阵，以计算全基因组的TAD分离评分。最后，在关注区域绘制了域，循环和TAD分数数据。 - 切割和标签分析 最初在Henicoff Lab中开发的剪切数据处理和分析管道已被定制和实施，用于来自野生型或强力霉素处理的鼠标角质形成细胞的数据。经过预处理后，将读取与Bowtie2对齐MM10基因组。 SEACR和MACS2均用于峰值通话。收集BAM文件的计数并用作差异表达基因（DEG）分析的DESEQ2的输入。 - 单元多组分分析 Seurat多模式管道已被定制，并应用于通过分化小鼠肌肉细胞产生的多模式实验。将多OMIC数据集重新调整为MM10。首先，清洁了RNA-Seq计数矩阵和ATAC-SEQ峰矩阵。接下来，构建了加权最近的邻居（WNN）图，以了解每个单元格中每个数据模式的相对效用。 r包装Seurat和Signac用于数据缩放，转换，聚类，尺寸降低，差异表达分析和大多数可视化。 R包装单封作用于轨迹分析。 - 构建更强大的RNA-seq数据分析管道 该管道使用星（而不是Tophat）映射批量RNA读取和DESEQ2进行下游分析 - 建造的R套件用于途径和基因集富集分析 根据我们以前的工作，已经开发了一个新的R软件包（RichPathr），用于途径和基因集富集分析。它具有强大但用户友好的友好型，它基于流行的RERHICHR PATHWAY ANARESSION WEB工具，使多个基于基因列表的分析成为可能。该软件包提供了多个实用程序，用于富集数据操纵和可视化。