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Defining malignant hematopoiesis via single-cell multi-omics

通过单细胞多组学定义恶性造血

基本信息

批准号：
10911748
负责人：
Seung Ha Nam
金额：
$ 10.52万
依托单位：
WEILL MEDICAL COLL OF CORNELL UNIV
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-15 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10911748
关键词：
Acceleration Admixture Advisory Committees Affect Anatomy Appointment Biochemical Biological Assay Biomedical Research Blood Blood Cells Bone Marrow CD34 gene Cell Cycle Cell physiology Cell surface Cells Chromatin Clinical Communities Complex Core Facility DNA DNA Sequence Alteration Data Dependence Development Diagnostic Disease Environment Environmental Risk Factor Epigenetic Process Exhibits Faculty Funding Gene Expression Profile Gene Mutation Genes Genetic Genetic Transcription Genome Genomic medicine Genomics Genotype Hematological Disease Hematopathology Hematopoiesis Hematopoietic Hematopoietic Neoplasms Hematopoietic stem cells Human Immune Immunologic Factors Individual Inorganic Chemistry Institution Intrinsic factor Investigation Laboratories Link MPL gene Malignant - descriptor Medicine Megakaryocytes Memorial Sloan-Kettering Cancer Center Mentors Modernization Molecular Molecular Genetics Morphology Mutate Mutation Myelogenous Myeloproliferative disease NF-kappa B Nature Neoplastic Processes New York Outcome Output Pathology Pathway interactions Patients Peer Review Physicians Population Process Production Protein Secretion Proteins Publications Research Research Personnel Research Training Resources Sampling Scientific Advances and Accomplishments Scientist Shapes Signal Transduction Somatic Mutation Specimen T-Lymphocyte Technology Testing Therapeutic Intervention Tissues Training Translational Research Trees United States National Institutes of Health biobank calreticulin cell type clinical phenotype clinical training college cytokine directed differentiation disease phenotype doctoral student driver mutation epigenome epigenomics forging hematopoietic differentiation immunomodulatory therapies improved innovation insight medical schools medical specialties molecular array mouse model multidisciplinary multiple omics mutant neoplastic neoplastic cell next generation novel personalized medicine progenitor programs response single cell sequencing skills stem cells targeted treatment tool transcription factor transcriptome transcriptomics undergraduate student

项目摘要

PROJECT SUMMARY / ABSTRACT Clonal blood differentiation through the acquisition of somatic mutations result in abnormal accumulation of blood components and clinically manifest as myeloid disorders. The study of how these somatic mutations perturb the differentiation trajectories in human hematopoiesis is often challenged by the admixture of normal hematopoietic cells with the neoplastic cells that cannot be distinguished by cell surface markers. To overcome this limitation, we developed a novel single-cell multi-omics Genotyping of Transcriptomes (GoT) platform that directly links somatic genotypes with transcriptomes of thousands of single cells. Thus, GoT enabled the comparison of mutant and wildtype cells within the same sample in the context of progenitor identities, thereby turning the co-mingling of mutant and wildtype hematopoiesis from a limitation to an advantage. As proof of principle, GoT was applied to CD34+ progenitor cells from patients with calreticulin- mutated myeloproliferative neoplasms (MPN), revealing key pathways that were aberrantly activated in the mutant cells, such as a robust unfolded protein response in the megakaryocytic progenitors, on the one way, and NF-KB pathway in stem cell-enriched populations, on the other. Overall, GoT revealed that the transcriptional impact of calreticulin mutations is highly variable as a function of progenitor identity – which bears significant implications for therapy by enabling the discovery of targetable pathways specific to the earliest stem cells. Thus, to demonstrate the cell identity-dependency across other key driver mutations, as a fundamental concept in myeloid disorders, I will apply GoT to thrombopoietin receptor-mutated progenitor cells and to clonally-diverse cells from MPN samples (Aim 1). Next, in order to define cell extrinsic determinants of somatic mutation impact, I will determine the immune niche interactions with calreticulin-mutant and wildtype progenitor cells, as well as the impact of immunomodulatory therapy on these interactions (Aim 2). Finally, I will test the hypothesis that the cell’s epigenome precedes the cell identity-dependency of somatic mutation effects, by developing and applying a novel single-cell platform that integrates somatic genotyping with chromatin accessibility states of progenitor cells (Aim 3). Thus, I will define the genetic, epigenetic, transcriptional and environmental factors that culminate in the clinical output of somatic mutations in human hematopoiesis. These studies will, therefore, unveil not only fundamental concepts in clonal hematopoietic differentiation but also specific targets for therapeutic intervention.

项目总结/摘要通过获得体细胞突变的克隆血液分化导致异常积累，血液成分和临床表现为骨髓疾病。研究这些体细胞突变干扰人类造血中的分化轨迹通常受到正常造血细胞和造血干细胞的混合物的挑战。造血细胞与不能通过细胞表面标志物区分的肿瘤细胞。到为了克服这一局限性，我们开发了一种新的单细胞多组学转录组基因分型（GoT）这是一个将体细胞基因型与数千个单细胞的转录组直接联系起来的平台。因此，GoT 使得能够在祖细胞背景下比较同一样品中的突变型和野生型细胞。身份，从而将突变体和野生型造血的共混合从限制变为限制。优势作为原理的证明，将GoT应用于来自钙网蛋白缺乏患者的CD 34+祖细胞。突变的骨髓增生性肿瘤（MPN），揭示了在骨髓增生性肿瘤中异常激活的关键通路。突变细胞，如巨核细胞祖细胞中强烈的未折叠蛋白反应，另一方面，干细胞富集群体中的NF-κ B途径。总的来说，GoT透露，钙网蛋白突变的转录影响因祖细胞身份的不同而高度可变--这通过能够发现特异于肿瘤的靶向途径，早期干细胞因此，为了证明跨其他关键驱动突变的细胞身份依赖性，如作为髓系疾病的基本概念，我将把GoT应用于血小板生成素受体突变的祖细胞细胞和来自MPN样品的克隆多样性细胞（目的1）。接下来，为了定义细胞外部决定因素的体细胞突变的影响，我将确定与钙网蛋白突变体的免疫生态位相互作用和野生型祖细胞，以及免疫调节治疗对这些相互作用的影响（目的 2）。最后，我将测试细胞的表观基因组先于细胞的身份依赖性的假设，体细胞突变效应，通过开发和应用一种新的单细胞平台，用祖细胞的染色质可及性状态进行基因分型（Aim 3）。因此，我将定义基因，表观遗传、转录和环境因素，最终导致体细胞突变的临床输出在人类造血系统中。因此，这些研究不仅揭示了克隆技术的基本概念，造血分化以及治疗干预的特异性靶点。