Long noncoding RNAs in innate lymphoid cell biology

先天淋巴细胞生物学中的长非编码RNA

基本信息

批准号：
9329977
负责人：
Walter Mowel
金额：
$ 4.4万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-06-01 至 2019-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9329977
关键词：
ATAC-seq Address Affect Alpha Cell Antigen Receptors Apoptosis Asthma Bacterial Infections Bioinformatics Biological Process Biological Response Modifiers Biology Bone Marrow CD4 Positive T Lymphocytes CRISPR/Cas technology Cell Proliferation Cells Cellular biology Chromatin Code Defect Development Disease Ectopic Expression Embryonic Development Functional disorder Future Gene Expression Gene Expression Regulation Genes Genetic Polymorphism Genetic Transcription Genome Genomic Segment Helminths Helper-Inducer T-Lymphocyte Homeostasis Human Human Genome Hypersensitivity ID2 gene IL2RB gene Immune response Immune system Immunologic Monitoring Immunologics Infection Inflammation Inflammatory Inflammatory Bowel Diseases Insulin Resistance Interleukin-15 Knowledge Lead Listeria monocytogenes Lymphocyte Lymphoid Lymphoid Cell Malignant Neoplasms Mediator of activation protein Mus Myelogenous Natural Killer Cells Obesity Pathology Phenotype Play Population Poxviridae Proteins RNA Regulation Regulator Genes Role Signal Transduction Techniques Testing Therapeutic Tissues Toxoplasma gondii Transcript Transcription Repressor/Corepressor Untranslated RNA Virus Diseases Western Blotting base cell type cytokine experimental study immunoregulation in vivo novel novel therapeutics pathogen progenitor programs response targeted treatment transcription factor

项目摘要

Project Summary: Innate lymphoid cells (ILCs) are recently described groups of innate lymphocytes critical for defense against a variety of pathogens, and their dysfunction has been associated with multiple pathologies. Therefore, understanding how innate lymphoid cells are regulated in vivo is key to developing novel treatments for a variety of diseases. It has become clear recently that although the majority of the human genome does not encode for proteins, noncoding regions are transcribed nonetheless. Indeed, long intergenic noncoding RNA (lincRNA) transcripts have been shown to have key regulatory function in a variety of contexts, such as embryonic development. However, the roles of lincRNAs in the immune system in vivo are not well understood. Importantly, the loci encoding lincRNAs in mice and humans are often conserved. Furthermore, the expression of lincRNAs is often regulated in a cell type-specific manner, more so than protein coding genes. This implies both that lincRNAs play important roles in regulating specific cells in mice and humans, and that they may be useful targets in future therapeutics. Therefore, I hypothesize that cell type-specific lincRNA expression in ILCs is critical for their homeostasis. To this end, we found a specific lincRNA, Ak083360, that is expressed in group 1 ILCs, and in the absence of Ak083360 I have found that both the numbers and function of group 1 ILCs are significantly reduced in multiple tissues. Furthermore, I found that expression of the Id2 transcript is greatly reduced in Ak083360-/- NK cells. Thus, I hypothesize that Ak083360 is critical for the homeostasis of group 1 ILCs through regulation of group 1 ILC development, and that it does this through specific regulation of the Id2 gene. To test this hypothesis, I will determine both the developmental stages and biological process, such as cell proliferation or apoptosis, that are dysregulated in Ak083360-/- mice. I will also determine whether Ak083360 is required for group 1 ILC responses in inflammatory settings. Furthermore, I found that the expression of the Id2 gene is altered in Ak083360-deficient group 1 ILCs, and will determine whether dysregulation of Id2 expression is responsible for this phenotype. Finally, I predict that Ak083360 regulates chromatin accessibility at the Id2 locus. To test this, I will determine the state of chromatin accessibility in Ak083360-/- group 1 ILCs using ATAC-seq, and will combine this with RNA pulldown and Western blotting to determine if Ak083360 interacts with specific protein partners. Altogether, successful completion of the described experiments will further our understanding of both gene regulation by lincRNAs in general and specific factors regulating ILC populations.

项目概要：先天淋巴细胞（ILC）是最近描述的先天淋巴细胞群，对于防御病毒至关重要。多种病原体，其功能障碍与多种病理有关。所以，了解先天淋巴细胞在体内如何调节是开发新疗法的关键各种疾病。最近已经清楚的是，尽管大多数人类基因组并不编码蛋白质，非编码区仍然被转录。事实上，长基因间非编码RNA (lincRNA) 转录本已被证明在多种情况下具有关键的调节功能，例如胚胎发育。然而，lincRNA在体内免疫系统中的作用尚不清楚明白了。重要的是，小鼠和人类中编码 lincRNA 的基因座通常是保守的。此外， lincRNA 的表达通常以细胞类型特异性的方式受到调节，比蛋白质编码的调节更明显基因。这意味着 lincRNA 在调节小鼠和人类的特定细胞中发挥着重要作用，并且它们可能是未来治疗的有用靶标。因此，我假设细胞类型特异性 ILC 中的 lincRNA 表达对其稳态至关重要。为此，我们找到了一个特异的lincRNA， Ak083360，在第 1 组 ILC 中表达，在没有 Ak083360 的情况下，我发现多个组织中第 1 组 ILC 的数量和功能显着减少。此外，我发现 Ak083360-/- NK 细胞中 Id2 转录物的表达大大降低。因此，我假设 Ak083360 通过调节第 1 组 ILC 的发育，对于第 1 组 ILC 的稳态至关重要，并且它确实这是通过 Id2 基因的特定调节实现的。为了检验这个假设，我将确定发育 Ak083360-/- 中失调的阶段和生物过程，例如细胞增殖或凋亡老鼠。我还将确定 Ak083360 是否是炎症环境中第 1 组 ILC 反应所必需的。此外，我发现 Id2 基因的表达在 Ak083360 缺陷的 1 组 ILC 中发生了改变，并且将确定 Id2 表达失调是否是造成这种表型的原因。最后，我预测 Ak083360 调节 Id2 位点的染色质可及性。为了测试这一点，我将确定染色质的状态使用 ATAC-seq 在 Ak083360-/- 组 1 ILC 中进行可访问性，并将其与 RNA pulldown 结合起来通过蛋白质印迹法确定 Ak083360 是否与特定蛋白伴侣相互作用。总而言之，成功完成所描述的实验将进一步我们对 lincRNA 基因调控的理解调节 ILC 群体的一般和特定因素。