Regulation of Cellular Proliferation by Novel Mitochondrial-Encoded Tumor Suppressors

新型线粒体编码肿瘤抑制剂对细胞增殖的调节

基本信息

批准号：
10389994
负责人：
Changhan Lee
金额：
$ 16.74万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
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：
2020-09-01 至 2024-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10389994
关键词：
ATAC-seq Adenosine Monophosphate Affect Amino Acids Bacteria Basic Science Binding Bioinformatics Cancer Model Cell Cycle Cell Nucleus Cell Proliferation Cell Separation Cell Survival Cell physiology Cells Cellular Stress Chromatin Code Communication Computer Analysis Computing Methodologies Coupled DNA DNA Binding Data Developmental Therapeutics Program Electron Transport Endothelium Eukaryota Eukaryotic Cell Evolution Exhibits FDA approved Foundations Gene Expression Genes Genetic Genetic Diseases Genome Genomic approach Genomics Homeostasis In Vitro Insulin Resistance Language Longevity Machine Learning Malignant - descriptor Malignant Neoplasms Maps Mediating Metabolic Metabolic stress Metabolism Mitochondria Mitochondrial DNA Modeling Molecular Molecular Biology Techniques Molecular Genetics Molecular and Cellular Biology Mus Names Normal Cell Normal tissue morphology Nuclear Nuclear Translocation Nutrient Open Reading Frames Organelles Osteoporosis Pathway interactions Patients Peptides Pharmaceutical Preparations Process Property Protein Kinase Proteins Proteomics Publishing RNA Regulation Reporting Resistance Ribosomal RNA Ribosomes Role Signal Transduction Site-Directed Mutagenesis Source Stress System TP53 gene Testing The Cancer Genome Atlas Time Tissue Microarray Tissues Toxic effect Treatment Efficacy Tumor Suppressor Proteins age related antitumor effect base cancer cell cancer genome cancer type cell growth regulation cell type chemotherapy chromatin immunoprecipitation combinatorial comparative diet-induced obesity exhaustion functional genomics genomic data immune function improved in vivo loss of function mitochondrial genome mouse model muscle metabolism mutant new therapeutic target novel prevent response sensor single-cell RNA sequencing therapeutic development tumor

项目摘要

ABSTRACT Cellular compartments are coordinated through a dynamic bidirectional communication network amongst various organelles. Here, we focus on the communication between mitochondria and the nucleus, organelles that each possess their own genomes. The mitochondrial and nuclear genomes have co-evolved for over a billion years and have likely required close communication and cross-regulation. However, whereas mitochondria are known to be regulated by over 1,000 nuclear-encoded proteins, but there is currently no known mitochondrial-encoded factor that actively communicates to and regulates the nucleus. We have recently identified a novel gene encoded within the mitochondrial DNA and named it MOTS-c (Mitochondrial ORF within the Twelve S rRNA type-c). MOTS-c is a small 16 amino acid peptide that regulates metabolic homeostasis, in part, via the master nutrient sensor AMPK (adenosine monophosphate-activated protein kinase). We recently reported that MOTS-c can translocate into the nucleus in response to metabolic stress to bind to chromatin and regulate nuclear gene expression. Further, our preliminary study using a multi-pronged approach, including single cell RNA-seq, bioinformatics (including machine learning), chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR), and cell sorting, showed that MOTS-c can regulate cellular proliferation; MOTS-c targeted the p53/p21 pathway and ribosomal processes. Considering the important metabolic role of mitochondria in cellular proliferation processes (29), a critical question that remains largely enigmatic is how mitochondrial-encoded factors communicate to the nucleus to coordinate the metabolic shift with gene expression during proliferation. Notably, rapidly dividing cancer cells had undetectable levels of MOTS-c or nuclear-translocation deficiency, suggesting loss of mito-nuclear communication by MOTS-c. Together, cancer may be a genetic disease in which our two genomes exist in a state of disrupted bi-directional communication/regulation, and may serve as a unique model to start understanding the role of MOTS-c in cellular proliferation. Because MOTS-c expression/function was dysregulated and that MOTS-c can negatively regulate cell cycle/proliferation, we hypothesize that MOTS-c is a mitochondrial-encoded tumor suppressor, the first of its kind to be identified, that directly regulates the nucleus to coordinate cellular metabolism with proliferation. We propose three aims to test this hypothesis. First, we will characterize MOTS-c as a tumor suppressor that regulates cell proliferation at the molecular, cellular, genetic level. Second, we will comprehensively map the MOTS-c-dependent functional nuclear genomic landscape using multiple complimentary genomics approach, including single cell RNA-seq, ATAC-seq (chromatin accessibility), and genomic footprinting using ChIP-seq. The data from each genomic approach will be integrated using cutting-edge computational methods, including machine learning, to decipher the message(s) MOTS- c delivers to the nuclear genome to regulate cancer cell proliferation and survival. Lastly, we will determine how MOTS- c-mediated communication to the nucleus can differentially regulate cellular proliferation and stress resistance in normal and malignant cells using mouse models of cancer. If successful, we predict that our study will have broad and lasting impact on (i) basic research by introducing the paradigm-shifting concept of mitochondrial-encoded tumor suppressors that coordinate cellular metabolism and proliferation and (ii) therapeutic development by revealing mtDNA as a source of novel drug targets (currently there are no FDA-approved drugs based on the mitochondrial genome).

抽象的蜂窝区室通过动态双向通信网络在各个区域之间进行协调细胞器。在这里，我们重点关注线粒体和细胞核之间的通讯，每个细胞器拥有自己的基因组。线粒体和核基因组已经共同进化了十亿多年，可能需要密切沟通和交叉监管。然而，尽管已知线粒体受 1,000 多种核编码蛋白调节，但目前尚无已知的线粒体编码因子积极地与细胞核沟通并进行调节。我们最近发现了一个新的基因编码线粒体 DNA 并将其命名为 MOTS-c（十二 S rRNA c 型线粒体 ORF）。 MOTS-c 是 16 个氨基酸小肽，部分通过主营养传感器 AMPK 调节代谢稳态（腺苷单磷酸激活蛋白激酶）。我们最近报道 MOTS-c 可以易位到细胞核响应代谢应激，与染色质结合并调节核基因表达。此外，我们的初步研究采用多管齐下的方法，包括单细胞RNA-seq、生物信息学（包括机器学习）学习）、染色质免疫沉淀 (ChIP) 结合定量 PCR (qPCR) 和细胞分选，显示 MOTS-c可以调节细胞增殖； MOTS-c 针对 p53/p21 途径和核糖体过程。考虑到线粒体在细胞增殖过程中的重要代谢作用 (29)，一个关键问题线粒体编码因子如何与细胞核通讯以协调增殖过程中代谢随基因表达的变化。值得注意的是，快速分裂的癌细胞的水平无法检测到 MOTS-c 或核易位缺陷，表明 MOTS-c 导致线粒体-核通讯丧失。总之，癌症可能是一种遗传疾病，其中我们的两个基因组以双向破坏的状态存在。通信/调节，并且可以作为开始了解 MOTS-c 在细胞中的作用的独特模型增殖。因为 MOTS-c 表达/功能失调，并且 MOTS-c 可以负向调节细胞周期/增殖，我们假设 MOTS-c 是一种线粒体编码的肿瘤抑制因子，这是同类中的第一个待鉴定，它直接调节细胞核以协调细胞代谢与增殖。我们提出三个旨在检验这一假设。首先，我们将 MOTS-c 描述为一种肿瘤抑制因子，可调节细胞增殖分子、细胞、遗传水平。其次，我们将全面绘制 MOTS-c 依赖的功能核图谱。使用多种互补基因组学方法的基因组景观，包括单细胞 RNA-seq、ATAC-seq （染色质可及性），以及使用 ChIP-seq 进行基因组足迹分析。每种基因组方法的数据将是使用包括机器学习在内的尖端计算方法进行集成，以破译消息 MOTS- c 传递至核基因组以调节癌细胞增殖和存活。最后，我们将确定 MOTS- c介导的细胞核通讯可以差异性地调节正常细胞的增殖和应激抵抗和使用小鼠癌症模型的恶性细胞。如果成功，我们预计我们的研究将通过引入以下内容对 (i) 基础研究产生广泛而持久的影响：线粒体编码的肿瘤抑制因子的范式转换概念，协调细胞代谢和增殖和（ii）通过揭示 mtDNA 作为新药物靶点的来源来进行治疗开发（目前有不是 FDA 批准的基于线粒体基因组的药物）。