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Biological and cancer-associated role of epitranscriptomic gene expression regulation

表观转录组基因表达调控的生物学和癌症相关作用

基本信息

批准号：
10016235
负责人：
Deniz Nesli Dolcen
金额：
$ 4.55万
依托单位：
UNIVERSITY OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-11 至 2022-09-11
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10016235
关键词：
Binding Proteins Biological Breast Cancer Cell Breast Cancer Model Breast Cancer cell line Cancer Biology Cell Culture Techniques Cell Death Cell Survival Cells Cellular Stress Response Consumption DNA DNA Modification Process Data Development Epigenetic Process Eukaryota Exhibits Exposure to Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Histones Human Hypoxia In Vitro Individual Link MDA MB 231 Malignant Neoplasms Mass Spectrum Analysis Mediating Messenger RNA Methylation Methyltransferase Modeling Modernization Modification Mus Neoplasm Metastasis Niacinamide Nicotinamide N-Methyltransferase Oncogenic Pathology Pathway interactions Patients Pharmacology Phenotype Physiology Play Polymerase Postdoctoral Fellow Process Proteome RNA RNA methylation Rattus Regulator Genes Relapse Research Research Project Grants Role S-Adenosylhomocysteine Small Interfering RNA Sprague-Dawley Rats Stimulus Systemic Therapy Testing Therapeutic Agents Transcript Translational Regulation Urine Xenograft procedure cancer cell cancer gene expression cancer stem cell cancer therapy differential expression epitranscriptomics genetic regulatory protein histone modification in vivo knock-down malignant breast neoplasm methylome mouse model novel nutrient deprivation prevent protein expression response single-cell RNA sequencing stem-like cell stressor trait triple-negative invasive breast carcinoma tumor tumor growth tumor microenvironment tumor progression

项目摘要

PROJECT SUMMARY My lab discovered that NNMT is a direct GR transcriptional target gene in TNBC. I then observed relatively high NNMT expression in several aggressive patient-derived TNBC cell lines. NNMT consumes the universal methyl donor S-adenosyl methionine (SAM) for methylation of nicotinamide. High NNMT activity depletes SAM; as a result, methyltransferase targets are hypomethylated in cells with high NNMT expression. NNMT-induced DNA and histone hypomethylation have been shown to result in oncogenic gene expression in cancer cells but NNMT mechanism of action in TNBC biology remains unclear. A link between NNMT expression and mRNA hypomethylation has not previously been established as a mechanism contributing to cancer progression. N6- methyladenosine (m6A) is an abundant and reversible RNA modification in eukaryotes. Our collaborator Dr. Chuan He discovered that m6A-binding proteins mediate translational regulation by altering stability and translational efficiency of m6A-modifed mRNAs. Importantly, altered m6A mRNA methylation is implicated in the progression of several human cancers via causing changes in post-transcriptional gene expression of cancer pathways. To our knowledge, I am the first to characterize the m6A methylome of a patient-derived TNBC cell line model (MDA-MB-231): ~ 7000 m6A-modified transcripts are significantly enriched for pathways involved in cellular stress response, cell death and cell survival. In addition, I have data suggesting that NNMT activity in the MDA-MB-231 TNBC cell line results in 1) reduced m6A modification of mRNAs regulating key cancer pathways and 2) increased in vivo tumor-growth. In my dissertation research, I am testing the hypothesis that NNMT activity in TNBC cells results in 1) reduced m6A mRNA modification associated with altered protein expression of pathways mediating cellular stress response and 2) cancer stem cell-like traits associated with survival, metastatic potential and increased in vivo tumor-forming capacity. During my postdoctoral research, I aim to test whether epitranscriptomic gene expression regulates dynamic cellular phenotypes including adaptation to the changing microenvironment. I will first characterize the actively transcribed genes with polymerase ChIPseq and perform whole proteome quantification with mass spectrometry in cells exposed to distinct microenvironmental stressors (e.g. nutrient deprivation, hypoxia). I will then determine whether differential transcription of genes correlate with protein expression in different cellular states. If there is not a strong correlation, I will perform individual siRNA knockdown of all known m6A- regulatory genes and determine the effect on protein expression. I will then utilize patient-derived xenograft mouse models and the Sprague Dowley rat model of spontaneous breast cancer to determine whether the m6A-regulatory proteins are differentially expressed in distinct tumor regions with single-cell RNA sequencing.

项目总结