Integrated Large-Scale, Single-Cell Transcriptomic and Epigenomic Profiling to Understand Mitochondrial Heteroplasmy
Abstract
Peer Reviewed Medical Research Program Topic Area: Mitochondrial Disease Project Overview: A fundamental question in mitochondrial biology and disease is how variations of mitochondrial DNA (mtDNA) heteroplasmy cause significant phenotypic heterogeneity. mtDNA heteroplasmy refers to the state that a specific mtDNA mutation can be present only in some mtDNA or mitochondria, creating an intracellular mixture of mutant and normal mtDNA. It is now well-established that information of mtDNA heteroplasmy status can be transmitted to the nucleus to induce significant changes in nuclear transcriptome (gene expression) and epigenome (modifications of DNA and associated proteins). However, such changes at the whole genome level remain little understood. Here we propose to use single-cell RNA sequencing (scRNA-Seq) or Assay for Transposase-Accessible Chromatin using sequencing (scATAC-Seq) technologies to comprehensively investigate how variations of mtDNA heteroplasmy affect nuclear transcriptome and epigenome at the single-cell resolution, and reveal and validate the underlying mechanism. Statement of Problem: Though each cell in our body has only two copies of nDNA, it can contain hundreds of mitochondria, with up to thousands of copies of mtDNA per mitochondrion. A specific mtDNA mutation can be present only in some mtDNA or mitochondria, creating an intracellular mixture of mutant and normal mtDNA, a state known as heteroplasmy. Even small changes in the mtDNA heteroplasmic levels can have significant impact on the manifestation and disease severity of patients affected by the mtDNA mutation. Therefore, a fundamental question in mitochondrial biology and disease is how variations of mtDNA heteroplasmy cause significant phenotypic heterogeneity. It is now known that information of mtDNA heteroplasmy status can transmit to the nucleus to induce significant changes in epigenomic state, gene transcription, and downstream cellular functions. However, such epigenetic and transcriptional changes at the whole genome level remain little understood. Innovation: Our studies proposed herein contain both conceptual and technological innovations: • We will reveal, for the first time to our knowledge, comprehensive genome-wide transcriptional and epigenetic changes caused by mtDNA heteroplasmy at the single-cell resolution, using state-of-the-art large-scale scRNA-Seq and scATAC-Seq methods. • We are using and developing advanced bioinformatics tools for integrated single-cell transcriptome and epigenome analysis. This will uncover the transcription regulators that open the chromatin and impact gene expression, thereby providing novel insights into how the information of mtDNA heteroplasmy status is transmitted to downstream nuclear transcriptional and epigenetic changes. • We have developed and are characterizing a series of new cell lines with different level of specific mtDNA heteroplasmy. These cell lines will be invaluable tools for the mitochondrial biology community to study mtDNA heteroplasmy. • Combining all these innovations together, our integrated, large-scale, single-cell transcriptomic and epigenomic analysis approach will help answer a fundamental question in mitochondrial biology and disease, that is, how variations of mtDNA heteroplasmy cause significant phenotypic heterogeneity. Impact: We believe that our proposed studies will generate significant scientific and clinical impact: • Our innovative single-cell transcriptome and epigenome approaches and integrated data analysis methods will significantly advance our understanding of mtDNA heteroplasmy and be generally applicable to many other areas of mitochondrial biology and disease. • Similarly, the cell lines we generated that contain different level of specific mtDNA heteroplasmy will be invaluable tools for the mitochondrial biology community to study mtDNA heteroplasmy. • Our proposed studies will bring novel insights into a fundamental ques
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Mar 10, 2021
- Source ID
- W81XWH2010042
Entities
People
- Liming Pei
Organizations
- United States Army