Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing

Abstract

Next-generation sequencing technologies have revolutionised the study of biological systems by enabling the examination of a broad range of tissues. Its application to single-cell genomics has generated a dynamic and evolving field with a vast amount of research highlighting heterogeneity in transcriptional, genetic and epigenomic state between cells. However, compared to these aspects of cellular heterogeneity, relatively little has been gleaned from single-cell datasets regarding cellular mitochondrial heterogeneity. Single-cell sequencing techniques can provide coverage of the mitochondrial genome which allows researchers to probe heteroplasmies at the level of the single cell, and observe interactions with cellular function. In this review, we give an overview of two popular single-cell modalities—single-cell RNA sequencing and single-cell ATAC sequencing—whose throughput and widespread usage offers researchers the chance to probe heteroplasmy combined with cell state in detailed resolution across thousands of cells. After summarising these technologies in the context of mitochondrial research, we give an overview of recent methods which have used these approaches for discovering mitochondrial heterogeneity. We conclude by highlighting current limitations of these approaches and open problems for future consideration.

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

“…For instance, they are relevant when analyzing mitochondrial disorders. New sequencing platforms have revolutionized diagnostics of such diseases, mainly exome and wholegenome approaches, including mitochondrial heteroplasmy [33]. Nevertheless, a holistic -omics approach is needed to generate more comprehensive results, also requiring new bioinformatics tools to properly analyze them [34][35][36][37][38].…”

“…That allows an unprecedented dissection of transcription within millions of individual cells. Both single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) have exciting applications [65][66][67][68][69][70][71][72][73][74][75][76][77], for instance: (i) discovering and characterizing cell type in health and diseases, such as cancer [13,[78][79][80][81][82][83][84][85][86][87][88][89], with implications in immunology [90], immune-mediated diseases [91], immunotherapy [92][93][94][95][96][97][98][99][100] and drug resistance [101]; (ii) deciphering the roles of such specific cell types in health and disease [102], including mitochondrial heteroplasmy [33]; and (iii) analyzing cell emergence, development and plasticity in tissues and organisms. These studies are also applied to study plant biology [103,104].…”

Mitochondrial Heterogeneity in Metabolic Diseases

“…Some potential players in reducing mitochondrial heterogeneity are bottleneck heteroplasmy, mitochondrial fusion, and fission and mitophagy ( Figure 5 ). Genetic bottlenecks lead to the rapid segregation of variants and if the variant takes over the population of mtDNA, homoplasmy results ( Figure 5 A) [ 120 ]. Contributors to bottleneck events may include mitochondrial fission or mitophagy ( Figure 5 B,C).…”

“…In the case of mitochondrial fusion, heterogeneity is diminished by the mixing and equilibrating of mitochondrial contents from different mitochondria ( Figure 5 B). As heteroplasmy increases, so too does the degree of mtDNA mutations [ 120 ]. Within the pool of mitochondria selected to be removed by mitophagy are damaged mitochondria and mitochondria carrying deleterious mutations in mtDNA ( Figure 5 C) [ 120 , 121 , 122 ].…”

“…As heteroplasmy increases, so too does the degree of mtDNA mutations [ 120 ]. Within the pool of mitochondria selected to be removed by mitophagy are damaged mitochondria and mitochondria carrying deleterious mutations in mtDNA ( Figure 5 C) [ 120 , 121 , 122 ]. Overall, genetic bottlenecks, fusion and fission, and mitophagy may reduce intracellular heterogeneity by removing variants encoding various mitochondrial subpopulations.…”