Discovery of cell-type-specific mtDNA common deletion in nasopharyngeal carcinoma

Abstract

The human mitochondrial genome (mtDNA) plays a key role in maintaining cellular functions. However, mtDNA is vulnerable to mutations due to the lack of protective histones and low efficiency in DNA repair mechanisms. In previous studies, a common deletion mutation in the mitochondrial genome (mtDNA-CD) was identified in nasopharyngeal carcinoma (NPC) patient samples. However, bulk sequencing protocols employed in past studies were unable to distinguish whether those mtDNA-CD were specific to the cancer cells or from other non-cancer cell types in the samples. Single-cell RNA sequencing (scRNA-seq) technology has provided integral insights into cellular heterogeneity and revolutionised cell-type-specific analysis. In this study, we propose to use scRNA-seq data to identify cell-type-specific deletion signatures in NPC samples. Since there is a lack of bioinformatics tools available, we developed a custom computational pipeline to detect large-scale deletion mutations at the single-cell level. We utilised the mgatk-del-find module of the mgatk analytical pipeline to harness both clipped read profiles and secondary alignment reads to overcome the typical limitations of low sequencing depth and uneven read coverage in scRNA-seq data. We tested our pipeline on an NPC data set consisting of nine patients. Our result suggests the presence of mtDNA- CD mutations specific to malignant cancer cells in NPC tumour samples. Our observations support the presence of cell-type-specific mtDNA-CD, which enables us to better understand the genetic and molecular pathogenesis of cancer and the development of specific biomarkers for NPC.