A comprehensive characterization of rare mitochondrial DNA variants in neuroblastoma

Abstract

BackgroundNeuroblastoma, a tumor of the developing sympathetic nervous system, is a common childhood neoplasm that is often lethal. Mitochondrial DNA (mtDNA) mutations have been found in most tumors including neuroblastoma. We extracted mtDNA data from a cohort of neuroblastoma samples that had undergone Whole Exome Sequencing (WES) and also used snap-frozen samples in which mtDNA was entirely sequenced by Sanger technology. We next undertook the challenge of determining those mutations that are relevant to, or arisen during tumor development. The bioinformatics pipeline used to extract mitochondrial variants from matched tumor/blood samples was enriched by a set of filters inclusive of heteroplasmic fraction, nucleotide variability, and in silico prediction of pathogenicity.ResultsOur in silico multistep workflow applied both on WES and Sanger-sequenced neuroblastoma samples, allowed us to identify a limited burden of somatic and germline mitochondrial mutations with a potential pathogenic impact.ConclusionsThe few singleton germline and somatic mitochondrial mutations emerged, according to our in silico analysis, do not appear to impact on the development of neuroblastoma. Our findings are consistent with the hypothesis that most mitochondrial somatic mutations can be considered as ‘passengers’ and consequently have no discernible effect in this type of cancer.

Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light

“…Haplogroup identification made it possible to verify the quality of mitochondrial genome reconstruction (Diroma et al, ). Haplogroup defining variants filtering for prioritization has already been described (Santorsola et al, ) in studies of tumor cells (F.M.Calabrese et al, ) or in a cohort of individuals suspected of mitochondrial diseases (Patowary et al, ).…”

“…In oncology, comparison of germline and somatic mtDNA variants highlighted specific mtDNA variants requiring prioritization filters such as population frequency or haplogroup assignment (F.M.Calabrese et al, ). In a cohort with suspected mitochondrial disorders, filtering out haplogroup defining variants made it possible to prioritize mtDNA variants, to confirm the causality of well‐known variants for LHON (Santorsola et al, ) during performance evaluation of the prioritization criteria, or to highlight variants of interest in autism (Patowary et al, ), a disease, which may be linked to mitochondrial dysfunction.…”

MtDNA As a Cancer Marker: A Finally Closed Chapter?

“…Recent NGS approaches combined with sophisticated data analysis to select mutations of likely functional relevance, may shed a much more systematic light on the potential role of mtDNA mutations for tumor biology in the future. A group of researchers from Italy recently implemented a multistep bioinformatics analysis of NGS-based sequence data, which detected many, mostly low abundant heteroplasmic mtDNA mutations in glioblastomas and neuroblastomas, the vast majority of which was likely to represent merely passengers of the clonal cell expansion without any role for tumor growth [ 91 , 92 ]. The bioinformatics tool used, called MToolBox, had been recently developed [ 93 ] and consists of several layers of subsequent filters, intended to exclude irrelevant polymorphisms and to select or assign higher priority to mutations, which may deserve further analysis of a potential clinical role.…”

A Targeted Gene Panel for Circulating Tumor DNA Sequencing in Neuroblastoma

“…Recent whole genome sequencing analysis in a large cohort of neuroblastoma patients have identified a paucity of recurrent alterations with point mutations in ALK (8-10%) and in ATRX, being the most frequent (20,21). The limited burden of mitochondrial DNA mutations with potential pathogenic impact have also been assessed (22). Nevertheless, a recent work has highlighted the involvement of noncoding somatic variants, located in regulatory DNA regions, in neuroblastoma development (23).…”