Ultra-deep next generation mitochondrial genome sequencing reveals widespread heteroplasmy in Chinese hamster ovary cells

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Title: Ultra-deep next generation mitochondrial genome sequencing reveals widespread heteroplasmy in Chinese hamster ovary cells
Authors: Kelly, Paul S.
Clarke, Colin
Costello, Alan
Barron, Niall
et al.
Permanent link: http://hdl.handle.net/10197/10335
Date: 1-May-2017
Online since: 2019-05-08T08:34:52Z
Abstract: Recent sequencing of the Chinese hamster ovary (CHO) cell and Chinese hamster genomes has dramatically advanced our ability to understand the biology of these mammalian cell factories. In this study, we focus on the powerhouse of the CHO cell, the mitochondrion. Utilizing a high-resolution next generation sequencing approach we sequenced the Chinese hamster mitochondrial genome for the first time and surveyed the mutational landscape of CHO cell mitochondrial DNA (mtDNA). Depths of coverage ranging from ~3,319X to 8,056X enabled accurate identification of low frequency mutations (>1%), revealing that mtDNA heteroplasmy is widespread in CHO cells. A total of 197 variants at 130 individual nucleotide positions were identified across a panel of 22 cell lines with 81% of variants occurring at an allele frequency of between 1% and 99%. 89% of the heteroplasmic mutations identified were cell line specific with the majority of shared heteroplasmic SNPs and INDELs detected in clones from 2 cell line development projects originating from the same host cell line. The frequency of common predicted loss of function mutations varied significantly amongst the clones indicating that heteroplasmic mtDNA variation could lead to a continuous range of phenotypes and play a role in cell to cell, production run to production run and indeed clone to clone variation in CHO cell metabolism. Experiments that integrate mtDNA sequencing with metabolic flux analysis and metabolomics have the potential to improve cell line selection and enhance CHO cell metabolic phenotypes for biopharmaceutical manufacturing through rational mitochondrial genome engineering.
Funding Details: European Commission Horizon 2020
Science Foundation Ireland
Type of material: Journal Article
Journal: Metabolic Engineering
Volume: 41
Start page: 11
End page: 22
Copyright (published version): 2017 International Metabolic Engineering Society
Keywords: Chinese hamster ovaryBiopharmaceuticalMitochondrialHeteroplasmyNext generation sequencingGenomics
DOI: 10.1016/j.ymben.2017.02.001
Language: en
Status of Item: Peer reviewed
Appears in Collections:Chemical and Bioprocess Engineering Research Collection

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