Type

Journal Article

Authors

Niall Barron
Martin Clynes
Michael J Betenbaugh
Nicole Borth
Heena Dhiman
Justine Meiller
Craig Monger
Alan Costello
Colin Clarke
Paul S Kelly

Subjects

Biochemistry

Topics
low frequency next generation sequencing cho cells genome sequencing chinese hamster ovary cells cell lines high resolution reveals

Ultra-deep next generation mitochondrial genome sequencing reveals widespread heteroplasmy in Chinese hamster ovary cells. (2016)

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.
Collections Ireland -> Dublin City University -> PubMed

Full list of authors on original publication

Niall Barron, Martin Clynes, Michael J Betenbaugh, Nicole Borth, Heena Dhiman, Justine Meiller, Craig Monger, Alan Costello, Colin Clarke, Paul S Kelly

Experts in our system

1
Niall Barron
Dublin City University
Total Publications: 44
 
2
Martin Clynes
Dublin City University
Total Publications: 209
 
3
Craig Monger
Dublin City University
Total Publications: 3
 
4
Alan Costello
Dublin City University
Total Publications: 3
 
5
Colin Clarke
Dublin City University
Total Publications: 26
 
6
Paul S. Kelly
Dublin City University
Total Publications: 11