Whole-genome sequencing identifies genetic variances in culture-expanded human mesenchymal stem cells

Jun Cai; Xuexia Miao; Yueying Li; Cory Smith; Kitman Tsang; Linzhao Cheng; Qian-Fei Wang

doi:10.1016/j.stemcr.2014.05.019

Whole-genome sequencing identifies genetic variances in culture-expanded human mesenchymal stem cells

Stem Cell Reports. 2014 Aug 12;3(2):227-33. doi: 10.1016/j.stemcr.2014.05.019. Epub 2014 Jun 26.

Authors

Jun Cai¹, Xuexia Miao², Yueying Li¹, Cory Smith³, Kitman Tsang⁴, Linzhao Cheng⁵, Qian-Fei Wang⁶

Affiliations

¹ Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
² Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
³ Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Stem Cell Program, Institute for Cell Engineering, and Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁴ Stem Cell Program, Institute for Cell Engineering, and Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵ Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Stem Cell Program, Institute for Cell Engineering, and Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: lcheng2@jhmi.edu.
⁶ Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: wangqf@big.ac.cn.

Abstract

Culture-expanded human mesenchymal stem cells (MSCs) are increasingly used in clinics, yet full characterization of the genomic compositions of these cells is lacking. We present a whole-genome investigation on the genetic dynamics of cultured MSCs under ex vivo establishment (passage 1 [p1]) and serial expansion (p8 and p13). We detected no significant changes in copy-number alterations (CNAs) and low levels of single-nucleotide changes (SNCs) until p8. Strikingly, a significant number (677) of SNCs were found in p13 MSCs. Using a sensitive Droplet Digital PCR assay, we tested the nonsynonymous SNCs detected by whole-genome sequencing and found that they were preexisting low-frequency mutations in uncultured mononuclear cells (∼0.01%) and early-passage MSCs (0.1%-1% at p1 and p8) but reached 17%-36% in p13. Our data demonstrate that human MSCs maintain a stable genomic composition in the early stages of ex vivo culture but are subject to clonal growth upon extended expansion.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adult
Bone Marrow Cells / cytology
Cells, Cultured
DNA Copy Number Variations
Genome, Human
High-Throughput Nucleotide Sequencing
Humans
Induced Pluripotent Stem Cells / cytology
Induced Pluripotent Stem Cells / metabolism
Male
Mesenchymal Stem Cells / cytology
Mesenchymal Stem Cells / metabolism*
Polymorphism, Single Nucleotide
Sequence Analysis, DNA

Abstract

Publication types

MeSH terms

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