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

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.

Graphical abstract

Figure 1

Culture and Whole-Genome Sequencing of Adult Marrow MSCs and Derived iPSC Lines (A) Relationship of adult bone marrow cells, MSCs at various passages, and derived MSCs from the same healthy male donor. After depleting CD34⁺ hematopoietic progenitor cells, CD34⁻ marrow MNCs were used to establish adherent MSCs culture or used for sequencing analyses. The early MSC culture (p1) was used to either derive iPSC lines (E1 and E2) or further expand MSCs until p13. (B) Summary of the whole-genome sequencing data and the comparison of SNCs among cultured MSCs and iPSCs. The raw sequencing data of cell line E1 was derived from the parental study, and the numbers of SNCs for E1 were cited from a previous paper (Cheng et al., 2012).

Figure 2

Detection of the Rare SNC by Droplet Digital PCR (A) The confirmed frequencies of the coding SNCs in different stages of cells from in vivo (CD34⁻ cells) to ex vivo (p1, p8, and p13 MSCs). (B–D) Demonstration of frequency analysis by Droplet Digital PCR (ddPCR) for SNC #1 at p1 and p8 and #4 at p8. y axis: the signal intensities of FAM probe for the mutant allele; x axis: the signal intensities of VIC probe for the reference allele. Each scatter dot represents a PCR signal in a droplet. Counting of ddPCR signals for the mutation (red bar) and reference (blue bar) resulted in the frequency estimation of 0.12%, 10.19%, and 1.25%, respectively. The pink horizontal and vertical lines were automatically determined based on both cluster separation of the four-color dots and the calibration of nontemplate control in ddPCR experiments by the QX100 ddPCR system. The primers and probes designed for #1 and #4 were distinct, so the cutoff rule was unique for each SNC.

Figure 3

A Working Model of Clonal Expansion to Explain Observed SNCs in Culture-Expanded MSCs Derived from Adult Marrow Cells Close circles of different colors represent cells with distinct single-nucleotide changes (SNCs). The number of circles for each color indicates the frequency of distinct SNCs in the mixed cell population. Cells derived from the same ancestor are marked with an identical color along serial ex vivo culture passages (p1, passage 1; p8, passage 8; and p13, passage 13). The emergence of multiple low-frequency SNCs in primary MNCs (uncultured CD34⁻ cells) indicates the existence of small clones that carry unique private somatic mutations. In addition, culture-expanded human MSCs maintain a relatively stable genomic composition in the early stages of ex vivo culture (p1). However, drastically increased frequencies of pre-existing mutations suggest dominant clonal growth of two independent MSC populations (clone 1 and clone 2) upon extended expansion in p8 and p13.