De Novo Cancer Mutations Frequently Associate with Recurrent Chromosomal Abnormalities during Long-Term Human Pluripotent Stem Cell Culture

Cells. 2024 Aug 21;13(16):1395. doi: 10.3390/cells13161395.

Abstract

Human pluripotent stem cells (hPSCs) are pivotal in regenerative medicine, yet their in vitro expansion often leads to genetic abnormalities, raising concerns about their safety in clinical applications. This study analyzed ten human embryonic stem cell lines across multiple passages to elucidate the dynamics of chromosomal abnormalities and single-nucleotide variants (SNVs) in 380 cancer-related genes. Prolonged in vitro culture resulted in 80% of the lines acquiring gains of chromosome 20q or 1q, both known for conferring an in vitro growth advantage. 70% of lines also acquired other copy number variants (CNVs) outside the recurrent set. Additionally, we detected 122 SNVs in 88 genes, with all lines acquiring at least one de novo SNV during culture. Our findings showed higher loads of both CNVs and SNVs at later passages, which were due to the cumulative acquisition of mutations over a longer time in culture, and not to an increased rate of mutagenesis over time. Importantly, we observed that SNVs and rare CNVs followed the acquisition of chromosomal gains in 1q and 20q, while most of the low-passage and genetically balanced samples were devoid of cancer-associated mutations. This suggests that recurrent chromosomal abnormalities are potential drivers for the acquisition of other mutations.

Keywords: cancer-related genes; copy number variation; genetic instability; human pluripotent stem cells; single-nucleotide variants.

MeSH terms

  • Cell Culture Techniques / methods
  • Cell Line
  • Chromosome Aberrations*
  • DNA Copy Number Variations* / genetics
  • Human Embryonic Stem Cells / metabolism
  • Humans
  • Mutation* / genetics
  • Neoplasms* / genetics
  • Neoplasms* / pathology
  • Pluripotent Stem Cells* / metabolism
  • Polymorphism, Single Nucleotide / genetics

Grants and funding

Y.L. is a predoctoral fellow supported by the China Scholarship Council (CSC). M.C.D. is a predoctoral fellow supported by the 175 Military Hospital in Vietnam. M.R. and N.K. were supported by predoctoral fellowships from the Fonds voor Wetenschappelijk Onderzoek Vlaanderen (FWO, grant numbers 1133622N and 1169023N, respectively). This research was supported by the FWO (grant number G078423N) and the Methusalem Grant to Karen Sermon and to Claudia Spits (Vrije Universitet Brussel).