Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation

Abstract

Human pluripotent stem cells (hPSCs) have promising therapeutic applications due to their infinite capacity for self-renewal and pluripotency. Genomic stability is imperative for the clinical use of hPSCs; however, copy number variation (CNV), especially recurrent CNV at 20q11.21, may contribute genomic instability of hPSCs. Furthermore, the effects of CNVs in hPSCs at the whole-transcriptome scale are poorly understood. This study aimed to examine the functional in vivo and in vitro effects of frequently detected CNVs at 20q11.21 during early-stage differentiation of hPSCs. Comprehensive transcriptome profiling of abnormal hPSCs revealed that the differential gene expression patterns had a negative effect on differentiation potential. Transcriptional heterogeneity identified by single-cell RNA sequencing (scRNA-seq) of embryoid bodies from two different isogenic lines of hPSCs revealed alterations in differentiated cell distributions compared with that of normal cells. RNA-seq analysis of 22 teratomas identified several differentially expressed lineage-specific markers in hPSCs with CNVs, consistent with the histological results of the altered ecto/meso/endodermal ratio due to CNVs. Our results suggest that CNV amplification contributes to cell proliferation, apoptosis, and cell fate specification. This work shows the functional consequences of recurrent genetic abnormalities and thereby provides evidence to support the development of cell-based applications.

TPX2 prompts mitotic survival via the induction of BCL2L1 through YAP1 protein stabilization in human embryonic stem cells

“…This result is consistent with a recent study showing that human iPSCs with 20q11.21 CNV only have lesser commitment of the ectodermal lineage in teratoma with minor changes in the expression of genes in 20q11.21 loci 42 . Therefore, we propose that other cues to activate BCL2L1 promoter activity, such as YAP1 activation, would occur, leading to the acquisition of the survival advantage trait (e.g., YAP1 stabilization by Aurora A activity due to TPX2 induction).…”

TPX2 Amplification-Driven Aberrant Mitosis in Long-Term Cultured Human Embryonic Stem Cells

“…The amplification of sub-chromosomal 20q11.21 has emerged as a frequent variant in culture-adapted hPSCs (9), a discovery propelled by advances in single-nucleotide resolution of genome-wide approaches. Considering that 25% of normal karyotype hESC lines, including hPSCs with early passage (14), and our cell models (Figs. 2 and 3) revealed a gain of 20q11.21 (9), it is likely hard to detect this minimal amplicon using conventional cytogenetic testing methods (i.e., spectral karyotyping and G-band karyotyping).…”

“…In particular, BCL2L1 in 20q11.21 has been identified as a driver mutation for survival advantages in cultures (11, 12), which also results from an independent loss-of-function mutation in p53 (13). Other than the survival advantage conferred by the amplification of BCL2L1 or the TP53 mutation, the other genetic alterations have not been closely characterized, with a few notable exceptions (14), although various abnormal behaviors, such as tumor formation (15, 16) and impaired differentiation (17), in their progenies or hPSCs themselves were reported in animal models. Although CNV, including 20q11.21, occurs even in early passage (14, 18), the incidence of abnormal karyotypes may occur in a prolonged culture (19), suggesting that the induction of a set of gene(s) by CNV would lead to further chromosomal aberrations (20).…”

Oncogenic miR‐1825 promotes head and neck carcinogenesis via targeting FREM1

“…It has been shown that the 20q11.21 locus contains cancer‐associated genes with potential oncogenic properties, and amplification detected in this region in colorectal cancer leads to genomic instability and recurrent genetic abnormalities and contributes to cancer pathogenesis 44,45 . Jo et al found that copy number variation in the 20q11.21 region led to increased migration capacities, metastatic potential, aberrant differentiation tendencies, cell proliferation, and decreased sensitivity to apoptosis in many types of cancers and human pluripotent stem cells 46 . Given the facts that miR‐1825 resides within 20q11.21 chromosomal region, where has been notified as a recurrent gain of function abnormality in human embryonic and induced pluripotent stem cells 13,14 and that 20q11.21 amplification in human embryonic stem cells resulted in acquisition of a gene‐expression signature enriched for cancer‐related genes, 16,17 we suggested that miR‐1825 might promote cellular phenotypes related to cancer progression in HNSCC as well.…”