BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures

Abstract

Human embryonic stem cells (hESCs) regularly acquire nonrandom genomic aberrations during culture, raising concerns about their safe therapeutic application. The International Stem Cell Initiative identified a copy number variant (CNV) amplification of chromosome 20q11.21 in 25% of hESC lines displaying a normal karyotype. By comparing four cell lines paired for the presence or absence of this CNV, we show that those containing this amplicon have higher population doubling rates, attributable to enhanced cell survival through resistance to apoptosis. Of the three genes encoded within the minimal amplicon and expressed in hESCs, only overexpression of BCL2L1 (BCL-XL isoform) provides control cells with growth characteristics similar to those of CNV-containing cells, whereas inhibition of BCL-XL suppresses the growth advantage of CNV cells, establishing BCL2L1 as a driver mutation. Amplification of the 20q11.21 region is also detectable in human embryonal carcinoma cell lines and some teratocarcinomas, linking this mutation with malignant transformation.

Graphical abstract

Figure 1

Presence of 20q11.21 Gain in Four Test hESC Lines (A) Genomic qPCR assay using primer/probe pairs designed to introns of genes spanning the 20q11.21 locus (black bars) determines the amplicon length and copy number fold change. Genomic positions relate to USCS human genome assembly version hg19 (Kent et al., 2002). Cycle threshold values are normalized against RELL1 (first white bar) genomic values. RELL1 is located on chromosome 4, which displays a low incidence of genomic instability in hESCs. Two additional controls (white bars) confirm the suitability of the first control. All data are normalized against control hESCs. (B) Schematic representation of amplicon lengths for the four test hESC cell lines (red lines) positioned alongside genes contained within the 20q11.21 locus. The green dotted line and asterisk represent the minimal amplicon previously described in hESCs, and genes in blue are candidate genes located within the minimal amplicon and expressed in hESCs. See also Figure S1 and Table S4.

Figure 2

CNV and BCL-XL-Overexpressing hESCs Display Enhanced Growth Rates (A) Cell densities for hESCs lines: control (blue circle), CNV-containing (red circle), or overexpressing HM13 (orange circle), ID1 (purple circle), or BCL-XL (black circle). Cells were seeded at 8 × 10⁴ cells/cm² and cultured for 96 hr before total cell counts were obtained. Error bars: SEM from three independent experiments. Asterisks indicate statistical significance by two-tailed t test; ^∗p ≤ 0.05, ^∗∗p ≤ 0.01, ^∗∗∗p ≤ 0.001. (B) Cell competition assay between HES3 cells. HES3-GFP-expressing control cells were mixed at a 9:1 ratio with control cells, CNV cells, or HES cells overexpressing HM13, ID1, or BCL-XL. The GFP percentage was measured by flow cytometry over the course of ten passages (P). Error bars: SEM from three independent experiments. (C) The clonogenicity of CNV cells is reduced to normal levels by inhibition of BCL-XL using the compound ABT-263. Control cells (green wells) and CNV cells (red wells) were seeded at 1 × 10⁴ cells/cm² and cultured for 5–7 days. CNV cells were untreated (i) or treated with ABT-263 at 50 nM (ii), 100 nM (iii), 250 nM (iv), or 1,000 nM (v) concentrations. (D) Cell densities obtained for H1 CNV BCL-XL-shRNAi cells seeded at 8 × 10⁴ cells/cm² treated in the presence of 100 ng/ml doxycycline (Dox+), or not (Dox-), for 96 hr. Cells were seeded at 8 × 10⁴ cells/cm² and cultured for 96 hr before total cell counts were obtained. Error bars: SEM from three independent experiments. Asterisks indicate statistical significance by two-tailed t test (p < 0.005). See also Figure S2.

Figure 3

Cell Survival, not Cell Cycle, Influences the Growth Advantage for CNV and BCL-XL-Overexpressing hESCs In each panel, cells are labeled as control (blue circle), CNV-containing (red circle), overexpressing HM13 (yellow circle), overexpressing ID1 (purple circle), or overexpressing BCL-XL (black circle). (A) Cell-cycle distribution percentages for cells in G0/1, S, or G2/M phase. Error bars: SEM from three independent experiments. Asterisks indicate statistical significance by two-tailed t-test; ^∗p ≤ 0.05, ^∗∗p ≤ 0.01. (B) Actual cell division times. Each spot represents the time period between two cell divisions; mean average and SEM are indicated by black lines. A two-tailed t test analysis was performed to compare differences between test and control cells. Actual p values are provided for test cells with significant differences (p < 0.05). (C) Cell-fate maps based upon time-lapse movie observations over 24 hr for control cells (blue bars) and CNV cells (red bars), where fates are measured as living (•) or dead (†) cells. Percentage outcomes (50 randomly selected cells from ten fields per group) represent cell death (1), cell division with both daughter cells dying (2), cell does not divide but survives (3), cell division with only one daughter cell surviving (4), and cell division with both daughter cells surviving (5). For all four lines, control and CNV cells exhibited significantly different frequencies of outcomes 1 and 5 (χ² test, p < 0.05). (D) Cell-staining percentages for cleaved caspase-3. Measurements were taken over the course of 24 hr. Error bars: SEM from three independent experiments. Asterisks indicate significant differences between control and CNV cells by 6 hr (HES3, H1, ESI, ESI+BCL-XL) or 12 hr (Shef5); two-way ANOVA, p < 0.05. See also Figure S3.

Figure 4

Presence of 20q11.21 Amplicon and Increased BCL-XL Protein Expression in Several ECC Lines (A) Representative figures for FISH analysis of the nine ECCs. Orange probe, BCL2L1 spectrum; green probe, 20 p telomere spectrum. The number of BCL2L1 copies is indicated at the bottom right of each panel. Scale bar: ∼2 μm. (B) Western blot analysis for BCL-XL and Bcl-xS protein using a universal BCL-X antibody. Whole-cell lysates were prepared from hECCs. β-actin was used as a loading control. See also Figure S4.