Gain of 20q11.21 negatively affects ectoderm differentiation potential in human embryonic stem cells

Human pluripotent stem cells frequently acquire chromosomal abnormalities during in vitro culture, one of the most common being the amplification of 20q11.21, present in more than 20% of stem cell lines worldwide. Up to now, there is an important gap in our knowledge, as there are no studies describing in detail the effects of the same aberration in multiple carrier lines. Therefore, we aimed at establishing how the gain of 20q11.21 affects the differentiation process.
For this study, we used 10 hESC lines: 4 wild type, 5 with a gain of 20q11.21 and 1 transgenic line overexpressing Bcl-xL, the driver gene of the 20q11.21 cell culture take-over. Gene-expression microarray analysis showed that the mutant lines and the Bcl-xL-overexpressing line had a significantly lower gene expression of CHCHD2. CHCHD2 up-regulation has been associated to enhanced ectodermal differentiation by modulation of the TGFB1 signaling (Zhu et al., 2016). Therefore, we hypothesized that, if the opposite effect was also true, the hESC with a gain of 20q11.21 should present with decreased ectodermal differentiation. Experiments on all 10 lines (3-6 biological replicates) confirmed the above hypothesis, as lines with a 20q gain as well as the transgenic line consistently express lower levels of ectodermal markers after a 4-day ectoderm differentiation. Overall, the mesendoderm differentiation did not appear to be affected, but we identified one carrier subline of VUB03 that is endoderm differentiation deficient. To address this phenomenon in more detail we are currently performing DNA massive parallel sequencing on the line. Moreover, two of the carrier lines tested were sublines of VUB02 with two different variants, one of which carried an isochromosome 20. This line, next to the decreased ectoderm differentiation, showed high levels of residual undifferentiated cells.