Large-Scale Analysis of Loss-of-Imprinting in Human Pluripotent Stem Cells - AWARD NOMINEE

Introduction: Genomic imprinting is an epigenetic process resulting in a group of genes that are expressed only from one parental allele, while the other allele is silenced. Aberrations in imprinted genes are found in several developmental disorders. Loss-of-imprinting (LOI) may be associated with tumor formation. In addition to genetic aberrations, human pluripotent stem-cells (hPSCs) may acquire epigenetic abnormalities, such as LOI. Determining the extent in which LOI occurs in hPSCs has important consequences on the use of these cells in regenerative medicine and disease modeling.

Methods: We developed a new method to directly calculate the allelic usage of imprinted genes from existing RNA-sequencing data, by comparing biallelic expression of various imprinted genes in different PSC types. We utilized it to chart the landscape of LOI in 271 hPSC samples.

Results: More than one imprinted gene was biallelically-expressed in any given cell line. Reprogrammed hPSCs (induced PSCs and nuclear-transfer derived hPSCs) acquire significantly higher levels of LOI compared with embryonic stem cells. LOI results in over-expression of some imprinted genes and is associated with aberrant patterns of DNA methylation. The biallelic expression also persists during differentiation to both neural lineage and beta cells. Different imprinted genes vary with respect to LOI incidence, surprisingly, those controlled paternally being more prone to disruption.

Conclusions: The relatively high frequency of LOI observed in our analysis, along with the known involvement of imprinting in cancer and disease, substantiate the need to closely examine hPSCs for imprinting aberrations. Potential effects of longterm culture and manipulations on human embrys should also be considered.