Clone- and Gene-Specific Aberrations of Parental Imprinting in Human Induced Pluripotent Stem Cells

Abstract

Genomic imprinting is an epigenetic phenomenon whereby genes are expressed in a monoallelic manner, which is inherited either maternally or paternally. Expression of imprinted genes has been examined in human embryonic stem (ES) cells, and the cells show a substantial degree of genomic imprinting stability. Recently, human somatic cells were reprogrammed to a pluripotent state using various defined factors. These induced pluripotent stem (iPS) cells are thought to have a great potential for studying genetic diseases and to be a source of patient-specific stem cells. Thus, studying the expression of imprinted genes in these cells is important. We examined the allelic expression of various imprinted genes in several iPS cell lines and found polymorphisms in four genes. After analyzing parent-specific expression of these genes, we observed overall normal monoallelic expression in the iPS cell lines. However, we found biallelic expression of the H19 gene in one iPS cell line and biallelic expression of the KCNQ10T1 gene in another iPS cell line. We further analyzed the DNA methylation levels of the promoter region of the H19 gene and found that the cell line that showed biallelic expression had undergone extensive DNA demethylation. Additionally we studied the imprinting gene expression pattern of multiple human iPS cell lines via DNA microarray analyses and divided the pattern of expression into three groups: (a) genes that showed significantly stable levels of expression in iPS cells, (b) genes that showed a substantial degree of variability in expression in both human ES and iPS cells, and (c) genes that showed aberrant expression levels in some human iPS cell lines, as compared with human ES cells. In general, iPS cells have a rather stable expression of their imprinted genes. However, we found a significant number of cell lines with abnormal expression of imprinted genes, and thus we believe that imprinted genes should be examined for each cell line if it is to be used for studying genetic diseases or for the purpose of regenerative medicine. STEM CELLS

Genomic imprinting and its relevance to congenital disease, infertility, molar pregnancy and induced pluripotent stem cell

“…100 Clone-and gene-specific aberrations of imprinting were also reported in human iPS cells. 101 These studies underscore the importance of the imprint maintenance mechanism in cell reprogramming.…”

Induced pluripotent stem cell models of the genomic imprinting disorders Angelman and Prader–Willi syndromes

“…Because nuclear reprogramming of somatic cells into pluripotent stem cells may involve global erasure of epigenetic marks, it has been argued that the differential methylation that marks the PWS-IC could also be erased during reprogramming, making it difficult to generate an iPSC model of AS (14). In this regard, aberrant DNA methylation at the imprinted H19 and KCNQOT1 genes in iPSCs was recently reported (15). We assessed the methylation imprint in normal, AS, and PWS iPSCs by methylation-specific PCR (16,17).…”

Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming

“…Since the aberrant silencing of the Dlk1-Dio3 cluster is not frequent in cloned mice produced by nuclear transfer, the oocyte cytoplasm may contain a factor that protects the DMRs of this cluster from de novo DNA methylation. Clone-specific variations in the stability of mono-allelic expression of the imprinted genes were also reported in human iPS cells, but in this case various genes were affected (for example, H19 and KCNQ1OT1) [72].…”