Transforming Pluripotency: An Exon-Level Study of Malignancy-Specific Transcripts in Human Embryonal Carcinoma and Embryonic Stem Cells

Abstract

To circumvent difficulties of isolating pure populations of cancer stem cells (CSCs) for the purpose of identifying malignancy-specific gene expression, we have compared exon-resolution transcriptomic profiles of 5 embryonal carcinoma (EC) cell lines, a histological subtype of germ cell tumor (GCT), to their nonmalignant caricature, specifically 6 human embryonic stem (ES) cell lines. Both cell types are readily accessible, and were purified for undifferentiated cells only. We identified a set of 28 differentially expressed genes, many of which had cancer and stemness roles. Overexpression of the recently discovered pluripotency gene NR5A2 in malignant EC cells revealed an intriguing indication of how WNT-mediated dysregulation of pluripotency is involved with malignancy. Expression of these 28 genes was further explored within 2 publically available data sets of primary EC tumors and normal testis. At the exon-level, alternative splicing events were detected in ZNF195, DNMT3B, and PMF1, and alternative promoters were detected for ASH2L and ETV5. These events were validated by reverse transcriptase-polymerase chain reaction-based methods in EC and ES lines, where the alternative splicing event in the de novo DNA methyltransferase DNMT3B may have functional consequences. In conclusion, we have identified malignancy-specific gene expression differences within a rigorous pluripotent stem cell context. These findings are of particular interest for both GCT and ES cell biology, and, in general, to the concept of CSCs.

An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines

“…The assumption that SOX2 binds similar genomic loci in both hECCs and hESCs was based on the evidence supporting a phenotypic similarity between these cell types and further supported by functional studies which show that SOX2 has highly comparable roles in the maintenance and differentiation of these cell lines [23, 76]. Some differences do exist between hECC and hESCs on the genetic and transcriptomic level, but current research accepts that this is limited to the expression and alternative splicing of only a relatively small number of genes [77]. …”

“…ECCs have been previously used as a model to study cancer stemness, ESCs and embryonic development [37, 38, 40, 42, 77, 92]. As CSCs of embryonal carcinoma and teratocarcinoma, they have been subjects of cancer stemness studies, while their phenotypical similarities with ESCs have kept ECCs interesting to researchers who study embryonic development and ESC biology.…”

“…As CSCs of embryonal carcinoma and teratocarcinoma, they have been subjects of cancer stemness studies, while their phenotypical similarities with ESCs have kept ECCs interesting to researchers who study embryonic development and ESC biology. Recently, these fields have converged in research which utilises ECCs as a model to investigate ESC and iPSC tumourgenicity and cancer cells expressing embryonic biomarkers [42, 77, 93]. …”

An oncofetal and developmental perspective on testicular germ cell cancer

“…1B). Gene expression analysis of CIS and SE also showed overlapping expression patterns related to early embryogenesis and fetal germ cells [13,20,[79][80][81][82][83][84][85][86][87][88]. Despite their common origin, significant differences in gene expression were observed between the histological subtypes of invasive TGCC [14,82,85,[89][90][91].…”

Aza-deoxycytidine induces apoptosis or differentiation via DNMT3B and targets embryonal carcinoma cells but not their differentiated derivatives

“…The molecular similarity between CIS and gonocytes is further supported by low levels of DNA methylation and histone H3 lysine 9 dimethylation in CIS, which are consistent with low levels of those epigenetic marks in PGCs (Almstrup et al , 2010). An activation of embryonic programme similar to embryonic stem (ES) cells in CIS might lead to the development of teratocarcinoma stem cells (Almstrup et al , 2004; Skotheim et al , 2005; Kristensen et al , 2008; Alagaratnam et al , 2012). …”