A survey of human cancer-germline genes: Linking X chromosome localization, DNA methylation and sex-biased expression in early embryos

Human cancer-germline (CG) genes are a group of testis-specific genes that become aberrantly activated in various tumors. Ongoing studies aim to understand their functions in order to evaluate their potential as anti-cancer therapeutic targets. Evidence suggests the existence of subcategories of CG genes, depending on location on autosomal or sex chromosomes, reliance on DNA methylation for transcriptional regulation, and profile of expression during gametogenesis and early embryogenesis. To clarify this issue, we developed CTexploreR, a R/Bioconductor package that integrates an up-to-date reference list of human CG genes (n = 146) with multiple bulk and single-cell methylomic and transcriptomic datasets. Based on promoter methylation profiles and responsiveness to a DNA methylation inhibitor, 74% of the CG genes were classified as DNA methylation dependent (Methdep). Intriguingly, most X-linked CG genes (69/70) fell into this category, thereby implicating DNA methylation dependency in the well-documented over-representation of testis-specific genes on the X chromosome. We further observed that, whereas X-linked Methdep CG genes become demethylated and activated in pre-spermatogonia in the fetal testis, most of them resist DNA demethylation in female germ cells and remain therefore silent in fetal and adult oocytes. Importantly, a number of X-linked Methdep CG genes (e.g., FMR1NB, GAGE2A, MAGEB2/C2, PAGE2, VCX3A/B) maintained this maternal-specific imprinting after fertilization, and were expressed exclusively in female preimplantation embryos, which inherit a paternal X chromosome. Together, our study using the CTexploreR package has allowed us to show that X-linked CG genes undergo transient maternal imprinting and contribute therefore to transcriptional sexual dimorphism in early embryos.