Key tumor suppressor genes inactivated by “greater promoter” methylation and somatic mutations in head and neck cancer

Abstract

Tumor suppressor genes (TSGs) are commonly inactivated by somatic mutation and/or promoter methylation; yet, recent high-throughput genomic studies have not identified key TSGs inactivated by both mechanisms. We pursued an integrated molecular analysis based on methylation binding domain sequencing (MBD-seq), 450K Methylation arrays, whole exome sequencing, and whole genome gene expression arrays in primary head and neck squamous cell carcinoma (HNSCC) tumors and matched uvulopalatopharyngoplasty tissue samples (UPPPs). We uncovered 186 downregulated genes harboring cancer specific promoter methylation including PAX1 and PAX5 and we identified 10 key tumor suppressor genes (GABRB3, HOXC12, PARP15, SLCO4C1, CDKN2A, PAX1, PIK3AP1, HOXC6, PLCB1, and ZIC4) inactivated by both promoter methylation and/or somatic mutation. Among the novel tumor suppressor genes discovered with dual mechanisms of inactivation, we found a high frequency of genomic and epigenomic alterations in the PAX gene family of transcription factors, which selectively impact canonical NOTCH and TP53 pathways to determine cell fate, cell survival, and genome maintenance. Our results highlight the importance of assessing TSGs at the genomic and epigenomic level to identify key pathways in HNSCC, deregulated by simultaneous promoter methylation and somatic mutations.

HOXA9 is Underexpressed in Cervical Cancer Cells and its Restoration Decreases Proliferation, Migration and Expression of Epithelial-to-Mesenchymal Transition Genes

“…Regarding the HOXC cluster, we observed reduced expression of HOXC12 and -C13 in the CC-derived cell line HeLa. HOXC12 was recently proposed as a tumor suppressor gene downregulated by methylation in head and neck SCC (Guerrero-Preston et al, 2014). HOXC13 regulates the expression of keratins, and abnormal expression of this gene has been observed in malignant pilomatricoma (Jave-Suarez et al, 2002;Cribier et al, 2006); in SCC, expression of HOXC13 is augmented and modulated by histone methylation (Marcinkiewicz and Gudas, 2014b;Marcinkiewicz and Gudas, 2014a).…”

De novo DNA methylation by DNA methyltransferase 3a controls early effector CD8 + T-cell fate decisions following activation

“…1F). Meanwhile, the endogenous host CD8 + gp [33][34][35][36][37][38][39][40][41] -specific T cells in recipient DNMT3a KO mice showed the consistent increase in the CD127 + KLRG1 − memory precursor cells and decrease in the CD127 − KLRG1 + terminal effector cell population seen in the absence of WT P14 adoptive transfer (Fig. 1F).…”

“…1E). Conversely, when WT P14 TCR-Tg cells (specific to LCMV gp [33][34][35][36][37][38][39][40][41] ) were transferred into a WT or DNTM3a KO host, the P14 effector/memory precursor balance developed normally (Fig. 1F).…”

“…LCMV-infected WT and DNMT3a KO mice were assessed for their CD8 + T-cell memory response 60 d after infection. Indeed, DNMT3a KO mice had increased numbers of gp [33][34][35][36][37][38][39][40][41] -specific CD8 + T cells compared with WT mice as assessed by tetramer staining ( Fig. 2A) and cytokine secretion (Fig.…”

“…Mice were infected with virus and immunodominant CD8 + T-cell responses were assessed by MHC I viral epitope-tetramer staining: H-2K b -restricted Ova 257-264 , H-2D b -restricted influenza nucleoprotein [366][367][368][369][370][371][372][373][374] , and H-2D brestricted LCMV gp [33][34][35][36][37][38][39][40][41] . At the peak of the CD8 + T-cell response to each type of infection (VacOva = day 7, influenza and LCMV = day 10), no significant differences in the absolute numbers of CD8 + -tetramer + cells were noted between WT and DNMT3a KO mice ( Fig.…”