Update on the role and therapeutic potential of polycomb repressive complexes in (biliary tract) cancer

Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification

Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.

Polycomb group proteins in cancer: multifaceted functions and strategies for modulation

Polycomb repressive complexes (PRCs) are a heterogenous collection of dozens, if not hundreds, of protein complexes composed of various combinations of subunits. PRCs are transcriptional repressors important for cell-type specificity during development, and as such, are commonly mis-regulated in cancer. PRCs are broadly characterized as PRC1 with histone ubiquitin ligase activity, or PRC2 with histone methyltransferase activity; however, the mechanism by which individual PRCs, particularly the highly diverse set of PRC1s, alter gene expression has not always been clear. Here we review the current understanding of how PRCs act, both individually and together, to establish and maintain gene repression, the biochemical contribution of individual PRC subunits, the mis-regulation of PRC function in different cancers, and the current strategies for modulating PRC activity. Increased mechanistic understanding of PRC function, as well as cancer-specific roles for individual PRC subunits, will uncover better targets and strategies for cancer therapies.