Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals 5 Distinct Subtypes of Colorectal Adenocarcinomas

Abstract

Background & Aims Colorectal cancer is an epigenetically heterogeneous disease, however, the extent and spectrum of the CpG island methylator phenotype (CIMP) is not clear. Methods Genome-scale methylation and transcript expression were measured by DNA Methylation and RNA expression microarray in 216 unselected colorectal cancers, and findings were validated using The Cancer Genome Atlas 450K and RNA sequencing data. Mutations in epigenetic regulators were assessed using CIMP-subtyped Cancer Genome Atlas exomes. Results CIMP-high cancers dichotomized into CIMP-H1 and CIMP-H2 based on methylation profile. KRAS mutation was associated significantly with CIMP-H2 cancers, but not CIMP-H1 cancers. Congruent with increasing methylation, there was a stepwise increase in patient age from 62 years in the CIMP-negative subgroup to 75 years in the CIMP-H1 subgroup ( P < .0001). CIMP-H1 predominantly comprised consensus molecular subtype 1 cancers (70%) whereas consensus molecular subtype 3 was over-represented in the CIMP-H2 subgroup (55%). Polycomb Repressive Complex-2 (PRC2)-marked loci were subjected to significant gene body methylation in CIMP cancers ( P < 1.6 × 10 -78 ). We identified oncogenes susceptible to gene body methylation and Wnt pathway antagonists resistant to gene body methylation. CIMP cluster–specific mutations were observed in chromatin remodeling genes, such as in the SWItch/Sucrose Non-Fermentable and Chromodomain Helicase DNA-Binding gene families. Conclusions There are 5 clinically and molecularly distinct subgroups of colorectal cancer. We show a striking association between CIMP and age, sex, and tumor location, and identify a role for gene body methylation in the progression of serrated neoplasia. These data support our recent findings that CIMP is uncommon in young patients and that BRAF mutant polyps in young patients may have limited potential for malignant progression.

APCMutation marks an aggressive subtype ofBRAFmutant colorectal cancers

“…This fits with the aggressive phenotype of these cancers. An alternative hypothesis, supported an age at diagnosis that is similar to conventional pathway cancers 18 and the morphology of our murine adenomas, is that polyps are initiated by APC, acquire a BRAF mutation. If this is the case such lesions must progress extremely rapidly to cancer as they are very rarely identified in large series of conventional adenomas.…”

“…DNA was isolated from whole blood using the salt precipitation method as previously reported 17 . Cancer samples were snap-frozen in liquid nitrogen and DNA extracted using the AllPrep DNA/RNA/Protein mini kit (QIAGEN, Germany) as previously reported 18 . Exome-sequencing libraries were generated using the Agilent SureSelect Human All Exon V4+UTR capture platform (Agilent, CA, USA).…”

<p>Curcumin Modifies Epithelial–Mesenchymal Transition in Colorectal Cancer Through Regulation of miR-200c/EPM5</p>

“…4 Epithelial-mesenchymal transition (EMT) has been considered as a key metastatic step, which is associated with poor prognosis in CRC. 5,6 EMT is a complex process including the dissolution of cell-cell junction and loss of apicobasolateral polarity, which resulted in the formation of migratory mesenchymal cells with invasive properties. 7,8 The decrease of E-cadherin expression and increase of VIM is generally accepted as a hallmark of the EMT process regulated by various transcriptional factors, such as ZEB1, ZEB2, TWIST, SLUG and SNAIL.…”

“…[9][10][11] In addition to these EMT transcriptional factors (EMT-TFs), recent evidence showed that microRNAs (miRNAs) are also critical for EMT regulation. 6,8 For instance, miRNAs from the miR-200 family repress EMT by directly targeting and downregulating ZEB1/ZEB1/ SNAIL/SLUG via miR-200-binding sites located within their 3′UTRs, resulting in enhanced E-cadherin expression and inhibition of cancer cell migration and motility. [12][13][14] On the contrary, theses EMT-TFs bind directly to the common promoter regions of the miR-200c family and cause transcriptional repression.…”

Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes

“…The CRC Subtyping Consortium introduced four consensus molecular subtypes (CMS1-4) for CRC, based on gene expression profiles of tumors. Recently, a study by Lochlan et al[53] investigated genome-scale DNA methylation in a large cohort of CRC patients and revealed five distinct CRC subtypes of colorectal adenocarcinomas with different therapeutic biomarkers for CRC treatment. This highlights the need for a better and more inclusive subtype classification approach to enable biomarker discovery and thus inform drug development for CRC.…”