External Validation of Consensus Molecular Subtyping of Colorectal Adenocarcinoma

Abstract

Background: Colorectal cancer (CRC) is the second most diagnosed cancer in New Zealand, and New Zealand has amongst the highest rates per capita of CRC in the world. CRC is a highly heterogeneous disease with varying clinical outcomes, morphology and treatment response. Various molecular classifications have been previously described with varying degrees of success in prognostication and predicting response to treatment, but none has been successful in establishing tailored treatments based on molecular profiling. In 2015, a large international consortium published a new classification system based on gene expression data. While this classification system shows considerable promise in subtyping CRC, it has yet to be adopted widely. We aim to validate this Consensus Molecular Subtype (CMS) classification system using CRC stored within the Cancer Society Tissue Bank (CSTB).

Method: More than 300 snap-frozen tumour tissue samples were available from the CSTB between 2002 to 2012. RNA was extracted from 20 milligram of tumour samples and sequenced using the Illumina HiSeq platform. Raw sequence reads were checked and mapped to human reference genome. Gene expression were quantified based on the number of reads mapped to particular gene loci. Gene Expression profiles from each patient was used as input data to the publicly available CRC subtype classifier from the Colorectal Cancer Subtyping Consortium (CRCSC) and subclassified into four individual subtypes. The clinicopathological, treatment, outcome and 5-year follow-up data were collected retrospectively from patient notes.

Results: Of the 306 patients, 19.3% were CMS1, 45.4% were CMS2, 13.1% were CMS3 and 5.2% were CMS4. 17% of CRCs were not classifiable. CMS1 tumours were mainly right-sided, node-negative, poorly-differentiated. CMS2 tumours were predominantly left-sided tumours found in male patients and were mainly Microsatellite stable (MSS). CMS4 tumours were mainly found in younger patients with left sided tumours and present at an advanced stage. The five-year survival rates for patients with CMS1, CMS2, CMS3 and CMS4 tumours were 74.6%, 71.2%, 67.5% and 43.8% respectively (P=0.03). There was no significant difference in the chemo-response rate between the four subtypes. When subtyping of hepatic metastasis was looked at 50% had incongruent classification. 75% of these patients received neoadjuvant therapy prior to hepatic resection (P = 0.02).

Conclusion: The CMS classification is reproducible on a large scale and showed distinct clinical and histological features within each subtype. Further clinical studies are required to assess responsiveness of each subtype to adjuvant therapy and targeted therapy and the subtype congruency in distant metastasis.