Analytical Validation of Multiplex Biomarker Assay to Stratify Colorectal Cancer into Molecular Subtypes

Ragulan, Chanthirika; Eason, Katherine; Fontana, Elisa; Nyamundanda, Gift; Tarazona, Noelia; Patil, Yatish; Poudel, Pawan; Lawlor, Rita T.; Rio, Maguy Del; Koo, Si-Lin; Tan, Wei; Sclafani, Francesco; Begum, Ruwaida; Mendes, Larissa Sena Teixeira; Martineau, Pierre; Scarpa, Aldo; Cervantes, Andrés; Tan, Iain Beehuat; Cunningham, David; Sadanandam, Anguraj

doi:10.1038/s41598-019-43492-0

Cited by 37 publications

(34 citation statements)

References 24 publications

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“…CRCassigner partitions tumors into the Inflammatory, Enterocyte, TA, Goblet-like and Stem-like subtypes. Because this system has received significant further development 34 , we studied the ability to represent CRCassigner subtypes with ColoType scores and subtypes, beginning in Cohort A training set. www.nature.com/scientificreports/ Using the published PAM algorithm ("Methods"), we computed the CRCassigner subtypes for Cohort A and compared these classifications with ColoType subtypes in the Cohort A training set ( Supplementary Table S3).…”

Section: Prediction Of Colotype Scores and Subtype For A Single New Smentioning

confidence: 99%

ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing

Buechler

Stephens

Hummon

et al. 2020

Sci Rep

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colorectal cancer (cRc) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for cMS subtyping. in this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1-4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, colotype was also implemented with targeted RnA-sequencing (illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNAsequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, colotype by targeted RnA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology. Colorectal cancer (CRC) is the fourth most common cancer in the U.S. and the second leading cause of cancer deaths. Attempts to reduce CRC deaths have been complicated by the molecular heterogeneity of the disease leading to differential responses to therapies. Over the past decade, numerous gene expression-based subtype systems were developed to better characterize CRC 1-6. To resolve potential disparities between these systems, the Colorectal Cancer Subtyping Consortium (CRCSC) published the consensus molecular subtypes (CMS), which partitioned CRC tumors into CMS1, CMS2, CMS3, CMS4 and a small set of unclassified tumors 7. Since publication of the CMS subtypes, numerous studies have explored how patients in different subtypes exhibit differential sensitivities to commonly used drugs 8-15 , contributing evidence to the clinical utility of CMS. Progress towards clinical application of the CMS subtypes has been limited by the complexity of the CMS subtyping method. CRCSC created the CMSclassifier computer application for CMS subtyping using expression of hundreds of genes from whole-genome data 7. The CMScaller application also uses whole-genome

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Section: Prediction Of Colotype Scores and Subtype For A Single New Smentioning

confidence: 99%

ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing

Buechler

Stephens

Hummon

et al. 2020

Sci Rep

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“…On CMS classification, 14%, 20%, 12% and 22% of patients in our cohort were classified, respectively, into CMS1, CMS2, CMS3 and CMS4, in line with previous reports. 11 However, subtyping was undetermined in 32% of our samples using the 'predicted CMS' classification, probably due to limited quality of samples or intratumoural heterogeneity. 18 Moreover, we have previously reported intratumoural heterogeneity associated with transcriptional subtype of CRCA classification representing the presence of more than one subtype within a sample.…”

Section: Discussionmentioning

confidence: 86%

“…[8][9][10] Our study aims at integrating novel biological factors into a multimodal approach to improve on our ability to pinpoint the risk of relapse. These include molecular alterations at multiple omic levels, such as plasma ctDNA, CDX2 staining, inflammation-associated cytokines and the Colorectal Cancer Assigner (CRCA) classification according to a novel validated assay, 11 as well as CMS classification using a new assay method. 12…”

Section: Key Questionsmentioning

confidence: 99%

Detection of postoperative plasma circulating tumour DNA and lack of CDX2 expression as markers of recurrence in patients with localised colon cancer

et al. 2020

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BackgroundColon cancer (CC) is a heterogeneous disease. Novel prognostic factors beyond pathological staging are required to accurately identify patients at higher risk of relapse. Integrating these new biological factors, such as plasma circulating tumour DNA (ctDNA), CDX2 staining, inflammation-associated cytokines and transcriptomic consensus molecular subtypes (CMS) classification, into a multimodal approach may improve our accuracy in determining risk of recurrence.MethodsOne hundred and fifty patients consecutively diagnosed with localised CC were prospectively enrolled in our study. ctDNA was tracked to detect minimal residual disease by droplet digital PCR. CDX2 expression was analysed by immunostaining. Plasma levels of cytokines potentially involved in disease progression were measured using ELISAs. A 96 custom gene panel for nCounter assay was used to classify CC into colorectal cancer assigner and CMS.ResultsMost patients were classified into CMS4 (37%) and CMS2 (28%), followed by CMS1 (20%) and CMS3 (15%) groups. CDX2-negative tumours were enriched in CMS1 and CMS4 subtypes. In univariable analysis, prognosis was influenced by primary tumour location, stage, vascular and perineural invasion together with high interleukin-6 plasma levels at baseline, tumours belonging to CMS 1 vs CMS2 +CMS3, ctDNA presence in plasma and CDX2 loss. However, only positive ctDNA in plasma samples (HR 13.64; p=0.002) and lack of CDX2 expression (HR 23.12; p=0.001) were found to be independent prognostic factors for disease-free survival in the multivariable model.ConclusionsctDNA detection after surgery and lack of CDX2 expression identified patients at very high risk of recurrence in localised CC.

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“…The NanoString platform uses short probes (35–50 nucleotides) to capture and quantify mRNA sequences and is therefore more compatible with fragmented RNA. Three recent studies have built customised NanoString probe sets and successfully classified panels of FFPE material according to CMS 75 , 87 , 131 . CMS classification between patient-matched FFPE and fresh frozen material was concordant, although sample size was limited 75 , 87 .…”

Section: Translation Of Cms To the Clinicmentioning

confidence: 99%

Exploring and modelling colon cancer inter-tumour heterogeneity: opportunities and challenges

2020

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Colon cancer inter-tumour heterogeneity is installed on multiple levels, ranging from (epi)genetic driver events to signalling pathway rewiring reflected by differential gene expression patterns. Although the existence of heterogeneity in colon cancer has been recognised for a longer period of time, it is sparingly incorporated as a determining factor in current clinical practice. Here we describe how unsupervised gene expression-based classification efforts, amongst which the consensus molecular subtypes (CMS), can stratify patients in biological subgroups associated with distinct disease outcome and responses to therapy. We will discuss what is needed to extend these subtyping efforts to the clinic and we will argue that preclinical models recapitulate CMS subtypes and can be of vital use to increase our understanding of treatment response and resistance and to discover novel targets for therapy.

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Analytical Validation of Multiplex Biomarker Assay to Stratify Colorectal Cancer into Molecular Subtypes

Cited by 37 publications

References 24 publications

ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing

ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing

Detection of postoperative plasma circulating tumour DNA and lack of CDX2 expression as markers of recurrence in patients with localised colon cancer

Exploring and modelling colon cancer inter-tumour heterogeneity: opportunities and challenges

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