The aims of this study were to determine if miRNA profiles could enhance prediction of pharmacological response compared to mutation alone. miRNAs are readily detectable in serum and plasma thus could be used in combination with mutations in liquid biopsies to support patient selection.

Unsupervised hierarchical clustering of a 50 cell line panel global miRNA profile revealed a subset of miRNAs with a striking reciprocal expression pattern. Expression of miR-192+ve (3 miRs), miR-125b+ve (3miRs) and miR-200-ve (3miRs) defined 3 main cell sub-types which were further divided into 5 subtypes by expression of miR31+ve.

Significantly, the miRNA sub-types are closely related to the five mRNA subtypes we had previously identified using iNMF (Schlicker et al, 2012) and to the subtypes identified in clinical CRC samples by Sadanandam et al 2013, Loboda et al, 2012 and Oh et al 2012. The miR192+ve subtype is an epithelial sub-type (iNMF sub-type 2 / Oh A-type) which has a gene expression pattern found in cells with transit amplifying phenotype, whereas the miR200 negative sub-type relates to the mesenchymal iNMF sub-type 1.1 and has a gene expression pattern similar to that found in CRC stem-like cells. Expression of miR125b is found in the stem-like subtype but also in mesenchymal sub-types with gene expression related to an inflammatory phenotype (iNMF sub-type 1.2, Oh B).

Analysis of differentially expressed genes between the sub-types revealed the miR-192+ve positive sub-type was discriminated from the miR-125b+ve by higher expression of several genes specifically associated with intestinal differentiation including HNF1a (TCF1) (3-fold) and HNF4a (TCF14) (13-fold) which drive expression of miR192 and CDX1 (71-fold), HNF4G (6-fold) ISX (12-fold), and IHH (24-fold).

TCGA clinical samples were also classified by the four mRNA methods and miRNAs differentially expressed between the sub-types analysed; all of the miRNAs identified in cell lines were statistically significantly differentially expressed in TCGA sub-types, however, there were additional miRNAs which clearly correlate with sub-types in clinical samples that have very low expression in cells.

Importantly, the miR-192+ve sub-type exhibited significantly greater sensitivity to EGFR TKIs, cetuximab and MEK targeted agents compared to the miR-200-ve and miR-125b+ve sub-types.

Taken together, the miR data enables segregation by differentiation status, this data enhances prediction of drug activity compared to mutation data alone and is of significance because miR expression and differentiation status are modulated by prior chemotherapy regimes.

Citation Format: Christine M. Chresta, Andreas Schlicker, Garry Beran, Georgia Cerillo, Lodewyk F. A. Wessels, George Orphanides. Reciprocal expression of miR-125b and miR-192/miR-200 families define clinically relevant sub-types of colorectal cancer with differential sensitivity to EGFR and MEK targeted agents. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5559. doi:10.1158/1538-7445.AM2014-5559