Gene expression signatures for colorectal cancer microsatellite status and HNPCC

Abstract

The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary nonpolyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI is correlated to prognosis and response to chemotherapy. Gene expression signatures as predictive markers are being developed for many cancers, and the identification of a signature for MMR deficiency would be of interest both clinically and biologically. To address this issue, we profiled the gene expression of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated the robustness of the signature by transferring it to a real-time RT-PCR platform. Using this platform, the signature was validated on an independent test set consisting of 47 tumours (10 MSI, 37 MSS), of which 45 were correctly classified. In a second step, we constructed a signature capable of separating MMR-deficient tumours into sporadic MSI and HNPCC cases, and validated this by a mathematical crossvalidation approach. The demonstration that this two-step classification approach can identify MSI as well as HNPCC cases merits further gene expression studies to identify prognostic signatures.

Mutations in the Circadian Gene CLOCK in Colorectal Cancer

“…The microarray data have been described previously (15). Briefly, 33 fresh-frozen MSI colorectal tumors and 15 normal mucosa samples were analyzed using standard Affymetrix protocols.…”

“…Gene expression was assessed using HG-U133A GeneChip oligonucleotide microarrays (Affymetrix; ref. 15). Mononucleotide repeats within the coding region of the genes that were underexpressed in MSI CRCs were searched by using public human genome databases (Ensembl and National Center for Biotechnology Information).…”

Dysregulation of the transcription factors SOX4, CBFB and SMARCC1 correlates with outcome of colorectal cancer

“…The samples were organised into two data sets. The first data set termed 'HG_U133A' is a subset of a previously published set of transcription profiles (Kruhoffer et al, 2005) and consisted of 10 adjacent normal mucosa and 80 colon cancer samples, comprising 53 stage II and 27 stage III cancers with a median age at diagnosis of 68.5 years (range 36 -87 years). The MSS/MSI status was known for 76 of the 80 cancers (25 MSI and 51 MSS).…”

“…The Human Genome U133A GeneChip array-based transcription profiles used in this study is a subset of a previously published set of transcription profiles (Kruhoffer et al, 2005). GC-content corrected robust multiarray analysis (GC-RMA) normalisation of the U133 plus 2.0 arrays and iterPLIER normalisation of the Exon 1.0 ST arrays were performed using the software packages ArrayAssist (Stratagene, La Jolla, CA, USA) and Expression Console v1.1 (Affymetrix), respectively.…”

“…The mechanism responsible for MSI is known to be a failure of the DNA mismatch repair system. Recently, whole-genome transcriptional profiling studies have shown that there are profound transcriptional differences between MSS and MSI cancers (Giacomini et al, 2005;Kruhoffer et al, 2005). However, the causal mechanisms for these differences remain unclear.…”