Carcinogenesis vol.27 no.3 pp.392–404, 2006 doi:10.1093/carcin/bgi237 Advance Access publication October 11, 2005 Oligonucleotide microarray analysis of distinct gene expression patterns in colorectal cancer tissues harboring BRAF and K-ras mutations Il-Jin Kim1,y, Hio Chung Kang1,2,y, Sang-Geun Jang1, Introduction Kun Kim1, Sun-A Ahn1, Hyun-Ju Yoon1, Sang Nam Yoon3 and Jae-Gahb Park1,2,3,Ã Colorectal cancer (CRC) is an important human cancer, and incidence rates of this cancer are increasing in Asian countries 1 Korean Hereditary Tumor Registry, Cancer Research Institute and such as Korea (1). CRC development is a multi-step process Downloaded from https://academic.oup.com/carcin/article/27/3/392/2476120 by guest on 27 September 2021 Cancer Research Center, Seoul National University, Seoul, Korea, (2) involving microsatellite instability (MSI), mutations in 2Research Institute and Hospital, National Cancer Center, 809 Madu-dong, Ilsan-gu, Goyang, Gyeonggi 411-764, Korea mismatch repair (MMR) of genes such as MLH1 and MSH2, and 3Department of Surgery, Seoul National University College of and mutations in APC, SMAD4,K-ras, TP53 and b-catenin Medicine, Seoul, Korea (2–9). Somatic BRAF mutations have been reported in ÃTo whom correspondence should be addressed. 5.1–18% of CRCs (10–12). BRAF is one of three serine/ E-mail: [email protected] threonine kinases (ARAF, BRAF, CRAF/RAF1) that act within Various types of human cancers harbor BRAF somatic the RAS–RAF–MEK–ERK–MAPK signaling pathway (13). mutations, leading researchers to seek molecular targets BRAF mutations have also been reported in 80% of primary for BRAF inhibitors. A mutually exclusive relationship melanomas (10), 68% of metastatic melanomas (14) and has been observed between the BRAF-V600E mutation 14–33% of ovarian carcinomas (10,15). Interestingly, a mutu- and K-ras mutations, suggesting that the BRAF-V600E ally exclusive relationship between the BRAF-V600E muta- mutation may differ from the other BRAF mutant types. tion and K-ras mutations has been found in most human Here, we used microarray analysis to examine differences cancers (10,12,16). In CRCs, BRAF-V600E mutations between the BRAF and K-ras mutant colorectal samples appeared to be associated with MMR deficiency and were and within the BRAF group (V600E versus non-V600E), not found in samples with K-ras mutations (12). This suggests in the hope that the identified gene sets could form the that the BRAF-V600E and K-ras mutations may have equival- basis for new target development. Eleven colorectal can- ent effects on tumorigenesis (12). However, other studies have cers (CRCs) with BRAF mutations and nine with K-ras shown that BRAF mutations were associated with MLH1 mutations were examined by high-density microarray promoter methylation but not MMR deficiency (17–19). analysis. We also tested whether other significant genetic Moreover, BRAF mutations were not found in MMR-deficient or clinical status involved in CRC development, such as hereditary non-polyposis colorectal cancer (HNPCC) samples APC and TP53 mutations, MSI and TNM-Duke’s staging, (18,19) but were found in sporadic CRCs, suggesting that were related with the observed BRAF-orK-ras associated BRAF may be involved in the carcinogenesis of non- expression profiles. Unsupervised two-way hierarchical inheritable CRCs (18,19). This is unexpected because it was clustering and multidimensional scaling revealed that believed that MMR-deficient phenotypes were associated with the differentially expressed genes clustered according to both sporadic and hereditary CRCs (18). Thus, researchers the mutation status of BRAF and K-ras, and that postulated that HNPCC patients could be screened for BRAF samples with the BRAF-V600E and non-V600E mutants mutations prior to MMR gene screening, as a weed-out tech- could be distinguished from each other by gene profiling. nique (18). Finally, BRAF mutations have been closely correl- Examination of TNM–Duke’s staging, MSI and mutations ated with methylator phenotypes in several genes including in APC and TP53 revealed that these significant muta- MLH1 (20), and BRAF mutations have been associated with tions could not account for the hierarchical clustering longer disease-free survival and a shorter duration of response results observed in our study. We herein identified to treatment was reported (21). Collectively, these observa- distinct gene expression patterns and gene sets that may tions seem to indicate that BRAF mutations could be used as form the basis for identification of BRAF-targeting therapeutic markers (18,20,21) and/or could be molecularly molecules or provide researchers with a better understand- targeted for development of new anticancer strategies. ing of the molecular pathogenesis underlying RAS–RAF A good example for molecularly targeted anti-cancer drug is signaling. imatinib (formerly STI-571), which inhibits the BCR–ABL kinase in chronic myeloid leukemia and KIT in gastrointestinal stromal tumors (GIST) (22). In fact, several candidate molecu- lar BRAF inhibitors have entered clinical trials (23,24). However, the V600E BRAF mutation clearly differs from the non-V600E BRAF mutations (10) in that V600E is independ- Abbreviations: CRC, colorectal cancer; GIST, gastrointestinal stromal ent of Ras signaling and elevates basal kinase activity without tumors; HNPCC, hereditary non-polyposis colorectal cancer; LOOCV, leave-one-out cross validation; MDS, multidimensional scaling; MMP1, K-ras mutations (10), while the non-V600E BRAF mutations matrix metalloproteinase 1; MMR, mismatch repair; MSI, microsatellite are Ras-dependent and are not mutually exclusive with K-ras instability; PAM, prediction analysis of microarrays; ROC, receiver operating mutations (10). As the V600E mutation accounts for 80% of characteristic; SPRED2, sprouty-related, EVH1 domain containing 2. all BRAF mutations (10), it would seem logical to search for yThese authors contributed equally to this work. V600E-specific molecular inhibitors. Carcinogenesis vol.27 no.3 # Oxford University Press 2005; all rights reserved. 392 Microarray analysis of CRCs with BRAF and K-ras mutations Microarray analysis is commonly used to screen genome- samples were run on an ABI 3100 sequencer (Applied Biosystems), and the wide gene expression profiles in human diseases, including Genescan software (Genotyper 2.1, ABI, Foster City, CA) was used to calcu- cancers (25–27). This technique can also be used to identify late the size of each fluorescent PCR product for MSI determination (38). new cancer subgroups (class discovery), to classify samples Sample hybridization using oligonucleotide microarrays into known cancer subgroups (class prediction) (28) and to The microarray experiments were performed according to our previous experi- predict the prognosis or therapeutic responsiveness of cancer mental protocol (39) with the addition of 10% DMSO (dimethyl sulfoxide) to patients (29,30). A previous microarray study revealed distinct the hybridization mixture. Briefly, the extracted total RNA was quantified by spectrophotometer (Beckman Coulter, Fullerton, CA), checked by 1% agarose gene expression patterns in BRCA1/2 mutant tissues sampled gel electrophoresis and then purified with an RNeasy kit (Qiagen, Valencia, from hereditary ovarian/breast cancer patients versus the non- CA). An aliquot of 40 ml of purified RNA was ethanol-precipitated with 3 M mutant group (BRCAx) (31,32). In CRCs, microarray analysis sodium acetate (pH 5.2), 1 ml of glycogen (5 mg/ml) and 100 ml of 100% was used to divide samples into two groups based on the ice-cold ethanol, and 20 mg of purified RNA was used to synthesize double- existence of MSI, which is an important marker in CRC (33). strand cDNAs using SuperScript II reverse transcriptase (Life Technologies, Rockville, MD) and an HPLC-purified T7-(dT)24 primer (Metabion, Germany). Recently, BRAF mutant melanoma samples were distinguished The synthesized double-strand cDNA was purified with a Qiagen DNA puri- from BRAF wild-type samples by supervised microarray ana- fication kit (Qiagen) and ethanol-precipitated with 1 ml of glycogen, 20 ml Downloaded from https://academic.oup.com/carcin/article/27/3/392/2476120 by guest on 27 September 2021 lysis (34), suggesting that gene expression profiling according of 7.5 M of ammonium acetate, and 100 ml of 100% ethanol. Biotinylated to BRAF status might be useful for the identification of cRNA was synthesized from the double-stranded cDNA using the GeneChip Expression 30-Amplification Reagents (Affymetrix), and then purified and molecular markers involved in RAS–RAS–MEK–ERK– fragmented. The fragmented cRNA was quantified, and 10 mg of cRNA was MAPK signaling. However, no previous work has used hybridized to the oligonucleotide microarray, which was subsequently washed microarray analysis to investigate the molecular differences and stained with streptavidin-phycoerythrin. Scanning was performed with an among samples with BRAF-V600E and non-V600E mutations, Affymetrix Scanner (Affymetrix). and K-ras mutations. Microarray data analysis Here, we examined whether microarray analysis was The scanned GeneChip data were analyzed with the GCOS 1.1 (GeneChip capable of distinguishing colorectal samples according to Operating Software, Affymetrix) and DMT 3.0 (Data Mining Tool, Affymet- BRAF and K-ras mutation status. Once these divisions were rix) programs. All genes present on the GeneChip were globally normalized established, we tested whether other significant genetic and adjusted to a user-specific target signal value (500). The Universal Human Reference RNA (Stratagene) sample was also hybridized to the microarray, changes involved in CRC development, such as APC and and its values served as the base line (control) for calculating the signal log TP53 mutations, MSI and TNM-Duke’s staging, were related ratios in the 20 CRC samples. After normalization, the present calls (P-calls) with the observed BRAF-orK-ras-associated expression generated by the DMT software were calculated for each gene in the 20 profiles. samples. Probes without a P-call from any of 20 samples were excluded from the analysis and 16 332 probes were left.