Assessment of the Changes in Mitochondrial Gene Polymorphism in Ulcerative Colitis and the Etiology of Ulcerative Colitis-associated Colorectal Cancer

BACKGROUND

Mitochondria are energy-producing organelles, and dysfunction in these organelles causes various types of disease. Although several studies have identified mutations in nuclear DNA that are associated with the etiology of ulcerative colitis (UC), information regarding mitochondrial DNA (mtDNA) in UC is limited. This study aimed to investigate the mitochondrial DNA polymorphism underlying the etiology of UC and UC-associated colorectal cancer.

MATERIALS AND METHODS

Next-generation sequencing was performed to assess mitochondrial DNA mutations in 12 patients with UC-associated cancer. The mtDNA mutations in the non-neoplastic mucosa, tumor tissues, and healthy controls were compared.

RESULTS

The incidence of mutations of nicotinamide adenine dinucleotide phosphate ubiquinone oxidase subunit, ATP synthetase, and tRNA was higher in non-neoplastic mucosa in those with UC compared with the healthy controls. However, no statistically significant differences were observed in mutations between the tumor tissues and non-neoplastic mucosa in UC.

CONCLUSION

Significant mutations in mtDNA were observed in the non-neoplastic mucosa of patients with UC-associated cancer.

CD44/CD133-Positive Colorectal Cancer Stem Cells are Sensitive to Trifluridine Exposure

Cancer stem cells (CSCs) are involved in metastatic colorectal cancer recurrence, but no effective therapy targeting these cells is currently available. Because trifluridine (FTD)/tipiracil therapy is used for refractory colorectal cancer, we sought to determine whether FTD is effective against CSC-like cells. CD44⁺CD133⁺ high-expressing and other populations of human DLD-1 colon cancer cells were separately isolated through fluorescence-activated cell sorting. The sphere-forming activity of each population and the anti-sphere-forming effects of FTD and fluorouracil (5-FU) on CD44⁺CD133⁺ cells were then measured. CD44⁺CD133⁺ DLD-1 cells formed substantially more spheres than other cells. Moreover, treating CD44⁺CD133⁺ DLD-1 cells with subtoxic concentrations of FTD (1 µM) inhibited sphere formation, and this was superior to the effect of subtoxic concentrations (1 µM) of 5-FU. The associated inhibition rates for FTD and 5-FU were 58.2% and 26.1%, respectively. Further, CD44⁺CD133⁺ DLD-1 cells expressed higher levels of thymidine kinase 1, which is responsible for FTD phosphorylation, than DLD-1 cells, and FTD was incorporated into the DNA of CD44⁺CD133⁺ DLD-1 cells. Thus, our data show that FTD treatment is effective against CSC-like cells and might be applied as CSC-targeting chemotherapy for tumor subtypes with high CD44 and CD133 expression.

ChIP-seq Analysis to Explore DNA Replication Profile in Trifluridine-treated Human Colorectal Cancer Cells In Vitro

BACKGROUND/AIM

Trifluridine (FTD) is a key component of the novel oral antitumor drug trifluridine/tipiracil that has been approved for the treatment of metastatic colorectal cancer. In this study, a comprehensive analysis of DNA replication profile in FTD-treated colon cancer cells was performed.

MATERIALS AND METHODS

HCT-116 cells were exposed to BrdU or FTD and subjected to DNA immunoprecipitation. Immunoprecipitated DNA was sequenced; the density of aligned reads along the genome was calculated. Peak finding, gene ontology, and motif analysis were performed using MACS, GREAT, and MEME, respectively.

RESULTS

We identified 6,043 and 5,080 high-confidence FTD and BrdU peaks in HCT-116 cells, respectively. Of 6,043 FTD peaks, 2,911 peaks were uncommon to BrdU. We observed that FTD was preferentially incorporated into genomic regions containing simple repeats, CpG islands, and gene bodies. Conserved motifs in FTD peaks contained dinucleotide repeats such as (GT)n.

CONCLUSION

Global FTD incorporation patterns delineated FTD, preferentially incorporating loci in cancer cells.

Abstract 2067: Trifluridine/tipiracil can overcome the resistance of gastric 5-fluorouracil-refractory cancer cells with various cancer driver-genes alterations in vitro and in vivo

Background: Trifluridine (FTD) is a key component of the antitumor drug combination trifluridine/tipiracil (FTD/TPI, also known as TAS-102), which is approved for the treatment of patients with metastatic colorectal cancer refractory to standard chemotherapies. Recently, a global phase III Trial (TAGS trial) revealed that FTD/TPI also prolongs overall survival in patients with metastatic gastric cancer. In this study, we explored the efficacy of FTD/TPI in 5-fluorouracil (5-FU)-resistant gastric cancer cell lines in vitro and in vivo, revealing their unique genomic signatures by a multi-omics profiling approach.

Method: 5-FU-resistant cell lines were established by continuously exposing the parent cell lines (MKN45, MKN74, and KATOIII) to escalating concentrations of 5-FU over a 1-year period. The sensitivities of the cell lines to FTD were evaluated by a cell growth inhibitory assay using crystal violet staining. Total RNA was purified using a silica membrane spin column-based centrifugation procedure. The extracted RNA was used to establish a cDNA library for transcriptome sequencing using a HiSeq 2500 platform. The resulting fastq files were used for mapping, gene mutation, and expression analysis. We especially focused on “pyrimidine metabolism” in Kyoto Encyclopedia of Genes and Genomes analysis.

Results: The KATOIII/5FU, MKN74/5FU, and MKN45/5FU were 2.4-fold, 4.7-fold, and 14.3-fold more resistant to 5-FU than their parent cell lines, respectively. MKN74/5FU and KATOIII/5FU did not show any cross-resistance to FTD, while TS-overexpressing MKN45/5FU showed partial cross-resistance to FTD in vitro. FTD/TPI exhibited significant antitumor activity in both MKN45/5FU and MKN74/5FU cells in vivo. As compared with corresponding parental cell lines, the transcriptome analysis revealed that ENTPD3 gene expression level changed by more than 2-fold in only MKN45/5FU, while ENTPD8 and ENPP3 gene expression changed by less than 0.5-fold in both MKN74/5FU and KATOIII/5FU. In addition, there are genes (UMPS, POLR2B, POLR2D, POLR2H, POLR2L, POLR2J2, POLR3G, PRIM1, POLE, and UPP1) that had non-synonymous mutation within their coding sequences. Interestingly, mutation status of POLR2L and PRIM1 in MKN45/5FU, of UMPS, POLR2D, and POLR2H in MKN74/5FU, of POLR2B, POLR2J2, and POLR3G in KATOIII/5FU differed from those of parental cell lines.

Conclusions: FTD/TPI was effective against 5-FU-resistant gastric cancer cells harboring various genetic alterations in vitro and in vivo. This might be a reason why FTD/TPI is expected to show significant benefits against heterogeneous metastatic gastric cancer in a clinical setting.

Citation Format: Kazuaki Matsuoka, Takashi Kobunai, Teiji Takechi. Trifluridine/tipiracil can overcome the resistance of gastric 5-fluorouracil-refractory cancer cells with various cancer driver-genes alterations in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2067.

Abstract 2886: ChIP-seq analysis to explore DNA replication profile in trifluridine-treated human colorectal cancer cells in vitro

Background: Trifluridine (FTD) is a key component of the novel oral antitumor drug trifluridine/tipiracil, which was approved for the treatment of patients with metastatic colorectal cancer refractory to standard chemotherapies. FTD, an antineoplastic thymidine analogue, is efficiently incorporated into the genomic DNA of tumor cells. However, the molecular mechanisms underlying its cytotoxic effects remain unclear. Therefore, the DNA replication profile in FTD-treated cells was comprehensively analyzed to explore the mode of FTD incorporation into the genomic DNA. Method: We generated the DNA replication profile in HCT-116 human colorectal cancer cells as follows: asynchronous cultures of HCT-116 were exposed to 5 μM 5-bromo-2′-deoxyuridine (BrdU), a non-cytotoxic control drug or FTD, for 4 h, harvested, and subjected to DNA immunoprecipitation using an anti-BrdU antibody. An input and immunoprecipitated DNA from each experiment were sequenced, and the sequence reads generated using Illumina sequencing were aligned uniquely to the human genome (hg19), allowing up to two mismatches using the BWA algorithm with default settings. The density of aligned reads along the genome was calculated and stored in a bigWig file for visualization in genome browsers. Peak finding and gene ontology analysis were performed using MACS and Genomic Regions Enrichment of Annotations Tool (GREAT). The 60-bp sequences surrounding the summits of the top 1000 peaks were analyzed for conserved motifs using the online program MEME. Results: In an antibody validation step, we observed significant FTD peaks over input DNA. We identified 6043 and 5080 high confident FTD and BrdU peaks in HCT-116 cells, respectively. Interestingly, 2911 of 6043 FTD peaks were uncommon to BrdU peaks, while 3232 peaks were common in FTD and BrdU. The FTD and BrdU peaks were not randomly distributed throughout the genome. Most FTD and BrdU peaks were ±5 kb or further away from transcription start sites. We identified the genes associated with distant peaks of FTD using GREAT. FTD peaks occurred near genes involved in extracellular matrix structural composition such as ACAN, BGN, CHAD, and COL12A1, while BrdU peaks were near genes involved in cysteine-type endopeptidase inhibitor activity such as ARRB1, BIRC7, LCN1, and CST1. Dinucleotide repeats such as TGTGTG were observed as conserved motifs in FTD-peak sequences. Conclusion: Global FTD incorporation patterns can delineate active replication loci, namely FTD preferentially incorporating loci, in human cancer cells. The DNA replication profile in FTD-treated cells differed from that in BrdU-treated cells. Thus, differences in the incorporation patterns of FTD and BrdU into the genomic DNA revealed the mechanisms of antitumor activities of FTD.

Citation Format: Takashi Kobunai, Kazuaki Matsuoka, Teiji Takechi. ChIP-seq analysis to explore DNA replication profile in trifluridine-treated human colorectal cancer cells in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2886.

Thymidine Kinase 1 Loss Confers Trifluridine Resistance without Affecting 5-Fluorouracil Metabolism and Cytotoxicity

Acquired resistance to therapeutic drugs is a serious problem for patients with cancer receiving systemic treatment. Experimentally, drug resistance is established in cell lines in vitro by repeated, continuous exposure to escalating concentrations of the drug; however, the precise mechanism underlying the acquired resistance is not always known. Here, it is demonstrated that the human colorectal cancer cell line DLD1 with acquired resistance to trifluridine (FTD), a key component of the novel, orally administered nucleoside analogue-type chemotherapeutic drug trifluridine/tipiracil, lacks functional thymidine kinase 1 (TK1) expression because of one nonsense mutation in the coding exon. Targeted disruption of the TK1 gene also conferred severe FTD resistance, indicating that the loss of TK1 protein expression is the primary cause of FTD resistance. Both FTD-resistant DLD1 cells and DLD1-TK1 ^-/- cells exhibited similar 5-fluorouracil (5-FU) sensitivity to that of the parental DLD1 line. The quantity of cellular pyrimidine nucleotides in these cells and the kinetics of thymidylate synthase ternary complex formation in 5-FU-treated cells is similar to DLD1 cells, indicating that 5-FU metabolism and cytotoxicity were unaffected. The current data provide molecular-based evidence that acquired resistance to FTD does not confer 5-FU resistance, implying that 5-FU-based chemotherapy would be effective even in tumors that become refractory to FTD during trifluridine/tipiracil treatment. Mol Cancer Res; 16(10); 1483-90. ©2018 AACR.

Colitic Cancer Develops Through Mutational Alteration Distinct from that in Sporadic Colorectal Cancer: A Comparative Analysis of Mutational Rates at Each Step

BACKGROUND

Patients with ulcerative colitis (UC) are at risk of UC-associated colorectal cancer (CRC); however, little is known about genetic alterations occurring during UC carcinogenesis. We examined mutational changes in patients with colitic cancer and the features that differed between the carcinogenesis of UC and sporadic CRC.

MATERIAL AND METHODS

Specimens were obtained from the non-neoplastic mucosa and cancer cells of 12 patients with colitic cancer. The mutational rate of oncogenes in colitic cancer was analyzed and compared to that of oncogenes in sporadic CRC.

RESULTS

We observed a lower mutation rate in adenomatous polyposis coli (APC) (16.7%(2/12) vs. 75.9%(161/212), respectively, p=0.0001) and KRAS (16.7%(2/12) vs. 42% (89/212), respectively, p=0.04) in colitic cancer than in sporadic CRC. With respect to cadherin 1 (CDH1) and fibroblast growth factor receptor 2 (FGFR2), the mutational rates for non-neoplastic colorectal mucosa were similar to those in sporadic CRC.

CONCLUSION

We demonstrated that mutational rates for APC and KRAS differ between colitic cancer and sporadic CRC. Furthermore, we revealed that CDH1 and FGFR2 become mutated at an earlier stage in colitic carcinogenesis than in sporadic CRC.

Increased Copy Number Variation of mtDNA in an Array-based Digital PCR Assay Predicts Ulcerative Colitis-associated Colorectal Cancer

AIM

Mitochondrial dysfunction plays a central role in carcinogenesis in numerous cancer-related diseases. We examined the copy number variation of mitochondrial DNA (mtDNA) and the expression of energy-producing genes in relation to ulcerative colitis (UC)-associated carcinogenesis.

MATERIALS AND METHODS

We studied 17 patients with UC-associated adenocarcinoma (UC-Ca) and 16 without UC-associated adenocarcinoma (UC-nonCa). The copy number of mtDNA in non-dysplastic mucosa in both groups was quantified by an array-based digital polymerase chain reaction (PCR) assay. Simultaneously, gene expression related to mitochondrial energy metabolism was determined by a PCR array.

RESULTS

We observed a higher copy number of mtDNA in non-dysplastic mucosa in the UC-Ca group compared to the UC-nonCa group (484.2 vs. 747.7 copies/cell, p=0.022). The sensitivity, specificity, positive predictive value, and negative predictive value for the detection of UC-associated adenocarcinoma by mtDNA copy number were 43.8%, 100%, 100%, and 60.9%, respectively. We observed an increased expression of mitochondrial genes related to energy metabolism together with an increased copy number of mtDNA.

CONCLUSION

Mitochondrial function and its metabolic process play essential roles in UC carcinogenesis and are possible risk markers for the development of colitic cancer.

Trifluridine/tipiracil overcomes the resistance of human gastric 5-fluorouracil-refractory cells with high thymidylate synthase expression

Trifluridine/tipiracil (FTD/TPI or TFTD, also known as TAS-102) is a combination of the antineoplastic thymidine analog, FTD, and thymidine phosphorylase inhibitor, TPI (molar ratio 1:0.5). FTD/TPI was approved in Japan, the United States, and the European Union for the treatment of unresectable advanced or recurrent colorectal cancer. We evaluated the in vitro and in vivo efficacy and mechanisms of action of FTD and FTD/TPI against 5-fluorouracil (5-FU)-resistant MKN45/5FU, MKN74/5FU, and KATOIII/5FU human gastric cancer cells overexpressing thymidylate synthase (TS) and their respective parent cell lines. MKN45/5FU and KATOIII/5FU cells were not cross-resistant to FTD, whereas MKN45/5FU cells were 3.7-fold more resistant than the parental cells in vitro. FTD was also incorporated into genomic DNA in a concentration-dependent manner in 5-FU-resistant and parental cells. Additionally, deoxyuridine monophosphate levels in MKN45/5FU cells after 24-h FTD treatment were 3.0-fold higher than those in parental cells, and FTD treatment for 72 h induced G2/M arrest in MKN45/5FU cells, unlike the S phase arrest in MKN45 cells. Thus, TS-overexpressing MKN45/5FU cells, but not MKN74/5FU and KATOIII/5FU cells, showed partial cross-resistance to FTD. However, FTD/TPI (administered orally twice a day) exhibited antitumor activity to the same extent in MKN45 and MKN45/5FU xenograft mouse models, overcoming in vitro cross-resistance to FTD. DNA incorporation rather than TS inhibition seems to be the main action of FTD under these in vivo conditions. Thus, FTD/TPI is a promising chemotherapeutic agent against gastric cancers recurring following 5-FU therapy.

Synergistic anticancer activity of a novel oral chemotherapeutic agent containing trifluridine and tipiracil in combination with anti-PD-1 blockade in microsatellite stable-type murine colorectal cancer cells

Trifluridine/tipiracil (FTD/TPI) is a combination of FTD, an antineoplastic thymidine-based nucleoside analog, and TPI, which acts to enhance the bioavailability of FTD in vivo. It is used to treat patients with unresectable advanced or recurrent colorectal cancer that is refractory to standard therapies. We investigated the anticancer activity of FTD/TPI combined with anti-mouse programed cell death 1 (PD-1) monoclonal antibody (mAb) against CMT-93 cells, which are microsatellite stable (MSS)-type murine colorectal cancer cells. Tumor growth inhibition (TGI) after treatment with anti-mouse PD-1 mAb monotherapy (0.1 mg, i.p., days 1, 5, 9) and FTD/TPI monotherapy (150 mg/kg/day, p.o., days 1-14) were 86.7% and 52.7%, respectively, and that of the combination was 98.4%. The TGI of the combination therapy was significantly greater than that of each monotherapy (P<0.05). The combination therapy caused complete tumor regression in four out of five mice without body-weight reduction, but neither of the monotherapies resulted in complete tumor regression. Low dose FTD/TPI (75 and 100 mg/kg) combined with anti-mouse PD-1 mAb also showed significant antitumor activity against CMT-93 tumors. Flow cytometric analysis revealed that a higher CD8⁺ T cell ratio among total lymphocytes and a lower regulatory T cells (Tregs) ratio in CD4⁺ T cells in the combination group compared with that in the control group. These results suggested that the combination therapy induced a cytotoxic response from infiltrated cytotoxic CD8⁺ T cells and reduced immunosuppressive activity as indicated by decreased Tregs. In this study, the combination therapy was found to have synergistically greater antitumor activity against CMT-93 cells. These preclinical findings indicated that FTD/TPI and anti-mouse PD-1 mAb combination therapy may be a promising treatment option, even for MSS-type colorectal cancer.

Abstract 1071: Efficacy of trifluridine/tipiracil + anti-mouse PD-1 antibody combination on mouse colorectal cancer model and related tumor immunomodulatory effects

Background: Trifluridine/tipiracil (FTD/TPI) is an oral nucleoside antitumor agent that is composed of trifluridine and tipiracil hydrochloride at a molecular ratio of 1:0.5. Checkpoint-blockade immunotherapies are particularly effective in patients with tumor T cell infiltrations. In this study, the antitumor effects of FTD/TPI + anti-mouse PD-1 antibody combination were studied in a syngeneic mouse model and the tumor-infiltrating lymphocyte (TIL) subsets were evaluated. Method: The mouse colorectal cancer cell line CMT-93 was subcutaneously implanted into C57BL/6 mice. Vehicle (0.5% Hydroxypropyl methylcellulose, 10 mL/kg, p.o.), FTD/TPI (75, 100, and 150 mg/kg/day, twice daily, days 1-14, p.o.), anti-mouse PD-1 antibody (clone RMP1-14; 0.1 mg/body; once daily, days 1, 5, and 9; i.p.), and FTD/TPI + anti-mouse PD-1 antibody combination were administered, and inhibitory activity was evaluated according to tumor-volume changes. Single-cell suspensions were prepared from collected tumors. Based on cell marker expression, CD4+ T cells, CD8+T cells, and regulatory T cells (Tregs) were identified using antibodies against CD4, CD8, CD25, and Foxp3, and subsets of TILs were evaluated by flow cytometry. Results: Both anti-mouse PD-1 antibody and FTD/TPI monotherapies were effective in vivo. Tumor-growth inhibition by anti-mouse PD-1 antibody was 81.7% at 0.1 mg/kg/day and that by FTD/TPI was 33.4%, 46.1%, and 59.5% at 75, 100, and 150 mg/kg/day, respectively. FTD/TPI + anti-mouse PD-1 antibody combination using FTD/TPI (75, 100, and 150 mg/kg/day) with anti-mouse PD-1 antibody (0.1 mg/kg/day) inhibited tumor growth at significantly higher rates (P &lt; 0.05; 91.8%, 95.7%, 98.4%, respectively) than monotherapy. Remarkably, the 150-mg/kg/day FTD/TPI + 0.1-mg/kg/day anti-mouse PD-1 antibody combination caused complete tumor regression in four/five mice without body-weight reduction or drug-related deaths; however, none of the monotherapies caused complete tumor regression. Flow cytometric analysis revealed a higher CD8+ T cell percentage among total lymphocytes and a lower Treg percentage in CD4+ T cells after combination therapy compared with the controls. Conclusion: FTD/TPI + anti-mouse PD-1 antibody combination was synergistically effective on CMT-93 mouse colon tumor. This combination increased CD8+ T cell percentages in whole lymphocyte and decreased Treg percentages in CD4+ T cell. This suggests that FTD/TPI + anti-mouse PD-1 antibody combination modulates tumor T cell populations and improves their antitumor activity.

Citation Format: Norihiko Suzuki, Hiroshi Tsukihara, Fumio Nakagawa, Takashi Kobunai, Teiji Takechi. Efficacy of trifluridine/tipiracil + anti-mouse PD-1 antibody combination on mouse colorectal cancer model and related tumor immunomodulatory effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1071. doi:10.1158/1538-7445.AM2017-1071

MicroRNA profiles involved in trifluridine resistance

Trifluridine (FTD) is a key component of the novel oral antitumor drug trifluridine/tipiracil, which is approved for the treatment of patients with metastatic colorectal cancer refractory to standard chemotherapies. A microRNA analysis of three colorectal cell lines was conducted to investigate causes of FTD resistance. Drug resistant sublines of DLD-1, HCT-116, and RKO cells were developed by continuous administration of increasing doses of FTD for 5 months. The let-7d-5p gene, which maps to chromosome 9q22.32, was downregulated in the FTD-resistant DLD-1 sublines. DLD-1 cells became more resistant to FTD when let-7d-5p was knocked down and more sensitive when let-7d-5p was overexpressed. The FTD-resistant sublines were not cross-resistant to 5-fluorouracil (5-FU); 5-FU sensitivity was affected only slightly when let-7d-5p as overexpressed or knocked down. These data indicate that let-7d-5p increases sensitivity of FTD but not 5-FU and that let-7d-5p is a potential clinical marker of treatment sensitivity.

Abstract 5175: Mutational and copy number profiling of cancer-related genes in 26 human tumor xenografts and their correlations with antitumor drug sensitivities

Background: Tumor responses to antitumor drugs are variable, but predicting these responses is important when selecting effective chemotherapy treatments. Our aim was to identify variations or alterations in gene copy number that influence cancer cells’ susceptibilities to standard chemotherapeutic agents. Methods: Twenty-six human cancer cell lines representing the five main tumor types were subcutaneously implanted into nude mice and tested for sensitivity to fluorinated pyrimidines (UFT, TS-1, 5’-DFUR, and capecitabine), CDDP, CPT-11, and paclitaxel. The cell lines included lung (AOI, LC-11, Lu-99, LX-1, LC-6, Lu-134, Lu-130), colon (KM12C, KM12C/FU, HCT-15, COL-1, CO-3), pancreas (PAN-3, PAN-4, PAN-12, H-48, MIAPaCa-2, BxPC-3), gastric (SC-2, ST-40, 4-1ST, SC-4) and breast (MC-2, MX-1, MDA-MB-435SHM, MDA-MD-231). Genomic DNA was prepared from frozen tumor tissues. Mutations in 48 genes from the TruSeq Amplicon Cancer Panel were screened using the MiSeq system (Illumina, San Diego, CA). Somatic copy number alterations were analyzed by high-density SNP arrays (Affymetrix, Santa Clara, CA). Results: Of the 225 amplicons (187 non-overlapping regions) in the cancer panel, 86% achieved a minimum average sequencing depth of 1000X and the average coverage across all target regions was 5374X. In 26 tumors, sequencing detected 55 somatic mutations in 18 out of 48 cancer related genes of high prognostic or therapeutic significance, such as TP53, APC, PTEN, and SMAD4. Mutation frequencies across 26 xenografts were 73.1% (TP53), 38.5% (KRAS), 15.4% (APC), 11.5% (SMAD4 and RET), 7.7% (BRAF, GNAS, and PTEN), and 3.8% (CTNNB1, GNAQ, HNF1A, HRAS, IDH1, KIT, NOTCH1, PIK3CA, SMO, and STK11). Tumor xenografts with TP53 mutations were significantly less sensitive to CDDP and CPT-11 than wild-type cell lines (P&lt;0.05). The APC mutation conferred resistance to paclitaxel. Copy number gain was observed at 23.1% (KRAS), 15.1% (EGFR), and 11.5% (JAK2 and CDK2NA). Copy number loss was observed at 30.8% (CDK2NA), 19.2% (SMAD4), and 15.4% (PTEN). Cell lines with more copies of CDK2NA and JAK2 were more sensitive to CDDP, while cell lines with fewer copies of PTEN were more sensitive to CDDP. Similarly, copy number gain of CDH1 conferred resistance to UFT, while copy number gain of KRAS sensitized tumors to 5’-DFUR. The copy number of 48 genes determined by the GeneChip array moderately agreed with those estimated by local GC-content adjusted coverage profiles in the sequencing analysis (average Pearson's correlation coefficient = 0.66, 95%CI = 0.54-0.69). Conclusions: Integrated analysis of mutational profiling and gene copy number may be useful to elucidate candidate genes influencing susceptibility of cancer cells to antitumor drugs.

Citation Format: Takashi Kobunai, Kenta Tsunekuni, Kazuaki Matsuoka, Hiroshi Tsukihara, Teiji Takechi. Mutational and copy number profiling of cancer-related genes in 26 human tumor xenografts and their correlations with antitumor drug sensitivities. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5175.

Prognostic impact of KRAS mutant type and MET amplification in metastatic and recurrent gastric cancer patients treated with first-line S-1 plus cisplatin chemotherapy

Receptor tyrosine kinase (RTK)-related genes, including HER2, EGFR, MET, FGFR2 and KRAS, are target molecules that are clinically beneficial in gastric cancer (GC). We investigated the correlation between RTK-related genes and the curative effect of first-line S-1 plus cisplatin (SP) combination chemotherapy in metastatic and recurrent GC. We enrolled 150 patients with histopathologically confirmed metastatic and recurrent GC treated with SP. KRAS mutation was detected using direct sequencing. DNA copy number was measured by real-time PCR. Formalin-fixed paraffin-embedded specimens were examined immunohistochemically for HER2, EGFR, FGFR2 and MET. Among 144 patients, KRAS mutation was detected in five (3.5%) at codon 12 and one (0.7%) at codon 13. FGFR2, EGFR, HER2, MET and KRAS gene amplification was suggested in 4.4%, 5.9%, 9%, 3.7% and 10.3% of patients, respectively. KRAS mutation, but not KRAS amplification, was associated with significantly shorter overall and progression-free survival. MET membranous overexpression was associated with a significantly higher tumor response. MET amplification was associated with significantly shorter overall survival. We show for the first time that KRAS mutation and MET amplification are promising predictive markers in metastatic and recurrent GC patients treated with SP. KRAS status may be a useful prognostic marker in patients treated with SP.

Genome-wide DNA Copy-number Analysis in ACTS-CC Trial of Adjuvant Chemotherapy for Stage III Colonic Cancer

BACKGROUND

The adjuvant chemotherapy trial of TS-1 for colon cancer phase III trial was designed to validate the non-inferiority of the oral fluoropyrimidine S-1 to uracil and tegafur/leucovorin as adjuvant chemotherapy for stage III colonic cancer. As a prospective biomarker study of this trial, DNA copy number was studied using formalin-fixed, paraffin-embedded specimens.

MATERIALS AND METHODS

FFPE blocks were obtained from 795 patients of the 1,535 patients enrolled in the study. The quality of extracted DNA was assessed using arbitrarily primed polymerase chain reaction and microfluidic analysis. Genomic copy-number alterations in cancer were analyzed by high-density single-nucleotide polymorphism arrays. Copy-number changes in Japanese patients with colonic cancer were compared with those in Western countries using data from a previously reported meta-analysis. We then compared genome-wide segment copy number and clinicopathological features of colorectal cancer.

RESULTS

Genome-wide copy number was analyzed in 161 samples and DNA copy-number alteration profiles showed frequent DNA copy-number gains at chromosome 7, 8q and 13, and losses at 4, 5q, 8p, 17p and 18q. The weighted kappa statistic from comparing copy-number alteration status with data from Western countries was 0.828 (95% confidence interval=0.786 -0.871). DNA copy-number alterations of 8,684 segments were compared with clinicopathological features in 161 patients. Location of the tumor correlated with genomic segments of chromosome 4, 5, 7, 8, 13, 14, 18 and 20. Differentiation of the tumor correlated with segments in chromosome 4, 6, 8, 11, 13, 14,15, 16, 17 and 20.

CONCLUSION

Somatic copy-number alteration profiles of stage III colonic cancer in the Japanese ACTS-CC trial closely agreed with the results of previous Western studies. Location and differentiation of the tumor correlated with DNA copy-number alterations. Our findings will facilitate understanding the characteristics of colonic cancer. Further investigation may contribute to the exploration of valid biomarkers.

Novel 5-fluorouracil-resistant human esophageal squamous cell carcinoma cells with dihydropyrimidine dehydrogenase overexpression

5-Fluorouracil (5-FU) is a key drug for the treatment of esophageal squamous cell carcinoma (ESCC); however, resistance to it remains a critical limitation to its clinical use. To clarify the mechanisms of 5-FU resistance of ESCC, we originally established 5-FU-resistant ESCC cells, TE-5R, by step-wise treatment with continuously increasing concentrations of 5-FU. The half maximal inhibitory concentration of 5-FU showed that TE-5R cells were 15.6-fold more resistant to 5-FU in comparison with parental TE-5 cells. TE-5R cells showed regional copy number amplification of chromosome 1p including the DPYD gene, as well as high mRNA and protein expressions of dihydropyrimidine dehydrogenase (DPD), an enzyme involved in 5-FU degradation. 5-FU treatment resulted in a significant decrease of the intracellular 5-FU concentration and increase of the concentration of α-fluoro-ureidopropionic acid (FUPA), a metabolite of 5-FU, in TE-5R compared with TE-5 cells in vitro. Conversely, gimeracil, a DPD inhibitor, markedly increased the intracellular 5-FU concentration, decreased the intracellular FUPA concentration, and attenuated 5-FU resistance of TE-5R cells. These results indicate that 5-FU resistance of TE-5R cells is due to the rapid degradation of 5-FU by DPD overexpression. The investigation of 5-FU-resistant ESCC with DPYD gene copy number amplification and consequent DPD overexpression may generate novel biological evidence to explore strategies against ESCC with 5-FU resistance.

Abstract 1981: Drug-tolerant gastric cancer cell subpopulation enriched by 5-fluorouracil acquires malignant phenotype

Background: Post-operative adjuvant chemotherapy for gastric cancer is a treatment for suppressing the growth of invisible cancer cells, but substantial numbers of patients experience recurrence despite of this therapy. We attempted to clarify the mechanism of cancer relapse after chemotherapy using 5-FU tolerant human gastric cancer cell line, MKN45.

Methods: Through a stepwise dose escalation of 5-fluorouracil (5-FU) for one year, a 5-FU-tolerant cell subpopulation, MKN45T, was established from a human gastric cancer cell line, MKN45. Nucleotide variation was screened with a panel of 46 cancer-associated genes, and western blot analyses were performed to examine whether known proteins were involved in the acquisition of the drug-tolerant phenotype. For molecular profiling, cancer cell subpopulations emerging as colonies in the presence of anticancer drugs including 5-FU, cisplatin, and docetaxel, “reverse-phase” protein arrays (RPPAs) were produced with the drug-tolerant 480 colonies. Subcutaneous or orthotopic xenografts of MKN45 and MKN45T to immunodeficient mice were performed to examine tumorigenicity.

Results: Western blot analysis revealed that most of protein expression levels were not visibly different between MKN45 and MKN45T, except that p53 showed slight reduction in MKN45T. Analysis of 46 cancer-associated genes revealed that all gene variations were identical in both MKN45 and MKN45T, suggesting that gene mutations had a limited effect on the acquisition of the drug-tolerant phenotype. RPPA analysis revealed that colonies from MKN45T exhibited a protein level increase in a 5-FU concentration-dependent manner in Atg5, Atg7, and PI3K, suggesting a functional association between drug-tolerance and autophagy/glucose metabolism. An orthotopic xenograft to the stomach demonstrated tumors in the stomach (9 out of 9, 100%), and lymph node and liver metastases only in MKN45T at a high frequency (6 out of 9, 67%). No difference in tumorigenicity was observed when MKN45 and MKN45T were transplanted subcutaneously. The orthotopic xenograft of MKN45T followed by administration of 5-FU (30mg/kg/day) for five post-xenograft days suppressed metastasis in 4 out of 5 mice (80%) at 42 post-xenograft days, indicating that chemotherapy is particularly effective if it is performed before initiating tumor formation.

Conclusion: Chemotherapy does not only reduce tumor size, but may also be selecting for tumors that are resistant to the chemotherapy. Our clinical experiences are well-explained by this observation, as relapse after chemotherapy is often chemotherapy resistant.

Citation Format: Kaoru Ishida, Satoshi S. Nishizuka, Kohei Kume, Mamoru Nukatsuka, Kei Sato, Fumitaka Endo, Hirokatsu Katagiri, Takashi Kobunai, Teiji Takechi, Keisuke Koeda, Go Wakabayashi. Drug-tolerant gastric cancer cell subpopulation enriched by 5-fluorouracil acquires malignant phenotype. [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 1981. doi:10.1158/1538-7445.AM2014-1981

Abstract 781: Efficacy of trifluridine for 5-fluorouracil-resistant human gastric cancer cell lines and their mechanisms

Background: TAS-102 is a novel oral nucleoside antitumor agent consisting of trifluridine (FTD) and tipiracil hydrochloride (TPI). TAS-102 was found to significantly improve the overall survival of patients with metastatic colorectal cancer who were refractory to treatment with a fluoropyrimidine, irinotecan, and oxaliplatin in a double-blind randomized phase II study. Although significant survival benefits from 5-fluorouracil (5-FU)-based chemotherapy have also been reported in patients with gastric cancer, many patients experience recurrences after several courses of 5-FU-based chemotherapy. The resistance of gastric tumors to 5-FU therapy is thus a major clinical problem. In this study, the efficacy of FTD against 5-FU-resistant human gastric cancer cell lines was investigated. Method: 5-FU-resistant cell lines established by continuously exposing the parent cell lines (MKN-45, MKN-74, and KATOIII) to escalating concentrations (1-5 μM) of 5-FU over a 1-year period were used. The sensitivities of the cell lines to FTD were evaluated using a crystal violet staining assay. To elucidate the mechanism by which resistance is overcome, the mRNA levels of TK1, which converts FTD into an active monophosphate form, and hENT1, which is involved in the cellular uptake of FTD, were determined using RT-PCR. Results: The resistant cell lines KATOIII/5FU, MKN74/5FU, and MKN45/5FU exhibited a 2.0-fold, 4.8-fold, and 14.2-fold resistance to 5-FU, compared with their parent cell lines, respectively. MKN-45/5FU also showed a 3.7-fold resistance to FTD, whereas MKN-74/5FU (1.0-fold) and KATOIII/5FU (1.2-fold) showed no cross-resistance to FTD. The TK1 mRNA level was decreased by 40% in the MKN-45/5FU cells, compared with the parent cell line. Furthermore, this cell line showed a 60% decrease in the mRNA level for hENT1. In contrast, the hENT1 mRNA level increased by 1.6-fold in the KATOIII/5FU cells, with a 50% decrease in the TK1 mRNA level. The TK1 and hENT1 mRNA levels in MKN-74/5FU were increased by 1.9-fold and 1.7-fold, respectively. Conclusion: FTD was able to overcome the resistance to 5-FU in 2 out of 3 resistant cell lines in vitro, with MKN45/5FU exhibiting a partial cross-resistance to FTD. These results suggest that TAS-102 might be a promising chemotherapeutic agent for the treatment of gastric cancer relapses after 5-FU-based treatment. Furthermore, TK1 and hENT1 might be involved in FTD-related cytotoxicity.

Citation Format: Kazuaki Matsuoka, Takashi Kobunai, Teiji Takechi. Efficacy of trifluridine for 5-fluorouracil-resistant human gastric cancer cell lines and their mechanisms. [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 781. doi:10.1158/1538-7445.AM2014-781

Abstract 4688: Landscape of DNA copy number alterations of stage III colon cancer in the ACTS-CC trial (TRICC0706), a phase III trial of adjuvant chemotherapy with S-1 and UFT/LV in Japan: A comparison with Western data

Background: The ACTS-CC trial is a phase III study of 1535 patients, designed to validate the noninferiority of S-1 to UFT/LV as adjuvant chemotherapy for stage III colon cancer. A genome-wide analysis of DNA copy number alterations was performed prospectively to identify predictive biomarkers and prognostic biomarkers. To accurately compare results between Japanese and Western clinical trials, it is important to investigate biological differences between Japanese and Western patients.

Purpose: To elucidate DNA copy number alteration profiles of stage III colon cancer in Japan as compared with those in Western countries.

Methods: Genomic DNA was extracted from 779 formalin-fixed, paraffin-embedded specimens. After quality assessment by arbitrary primed PCR, 162 samples were analyzed by high-density single-nucleotide polymorphism arrays (Affymetrix Human 250K StyI) according to the manufacturer's protocol. Copy number alterations in colon cancer in our study, estimated using a circular binary segmentation model, were compared with those of publically available data for colorectal or various other cancers in Western countries. First, concordance of the copy number gain or loss of each cytogenetic band with meta-analysis data reported by Diep et al. (Genes Chromosomes Cancer, 2006) was assessed by weighted kappa statistics. Next, copy number alterations of 43 focused cancer-related genes (APC, BRCA1, DCC, EGFR, FGFR2, MET, hMSH2, TP53, PTEN, etc.) were compared with those of 19 cancer subtypes (3131 cancer specimens) as reported by Beroukhim et al. (Nature, 2010)

Results: Changes occurring in at least 15% of cases were losses of 4, 5q, 8p, 15q, 17p, and 18q and gains of 7, 8q, 13, and 20. Loss of 18q was seen in 80% of samples. Over 700 colon cancer data in Western countries retrieved from a meta-analysis were compared with our results according to each cytogenetic position (total 193 cytogenetic bands). Weighted kappa statistics, 0.83, indicated that the copy number profiles agreed closely between Japan and Western countries. Moreover, the strongest correlations of copy number profiles for 43 focused genes were seen between our results and colorectal cancers in Western countries, among various cancer subtypes.

Conclusions: This is a preplanned analysis; eventually, clinical outcomes will be combined with biomarker analysis. Somatic copy number alteration profiles of stage III colon cancer in the ACTS-CC trial in Japan closely agreed with the results of previous Western studies.

Our findings will facilitate understanding the characteristics of colon cancer in Japan and extrapolation of the results of Japanese phase III trials to Western countries.

Citation Format: Toshiaki Ishikawa, Hiroyuki Uetake, Takashi Kobunai, Megumi Ishiguro, Shigeyuki Matsui, Kenichi Sugihara, ACTS-CC Trial Study Group. Landscape of DNA copy number alterations of stage III colon cancer in the ACTS-CC trial (TRICC0706), a phase III trial of adjuvant chemotherapy with S-1 and UFT/LV in Japan: A comparison with Western data. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4688. doi:10.1158/1538-7445.AM2013-4688

Abstract 990: Efficacy of various chemotherapeutic agents on 5-FU-resistant human gastric cancer cell lines and their mechanisms

Purpose: Four 5-fluorouracil (5-FU)-resistant human gastric cancer cell lines were established by the long-term exposure of parent cell lines (MKN45, MKN-74, KATO-III, and NCI-N87) to 5-FU. The cytotoxicity and mechanisms of several chemotherapeutic agents were then investigated using 5-FU-resistant gastric cancer cell lines.

Method: 5-FU-resistant cell lines were established by continuous exposure to escalating concentrations (1-5 μM) of 5-FU over a 1-year period. The sensitivities of the cell lines to chemotherapeutic agents (paclitaxel, docetaxel, cisplatin, oxaliplatin, epirubicin, and SN-38) were then evaluated using the WST-8 colorimetric assay. To elucidate the mechanisms of resistance, the gene expressions and copy numbers were measured using an Agilent Technologies whole human genome oligo DNA microarray and a CGH microarray. The protein and mRNA expressions of a target enzyme of 5-FU, thymidylate synthase (TS), were also investigated using western blotting and RT-PCR, respectively.

Results: The IC50 ratios of the 5-FU-resistant cell lines were 2.6 to 15.6 times higher than those of the parent cell lines in vitro. MKN-45/5-FU showed cross-resistance to cisplatin and oxaliplatin and KATO-III/5-FU showed cross-resistance to SN-38, while MKN-74/5-FU showed collateral sensitivities to docetaxel, cisplatin, and oxaliplatin, and NCI-N87/5-FU showed collateral sensitivities to cisplatin, oxaliplatin, SN-38, and epirubicin. RT-PCR showed that TS mRNA expression was higher in the parent cell lines than in the 5-FU-resistant cell lines, and the TS protein expression level was also higher in all the resistant cell lines. For MKN-45/5-FU and KATO-III/5-FU, not only the mRNA expression level but also the TS gene copy number was increased. Interestingly, the expression of MAP3K15, which is an apoptosis-facilitating factor, increased in NCI-N87/5-FU, which showed collateral sensitivity to cisplatin, oxaliplatin, SN-38, and epirubicin.

Conclusion: Analyzing the molecular mechanisms of 5-FU-resistant cell lines may be useful for the development of effective chemotherapy regimens for relapsed gastric cancer after 5-FU-based chemotherapy.

Citation Format: Mamoru Nukatsuka, Takashi Kobunai, Ayako Nakamura, Kazuhiko Hayashi, Teiji Takechi. Efficacy of various chemotherapeutic agents on 5-FU-resistant human gastric cancer cell lines and their mechanisms. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 990. doi:10.1158/1538-7445.AM2013-990

Abstract 991: Integrated analysis of gene expression, DNA copy number, and CpG island methylation of 5-fluorouracil-resistant human gastric cancer cell lines

Background: A major problem in chemotherapy is treatment failure due to anticancer drug resistance. A better understanding of mechanisms underlying acquired resistance may facilitate the development of an optimal second-line therapy for recurrent cancer. This study was designed to elucidate mechanisms underlying acquisition of 5-fluoroucacil (5-FU) resistance by human gastric cancer cells. Method: 5-FU resistant cell lines were established by continuously exposing parent cell lines (MKN45, MKN-74, KATO-III, and NCI-N87) to escalating concentrations (1-5 μM) of 5-FU over 1 year. To elucidate mechanisms of resistance, gene expression, DNA copy number, and DNA methylation were measured by Whole Human Genome 44K oligo DNA microarray, 244K CGH microarray, and 244K CpG Island Microarray (Agilent Technologies, Santa Clara, CA), respectively. Data analysis was done with GeneSpring GX™ software, version 11.0 (Agilent Technologies) and Partek genomic suite software, version 6.5 (Partek Inc., St. Louis, MO). Results: Each of the cell lines acquired high resistance to 5-FU, although the degree of resistance varied. IC50 of the 5-FU-resistant cell lines was 3.8- to 11.6-fold higher than that of the parent cell lines. On gene expression analysis, 3.0%, 2.3%, 1.4%, and 1.4% of 41,093 probes were differentially expressed with more than 5-fold changes in MKN45/FU, KATOIII/FU, NCI-N87/FU, and MKN74/FU as compared with their parental cell lines, respectively. Changes occurring in at least 3 cell lines were expressed by only 0.2% of probes. Copy number analysis revealed that DNA copy gains occurred at 16.6%, 6.7%, 5.1%, and 5.6% of all genomic segments elucidated in MKN45/FU, KATOIII/FU, NCI-N87/FU and MKN74/FU, respectively. The frequencies of DNA copy losses were 35.6%, 14.0%, 3.2%, and 8.9%, respectively. Methylation analysis revealed that the number of methylated CpG sites in NCI-N87/FU and MKN74/FU increased by 1.5 times as compared with the parental cell lines. In contrast, the numbers of methylated CpG sites in MKN45/FU and KATOIII/FU rarely changed (around 40% each). Conclusions: Mechanisms leading to acquired resistance against 5-FU differed among the 4 gastric cancer cell lines. Changes in copy number most frequently occurred in MKN45/FU cells. In NCI-N87/FU and MKN74/FU, the numbers of methylated CpG sites increased. Such genome-wide integrated analysis will facilitate an understanding of mechanisms for 5-FU acquired resistance and help to identify therapeutic target genes.

Citation Format: Takashi Kobunai, Ayako Nakamura, Mamoru Nukatsuka, Kazuhiko Hayashi, Teiji Takechi. Integrated analysis of gene expression, DNA copy number, and CpG island methylation of 5-fluorouracil-resistant human gastric cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 991. doi:10.1158/1538-7445.AM2013-991

Efficacy of combination chemotherapy using oral fluoropyrimidine S-1 with oxaliplatin (SOX) against colorectal cancer in vivo

Oxaliplatin is effective when used with 5-fluorouracil (5-FU) and leucovorin, or with capecitabine (COX) for the treatment of colorectal cancer. In this experiment, we investigated the optimal combination schedule and antitumor activity of oral S-1 with oxaliplatin combination therapy (SOX) against human colorectal cancer xenografts in vivo. Using human colon cancer COL-1-bearing nude mice, oxaliplatin was administered at a total dose of 8.3 mg/kg on day 1 alone, on day 8 alone, or in divided doses administered on days 1 and 8 with S-1 (6.9 mg/kg, days 1-14). The antitumor activity of SOX, administered according to the divided schedule was significantly superior to both monotherapies (p<0.01), and the toxicity was tolerable. However, administration on day 8 alone failed to significantly increase the antitumor activity, when compared with that of monotherapy, while administration on day 1 alone was toxic in this model. Next, the efficacy of SOX was compared with that of COX (360 mg/kg, days 1-14). The antitumor effect of SOX was significantly superior to that of COX (p<0.01), with an equivalent toxicity; moreover SOX suppressed COL-1 tumor growth for a longer period of time (2.2 times) than did COX. The antitumor activity of SOX against the 5-FU-resistant colorectal cancer cell line KM12C/5-FU was equivalent to that of COX. The evaluation of intermittent SOX administration in a clinical trial might be of critical value.

Predicting the response to preoperative radiation or chemoradiation by a microarray analysis of the gene expression profiles in rectal cancer

Preoperative radiotherapy or chemoradiotherapy (CRT) has become a standard treatment for patients with locally advanced rectal cancer. However, there is a wide spectrum of responses to preoperative CRT, ranging from none to complete. There has been intense interest in the identification of molecular biomarkers to predict the response to preoperative CRT, in order to spare potentially non-responsive patients from unnecessary treatment. However, no specific molecular biomarkers have yet been definitively proven to be predictive of the response to CRT. Instead of focusing on specific factors, microarray-based gene expression profiling technology enables the simultaneous analysis of large numbers of genes, and might therefore have immense potential for predicting the response to preoperative CRT. We herein review published studies using a microarray-based analysis to identify gene expression profiles associated with the response of rectal cancer to radiation or CRT. Although some studies have reported gene expression signatures capable of high predictive accuracy, the compositions of these signatures have differed considerably, with little gene overlap. However, considering the promising data regarding gene profiling in breast cancer, the microarray analysis could still have potential to improve the management of locally advanced rectal cancer. Increasing the number of patients analyzed for more accurate prediction and the extensive validation of predictive classifiers in prospective clinical trials are necessary before such profiling can be incorporated into future clinical practice.

Chromosomal instability (CIN) phenotype, CIN high or CIN low, predicts survival for colorectal cancer

PURPOSE

To examine whether chromosomal instability (CIN) phenotype, determined by the severity of CIN, can predict survival for stages II and III colorectal cancer (CRC).

PATIENTS AND METHODS

We determined microsatellite instability (MSI) and loss of heterozygosity (LOH) status in 1,103 patients (training [n = 845] and validation [n = 258] sets with stages II and III CRC). The LOH ratio was defined as the frequency of LOH in chromosomes 2p, 5q, 17p, and 18q. According to the LOH ratio, non-MSI high tumors were classified as CIN high (LOH ratio ≥ 33%) or CIN low (LOH ratio < 33%). CIN-high tumors were subclassified as CIN high (mild type; LOH ratio < 75%) or CIN high (severe type; LOH ratio ≥ 75%). We used microarrays to identify a gene signature that could classify the CIN phenotype and evaluated its ability to predict prognosis.

RESULTS

CIN high showed the worst survival (P < .001), whereas there was no significant difference between CIN low and MSI high. CIN high (severe type) showed poorer survival than CIN high (mild type; P < .001). Multivariate analysis revealed that CIN phenotype was an independent risk factor for disease-free and overall survival, respectively, in both the training (P < .001 and P = .0155) and validation sets (P < .001 and P = .0076). Microarray analysis also revealed that survival was significantly poorer in those with the CIN-high than in the CIN-low gene signature (P = .0203). In a validation of 290 independent CRCs (GSE14333), the CIN-high gene signature showed significantly poorer survival than the CIN-low signature (P = .0047).

CONCLUSION

The CIN phenotype is a predictive marker for survival and may be used to select high-risk patients with stages II and III CRC.

Abstract 4534: Large-scale DNA copy number analysis as a biomarker study in the ACTS-CC trial (TRICC0706), a phase III trial of adjuvant chemotherapy with S-1 and UFT/LV in stage III colon cancer in Japan

Background: The ACTS-CC trial is a phase III study designed to validate the non-inferiority of S-1 to UFT/LV, a standard treatment in Japan, as adjuvant chemotherapy for stage III colon cancer. The initial safety results were reported at ASCO 2011. In a biomarker study of the ACTS-CC trial, DNA copy number was studied using formalin fixed, paraffin-embedded (FFPE) specimens. Methods: Blocks of resected tumor specimens for this biomarker study were obtained after receiving informed consent from 779 of 1535 patients enrolled between April 2009 and January 2010. Laser-captured microdissection was performed to extract genomic DNA (gDNA) from 10-αm-thick FFPE specimens of colon cancer. DNA concentrations were measured by spectrophotometry (NanoDrop, Thermo Fisher Scientific Inc., Wilmington, DE). DNA quality was assessed and classified into 4 grades according to DNA fragment length by arbitrary primed PCR (AP-PCR) followed by microfluidic analysis (Bioanalyzer: Agilent Technology, Santa Clara, CA): grade-a, β700 bp; grade-b, &lt;700 bp and β400 bp; grade-c, &lt;400 bp and β200 bp; and grade-d, &lt;200 bp. Genomic copy-number alterations in cancer were analyzed by high-density single-nucleotide polymorphism (SNP) arrays (Human 250K StyI array, Affymetrix, Santa Clara, CA) using samples of grade-a or grade-b quality. For GeneChip arrays, 250 ng of DNA was used according to the manufacturer's protocols. Results: Initial DNA amount was sufficient for GeneChip assays in 647 of 779 samples. DNA quality assessment after AP-PCR revealed that the proportions of grade-a, grade-b, grade-c, and grade-d samples were 25.3%, 48.9%, 18.9%, and 6.9%, respectively. Samples of grade-a or grade-b DNA quality were used for target preparation. After complexity reduction by restricted enzymatic digestion followed by adaptor ligation, PCR amplification, and DNA purification, 162 of 647 purified PCR products were successfully amplified to 90 μg, sufficient for target hybridization. Throughout these stepwise processes, 162 of 779 samples were successfully analyzed by GeneChip. Somatic copy-number alterations of stage III colon cancer will be further investigated. Conclusions: Genome-wide copy number was successfully analyzed for only 21% of initial samples. However, this pre-planned study was designed to identify valid biomarkers. Not only 162 carefully selected genome-wide datasets to screen candidate loci associated with clinical outcomes, but also 617 genomic DNA samples usable as independent validation sets for real-time PCR-based assay were obtained.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4534. doi:1538-7445.AM2012-4534

Combination therapy using oral S-1 and targeted agents against human tumor xenografts in nude mice

In this study, combination therapies using the oral fluoropyrimidine tegafur-gimeracil-oteracil (S-1) with several targeted agents or antibodies, were evaluated. First, the effects of tyrosine kinase inhibitors (erlotinib hydrochloride, sorafenib tosilate and sunitinib malate) against human non-small cell lung cancer (NSCLC), breast cancer and colorectal cancer were evaluated in vivo. The effects of the combination of S-1 and targeted antibodies (bevacizumab and cetuximab) against human colorectal cancers was also evaluated in vivo. S-1 and the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, erlotinib, showed a significant inhibition of growth in human NSCLC (Lu-99 and PC-9 cell lines). The antitumor activity of the combination of S-1 and erlotinib against Lu-99 and PC-9 cancer cell lines was significantly superior to either monotherapy (P<0.05). Combination therapy using the multi-tyrosine kinase inhibitors, sorafenib or sunitinib, with S-1 against breast cancer (MX-1 cell line) and NSCLC (NCI-H460 cell line) was significantly superior to either monotherapy (P<0.01). The combination of the anti-vascular endothelial growth factor antibody bevacizumab or the anti-EGFR antibody, cetuximab, with S-1 against human colorectal cancer [Col-1, KM20C (bevacizumab) and DLD-1 (cetuximab) cell lines] and a 5-fluorouracil (5-FU)-resistant cell line (KM12C/5-FU) was significantly superior to either monotherapy (p<0.01). In particular, the growth of the Col-1 cells was completely inhibited by the combination of S-1 and bevacizumab. No toxic mortalities and no significant difference in the body weight changes of the animals treated with S-1 combined with the targeted agents or with the mono-therapies were observed; therefore, the treatments appeared to be well-tolerated. Our preclinical findings indicate that the combination therapies of S-1 and targeted agents are promising treatment options.

REG4, NEIL2, and BIRC5 gene expression correlates with gamma-radiation sensitivity in patients with rectal cancer receiving radiotherapy

AIM

The present study aimed to identify genes that influence the susceptibility of cancer cells to radiation.

MATERIALS AND METHODS

The sensitivities of eight colorectal cancer cell lines to gamma radiation were tested. Microarray data and cells with stable overexpression were used to identify candidate genes. Candidate genes correlating with radioresistance were validated with the use of 22 clinical specimens obtained before preoperative radiotherapy from patients with rectal cancer.

RESULTS

Regenerating islet-derived protein 4 (REG4) gene expression was 12-fold higher in radioresistant cells. REG4-overexpressing cells had higher survival rates and fewer DNA strand breaks after gamma irradiation. Expression of the antiapoptotic gene baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) and base excision-repair pathway gene nei endonuclease VIII-like 2 (NEIL2) in REG4-overexpressing cells, was also three to four times higher than that of the parental cell lines. REG4, BIRC5 and NEIL2 expression levels were significantly higher in non-responding patients (n=14) than in responders (n=8).

CONCLUSION

The REG4, BIRC5 and NEIL2 genes might be useful predictors of the sensitivity of cancer patients to radiotherapy.

Antitumour activity of S-1 in combination with cetuximab on human gastric cancer cell lines in vivo

This study aimed to assess the antitumour effect of a combination of cetuximab (Erbitux, a chimeric anti-epidermal growth factor receptor (EGFR) monoclonal antibody) and S-1, an oral 5-fluorouracil prodrug, on gastric cancer cell lines in vivo. Gastric cancer cell lines (SC-2 and SC-4) were transplanted subcutaneously into nude mice. In both cell lines, which have high EGFR expression and harbour K-ras wild-type alleles, treatment with a combination of cetuximab and oral S-1 resulted in significantly higher antitumour activity than treatment with cetuximab or S-1 alone. To investigate this potentiation of antitumour activity, the expression levels of thymidylate synthase (TYMS) were measured following administration of cetuximab. Cetuximab induced a decrease in expression of TYMS mRNA and protein. These findings suggest that cetuximab-mediated down-regulation of TYMS enhances the antitumour effect of S-1 and provide a rationale for designing novel combination chemotherapy regimens for patients with advanced gastric cancer.

Differential gene expression signatures between colorectal cancers with and without KRAS mutations: crosstalk between the KRAS pathway and other signalling pathways

PURPOSE

KRAS mutation is an important predictive marker in determining resistance to anti-Epidermal Growth Factor Receptor (EGFR) antibody therapies. In order to clarify whether not only KRAS related signalling pathways but also other signalling pathways are altered in patients with colorectal cancers (CRCs) with KRAS mutations, we examined the differences in the gene expression signatures between CRCs with and without KRAS mutation.

PATIENTS AND METHODS

One-hundred and thirteen patients who underwent a surgical resection of a primary CRC were examined. KRAS mutational status was determined using the Peptide Nucleic Acid (PNA)-clamp real-time polymerase chain reaction (PCR) TaqMan assay. Gene expression profiles were compared between CRCs with and without KRAS mutation using the Human Genome GeneChip array U133.

RESULTS

Among 113 CRCs, KRAS mutations were present in 35 tumours (31%). We identified 30 genes (probes) that were differentially expressed between CRCs with and without KRAS mutation (False Discovery Rate (FDR), p<0.01), by which we were able to predict the KRAS status with an accuracy of 90.3%. Thirty discriminating genes included TC21, paired-like homeodomain 1 (PITX1), Sprouty-2, dickkopf homologue 4 (DKK-4), SET and MYND domain containing 3 (SMYD3), mitogen-activated protein kinase kinase kinase 14 (MAP3K14) and c-mer Proto-oncogene tyrosine kinase (MerTK). These genes were related to not only KRAS related signalling pathway but also to other signalling pathways, such as the Wnt-signalling pathway, the NF-kappa B activation pathway and the TGF-beta signalling pathway.

CONCLUSIONS

KRAS mutant CRCs exhibited a distinct gene expression signature different from wild-type KRAS CRCs. Using human CRC samples, we were able to show that there is crosstalk between the KRAS-mediated pathway and other signalling pathways. These results are necessary to be taken into account in establishing chemotherapeutic strategies for patients with anti-EGFR-refractory KRAS mutant CRCs.

Predicting ulcerative colitis-associated colorectal cancer using reverse-transcription polymerase chain reaction analysis

BACKGROUND

Widespread genetic alterations are present not only in ulcerative colitis (UC)-associated neoplastic lesions but also in the adjacent normal colonic mucosa. This suggests that genetic changes in nonneoplastic mucosa might be effective markers for predicting the development of UC-associated cancer (UC-Ca). This study aimed to build a predictive model for the development of UC-Ca based on gene expression levels measured by reverse-transcription polymerase chain reaction (RT-PCR) analysis in nonneoplastic rectal mucosa.

PATIENTS AND METHODS

Fifty-three UC patients were examined, of which 10 had UC-Ca and 43 did not (UC-NonCa). In addition to the 40 genes and transcripts previously shown to be predictive for developing UC-Ca in our microarray studies, 149 new genes, reported to be important in carcinogenesis, were selected for low density array (LDA) analysis. The expression of a total of 189 genes was examined by RT-PCR in nonneoplastic rectal mucosa.

RESULTS

We identified 20 genes showing differential expression in UC-Ca and UC-NonCa patients, including cancer-related genes such as CYP27B1, RUNX3, SAMSN1, EDIL3, NOL3, CXCL9, ITGB2, and LYN. Using these 20 genes, we were able to build a predictive model that distinguished patients with and without UC-Ca with a high accuracy rate of 83% and a negative predictive value of 100%.

CONCLUSION

This predictive model suggests that it is possible to identify UC patients at a high risk of developing cancer. These results have important implications for improving the efficacy of surveillance by colonoscopy and suggest directions for future research into the molecular mechanisms of UC-associated cancer.

RUNX3 copy number predicts the development of UC-associated colorectal cancer

RUNX3 is a tumour suppressor gene that plays an important role in the development of various cancers. The present study aimed to compare RUNX3 mRNA expression levels and DNA copy numbers in the non-neoplastic rectal mucosa between ulcerative colitis (UC) patients with and without UC-associated colorectal cancer (UC-Ca). We further aimed to build a predictive model of the development of UC-Ca based on the RUNX3 DNA copy number. RUNX3 mRNA expression levels were quantified by RT-PCR. The hypermethylation and DNA copy number of RUNX3 were also determined. Thirty-five UC patients were examined, 17 of whom had UC-Ca (UC-Ca group) and 18 who did not (UC-NonCa group). The UC-Ca group had significantly lower mRUNX3 expression levels and smaller DNA copy numbers than the UC-NonCa group (p=0.04, p=0.0016, respectively). RUNX3 expression levels correlated with DNA copy numbers. Classification of the UC-Ca and UC-NonCa group based on DNA copy number gave an accuracy of 82.9%. RUNX3 expression levels in the non-neoplastic rectal mucosa was significantly decreased in the UC-Ca group and it is suggested that this was attributable to the decrease in RUNX3 DNA copy number. The present predictive model may be useful in the selection of high risk UC-Ca patients and to improve the efficacy of surveillance colonoscopy. The present study suggests that RUNX3 might play an important role in the development of UC-Ca.

Gene expression signature and the prediction of lymph node metastasis in colorectal cancer by DNA microarray

PURPOSE

Lymph node metastasis is an important factor in determining the outcome of colorectal cancer. If we can predict the presence of lymph node metastasis before surgery, it may help in deciding the need for surgical lymph node dissection or additional preoperative treatment modalities that might improve survival. Our objective here was to identify a set of discriminating genes that can be used for characterization and prediction of lymph node metastasis.

METHODS

Eighty-nine colorectal cancer patients were studied. Gene expression profiles of cancer were determined by human U133 Plus 2.0 GeneChip, and patients with and without lymph node metastasis were compared.

RESULTS

We identified 73 novel discriminating genes in which expression was significantly different between patients with and without lymph node metastasis. Using this gene set, we were able to establish a new model to predict the presence of lymph node metastasis with an accuracy of 88.4%. Discriminating genes were associated with various functions, including receptor activity and transcription regulatory activity. The list of genes included transmembrane glycoprotein, which has been reported to have a close relationship with lymph node metastasis in prostate cancer. Transmembrane glycoprotein showed significantly higher expression in patients with lymph node metastasis.

CONCLUSIONS

The present study suggests the possibility that gene expression profiling may be useful in predicting the presence of lymph node metastasis. Thus, gene expression profiling could help to establish individualized tailored therapy for colorectal cancer and provide insights into the development of novel therapeutic targets.

DNA methylation and sensitivity to antimetabolites in cancer cell lines

The prediction of the cellular direction of metabolic pathways toward either DNA synthesis or DNA methylation is crucial for determining the susceptibility of cancers to anti-metabolites such as fluorouracil (5-FU). We genotyped the methylenetetrahydrofolate reductase (MTHFR) gene in NCI-60 cancer cell lines, and identified the methylation status of 24 tumor suppressor genes using methylation-specific multiplex ligation-dependent probe amplification. The susceptibility of the cancer cell lines to seven antimetabolites was then determined. Cells homozygous for CC at MTHFR-A1298C were significantly more sensitive to cyclocytidine, cytarabine (AraC) and floxuridine than those with AA or AC (p=0.0215, p=0.0166, and p=0.0323, respectively), and carried more methylated tumor suppressor genes (p=0.0313). Among the 12 tumor suppressor genes which were methylated in >25% of cancer cell lines, the methylation status of TIMP3, APC and IGSF4 significantly correlated with sensitivity to pyrimidine synthesis inhibitors. In particular, cells with methylated TIMP3 had reduced mRNA levels and were significantly more sensitive to aphidicolin-glycinate, AraC and 5-FU than cells with unmethylated TIMP3. We speculate that MTHFR-A1298C homozygous CC might direct the methylation rather than the synthesis of DNA, and result in the methylation of several tumor suppressor genes such as TIMP3. These genes could be useful biological markers for predicting the efficacy of antimetabolites.

Folylpolyglutamate synthase and gamma-glutamyl hydrolase regulate leucovorin-enhanced 5-fluorouracil anticancer activity

Although 5-fluorouracil (5-FU) plus leucovorin (LV) is a standard chemotherapy regimen for colorectal cancer, the factors that determine the LV-mediated enhancement of the antitumor activity of 5-FU have remained unknown. We investigated the roles of folylpolyglutamate synthase (FPGS) and gamma-glutamyl hydrolase (GGH), which are the main enzymes involved in folate metabolism, in the effect of LV. LV enhanced the anticancer activity of 5-FU and the level of reduced folate in human colon cancer cells. Small-interfering RNA (siRNA) transfected into DLD-1 cells to downregulate FPGS reduced the basal level of reduced folate, the folate level after LV treatment, and the enhancement of 5-fluoro-2'-deoxyuridine (FdUrd)-induced cytotoxicity elicited by LV. By contrast, the downregulation of GGH by siRNA increased cellular sensitivity to FdUrd combined with LV. These results suggest that FPGS and GGH expression levels in tumors are determinants of the efficacy of LV in enhancing the antitumor activity of 5-FU.

Orotate phosphoribosyltransferase expression level in tumors is a potential determinant of the efficacy of 5-fluorouracil

Although the intratumoral expression levels of thymidylate synthase (TS) and dihydropyrimidine dehydrogenase (DPD) are known to affect the antitumor activity of 5-fluorouracil (5-FU), the importance of orotate phosphoribosyltransferase (OPRT) has remained unclear. This study investigated the relationship between intratumoral OPRT expression and the antitumor activity of 5-FU using human NCI60 cell lines with similar levels of TS and DPD messenger RNAs, as well as 31 tumor xenografts. The OPRT mRNA level was positively correlated with the 5-FU efficacy in these cell lines. In vitro, the 50% growth-inhibitory concentrations of 5-FU were closely correlated with the OPRT mRNA levels in cancer cell lines with similar levels of TS mRNAs when combined with a DPD inhibitor. Moreover, downregulation of OPRT with small-interfering RNA decreased the sensitivities of the cultured tumor cells to 5-FU. These results suggest that the OPRT expression level in tumors is an additional determinant of the efficacy of 5-FU.

Gene expression signature and the prediction of ulcerative colitis-associated colorectal cancer by DNA microarray

PURPOSE

Ulcerative colitis (UC) is associated with a high risk of colorectal cancer. To identify genes that could predict the development of cancer in UC, we conducted a DNA microarray analysis using nonneoplastic rectal mucosa of UC patients.

EXPERIMENTAL DESIGN

Gene expression in nonneoplastic mucosa of 53 UC patients were examined. Gene expression profiles were examined using human Genome U133 Plus 2.0 gene chip array (Affymetrix). Among 53 UC patients, 10 had UC-associated cancer (UC-Ca group) whereas 43 did not (UC-NonCa group).

RESULTS

By comparing gene expression profiles of nonneoplastic rectal mucosae between the UC-Ca and UC-NonCa groups, we could identify 40 genes that were differentially expressed between two groups. The list of discriminating genes included low-density lipoprotein receptor-related protein (LRP5 and LRP6). Previous studies suggested that LRP5 and LRP6 expression promotes cancer cell proliferation and tumorigenesis and are considered as candidate oncogenes. In the present study, both LRP5 and LRP6 showed significantly higher expression in the UC-Ca group, which suggests the importance of these genes in the development of UC-associated colorectal cancers. With the 40 selected discriminating genes, we did class prediction of the development of colorectal neoplasms in UC patients. Using the k-nearest neighbor method and the support vector machine, we could predict the development of UC-associated neoplasms with an accuracy of 86.8% and 98.1%, respectively.

CONCLUSIONS

These findings have important implications for the early detection of malignant lesions in UC and may provide directions for future research into the molecular mechanisms of UC-associated cancer.

Changes to the dihydropyrimidine dehydrogenase gene copy number influence the susceptibility of cancers to 5-FU-based drugs: Data mining of the NCI-DTP data sets and validation with human tumour xenografts

Patient response to the anti-tumour drug 5-fluorouracil (5-FU) is variable, but predicting the response rate is important for the selection of effective chemotherapy. Our aim was to identify alterations in DNA copy number that influence susceptibility of cancer cells to 5-FU-based drugs. The NCI public database was used to identify chromosome loci associated with drug sensitivity and DNA copy number. One of the 11 candidates, the cytogenetic band 1p21.3, harbours the dihydropyrimidine dehydrogenase (DPD) gene. To validate this finding, the DPD copy number and in vivo sensitivity to 5-FU-based drugs were determined in 31 human tumour xenografts. Those xenografts demonstrating low sensitivity had significantly higher DPD copy numbers than highly sensitive tumours (P<0.002). Moreover, DPD mRNA expression levels were significantly correlated with DPD copy numbers (P<0.046). An assessment of copy number may be a more precise method of predicting the sensitivity of cancer patients to 5-FU related drugs.

Distal colorectal cancers with microsatellite instability (MSI) display distinct gene expression profiles that are different from proximal MSI cancers

Promoter methylation of the mismatch repair gene plays a key role in sporadic microsatellite instability (MSI) colorectal cancers. However, promoter methylation often occurs in proximal colon cancers, and molecular phenotypes underlying MSI cancers in distal colon have not been fully clarified. Our goal was to clarify the difference between MSI and microsatellite stability (MSS) cancers and, furthermore, to determine distinct characteristics of proximal and distal MSI cancers. By DNA microarray analysis of 84 cancers (33 MSI and 51 MSS), we identified discriminating genes (177 probe sets), which predicted MSI status with a high accuracy rate (97.6%). These genes were related to phenotypic characteristics of MSI cancers. Next, we identified 24 probe sets that were differentially expressed in proximal and distal MSI cancers. These genes included promoter methylation-mediated genes, whose expression was significantly down-regulated in proximal MSI cancers. Among discriminating genes between MSI and MSS, nine methylation-mediated genes showed down-regulation in MSI cancers. Of these, 7 (77.8%) showed down-regulation in proximal MSI cancers. Furthermore, methylation-specific PCR confirmed that frequency of hMLH1 promoter methylation was significantly higher in proximal MSI cancers (P = 0.0317). These results suggested that there is a difference between proximal and distal MSI cancers in methylation-mediated influence on gene silencing. In conclusion, using DNA microarray, we could distinguish MSI and MSS cancers. We also showed distinct characteristics of proximal and distal MSI cancers. The inactivation form of hMLH, per se, differed between proximal and distal MSI cancers. These results suggested that distal MSI cancers constitute a distinct subgroup of sporadic MSI cancers.