DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up
- 454 Downloads
DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study.
Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up.
DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and TGF-β and apoptosis signaling, were found to be most significantly affected.
Our results suggest that CNAs in CRC tumor tissues are associated with concomitant changes in the expression of cancer-related genes. In other genes epigenetic mechanism may be at work. Up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, appear to be associated with a poor survival. These alterations may, in addition to Dukes' staging, be employed as new prognostic biomarkers for the prediction of clinical outcome in CRC patients.
KeywordsColorectal cancer DNA copy number alterations Comparative genomic hybridization (CGH) Gene expression alterations Disease-free survival
This project was financially supported by the AIRC (Associazione Italiana per la Ricerca sul Cancro) REGIONAL GRANT 2005.
CL, EB, CDF, PD, FT conceived and designed the experiments. EB and CL wrote the paper. The following authors performed the experiments: EB and CDF: a-CGH analysis, CL: GE analysis, FA: statistical analyses of a-CGH data, CC, ST and CL: a-CGH and GE data analyses, MF, FG and FT: patient recruitment, follow-up and samples collection, LM: histopathological evaluations.
Compliance with ethical standards
This study was conducted in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. A written informed consent was obtained from all patients involved in the study.
Conflict of interest
The authors declare that they have no conflict of interest.
- 2.H.R. Oh, C.H. An, N.J. Yoo, S.H. Lee, Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity - a short report. Cell. Oncol. 37(6), 455–61 (2014)Google Scholar
- 4.T. Ried, R. Knutzen, R. Steinbeck, H. Blegen, E. Schröck, K. Heselmeyer, S. du Manoir, G. Auer, Comparative genomic hybridization reveals a specific pattern of chromosomal gains and losses during the genesis of colorectal tumors. Genes Chromosomes Cancer 15(4), 234–245 (1996)CrossRefPubMedGoogle Scholar
- 9.S. Lassmann, R. Weis, F. Makowiec, J. Roth, M. Danciu, U. Hopt, M. Werner, C.G.H. Array, Identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas. J. Mol. Med. (Berl) 85(3), 293–304 (2007)CrossRefGoogle Scholar
- 11.Q.J. He, W.F. Zeng, J.S. Sham, D. Xie, X.W. Yang, H.L. Lin, W.H. Zhan, F. Lin, S.D. Zeng, D. Nie, L.F. Ma, C.J. Li, S. Lu, X.Y. Guan, Recurrent genetic alterations in 26 colorectal carcinomas and 21 adenomas from Chinese patients. Cancer Genet. Cytogenet. 144(2), 112–118 (2003)CrossRefPubMedGoogle Scholar
- 12.L. Marisa, A. de Reyniès, A. Duval, J. Selves, M.P. Gaub, L. Vescovo, M.C. Etienne-Grimaldi, R. Schiappa, D. Guenot, M. Ayadi, S. Kirzin, M. Chazal, J.F. Fléjou, D. Benchimol, A. Berger, A. Lagarde, E. Pencreach, F. Piard, D. Elias, Y. Parc, S. Olschwang, G. Milano, P. Laurent-Puig, V. Boige, Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 10(5), e1001453 (2013)CrossRefPubMedPubMedCentralGoogle Scholar
- 14.D. Cavalieri, P. Dolara, E. Mini, C. Luceri, C. Castagnini, S. Toti, K. Maciag, C. De Filippo, S. Nobili, M. Morganti, C. Napoli, G. Tonini, M. Baccini, A. Biggeri, F. Tonelli, R. Valanzano, C. Orlando, S. Gelmini, F. Cianchi, L. Messerini, L. Luzzatto, Analysis of gene expression profiles reveals novel correlations with the clinical course of colorectal cancer. Oncol. Res. 16(11), 535–548 (2007)CrossRefPubMedGoogle Scholar
- 15.M. Grade, P. Hörmann, S. Becker, A.B. Hummon, D. Wangsa, S. Varma, R. Simon, T. Liersch, H. Becker, M.J. Difilippantonio, B.M. Ghadimi, T. Ried, Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas. Cancer Res. 67(1), 41–56 (2007)CrossRefPubMedPubMedCentralGoogle Scholar
- 20.K.K. Lagerstedt, E. Kristiansson, C. Lönnroth, M. Andersson, B.M. Iresjö, A. Gustafsson, E. Hansson, U. Kressner, S. Nordgren, F. Enlund, K. Lundholm, Genes with relevance for early to late progression of colon carcinoma based on combined genomic and transcriptomic information from the same patients. Cancer Inform. 9, 79–91 (2010)PubMedPubMedCentralGoogle Scholar
- 21.M. Sheffer, M.D. Bacolod, O. Zuk, S.F. Giardina, H. Pincas, F. Barany, P.B. Paty, W.L. Gerald, D.A. Notterman, E. Domany, Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Proc. Natl. Acad. Sci. U. S. A. 106(17), 7131–7136 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
- 22.D. Tsafrir, M. Bacolod, Z. Selvanayagam, I. Tsafrir, J. Shia, Z. Zeng, H. Liu, C. Krier, R.F. Stengel, F. Barany, W.L. Gerald, P.B. Paty, E. Domany, D.A. Notterman, Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res. 66(4), 2129–2137 (2006)CrossRefPubMedGoogle Scholar
- 23.J. Camps, Q.T. Nguyen, H.M. Padilla-Nash, T. Knutsen, N.E. McNeil, D. Wangsa, A.B. Hummon, M. Grade, T. Ried, M.J. Difilippantonio, Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer. Genes Chromosomes Cancer 48(11), 1002–1017 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
- 24.L.W. Loo, M. Tiirikainen, I. Cheng, A. Lum-Jones, A. Seifried, J.M. Church, R. Gryfe, D.J. Weisenberger, N.M. Lindor, S. Gallinger, R.W. Haile, D.J. Duggan, S.N. Thibodeau, G. Casey, L. Le Marchand, Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable CpG island methylator phenotype-negative colon cancer. Genes Chromosomes Cancer 52(5), 450–466 (2013)CrossRefPubMedPubMedCentralGoogle Scholar
- 29.Y. Tang, A. Puri, M.D. Ricketts, T.S. Rai, J. Hoffmann, E. Hoi, P.D. Adams, D.C.R. Schultz, Marmorstein Identification of an ubinuclein 1 region required for stability and function of the human HIRA/UBN1/CABIN1/ASF1a histone H3.3 chaperone complex. Biochemistry 51(12), 2366–2377 (2012)CrossRefPubMedPubMedCentralGoogle Scholar
- 31.K. Vazquez-Santillan, J. Melendez-Zajgla, L. Jimenez-Hernandez, G. Martínez-Ruiz, V. Maldonado, NF-kB signaling in cancer stem cells: a promising therapeutic target? Cell. Oncol. 38(5), 327–39 (2015)Google Scholar
- 34.R. Liao, J. Sun, H. Wu, Y. Yi, J.X. Wang, H.W. He, X.Y. Cai, J. Zhou, Y.F. Cheng, J. Fan, S.J. Qiu, High expression of IL-17 and IL-17RE associate with poor prognosis of hepatocellular carcinoma. J. Exp. Clin. Cancer Res. 11, 32–33 (2013)Google Scholar
- 37.K. Wang, M.K. Kim, G. Di Caro, J. Wong, S. Shalapour, J. Wan, W. Zhang, Z. Zhong, E. Sanchez-Lopez, L.W. Wu, K. Taniguchi, Y. Feng, E. Fearon, S.I. Grivennikov, M. Karin, Interleukin-17 receptor a signaling in transformed enterocytes promotes early colorectal tumorigenesis. Immunity 41(6), 1052–1063 (2014)CrossRefPubMedPubMedCentralGoogle Scholar
- 41.I. Hlavata, B. Mohelnikova-Duchonova, R. Vaclavikova, V. Liska, P. Pitule, P. Novak, J. Bruha, O. Vycital, L. Holubec, V. Treska, P. Vodicka, P. Soucek, The role of ABC transporters in progression and clinical outcome of colorectal cancer. Mutagenesis 27(2), 187–196 (2012)CrossRefPubMedGoogle Scholar
- 44.S.M. Kessler, J. Pokorny, V. Zimmer, S. Laggai, F. Lammert, R.M. Bohle, A.K. Kiemer, IGF2 mRNA binding protein p62/IMP2-2 in hepatocellular carcinoma: antiapoptotic action is independent of IGF2/PI3K signaling. Am. J. Physiol. Gastrointest. Liver Physiol. 304(4), G328–336 (2013)CrossRefPubMedGoogle Scholar
- 45.B.M. Wolpin, K. Ng, A.X. Zhu, T. Abrams, P.C. Enzinger, N.J. McCleary, D. Schrag, E.L. Kwak, J.N. Allen, P. Bhargava, J.A. Chan, W. Goessling, L.S. Blaszkowsky, J.G. Supko, M. Elliot, K. Sato, E. Regan, J.A. Meyerhardt, C.S. Fuchs, Multicenter phase II study of tivozanib (AV-951) and everolimus (RAD001) for patients with refractory, metastatic colorectal cancer. Oncologist 18(4), 377–378 (2013)CrossRefPubMedPubMedCentralGoogle Scholar
- 46.Z. Niu, J. Wang, S. Muhammad, W. Niu, E. Liu, C. Peng, B. Liang, Q. Sun, S. Obo, Z. He, S. Liu, X. Zou, J. Niu, Protein expression of eIF4E and integrin αvβ6 in colon cancer can predict clinical significance, reveal their correlation and imply possible mechanism of interaction. Cell Biosci. 4, 23 (2014)CrossRefPubMedPubMedCentralGoogle Scholar
- 48.F. Puca, M. Colamaio, A. Federico, M. Gemei, N. Tosti, A.U. Bastos, L. Del Vecchio, S. Pece, S. Battista, A. Fusco, HMGA1 silencing restores normal stem cell characteristics in colon cancer stem cells by increasing p53 levels. Oncotarget 5(10), 3234–3245 (2014)CrossRefPubMedPubMedCentralGoogle Scholar
- 49.A.Z. Gimeno-García, A. Santana-Rodríguez, A. Jiménez, A. Parra-Blanco, D. Nicolás-Pérez, C. Paz-Cabrera, F. Díaz-González, C. Medina, L. Díaz-Flores, E. Quintero, Up-regulation of gelatinases in the colorectal adenoma-carcinoma sequence. Eur. J. Cancer 42(18), 3246–3252 (2006)CrossRefPubMedGoogle Scholar
- 51.Y. Takahashi, Y. Ishii, Y. Nishida, M. Ikarashi, T. Nagata, T. Nakamura, S. Yamamori, S. Asai, Detection of aberrations of ubiquitin-conjugating enzyme E2C gene (UBE2C) in advanced colon cancer with liver metastases by DNA microarray and two-color FISH. Cancer Genet. Cytogenet. 168(1), 30–35 (2006)CrossRefPubMedGoogle Scholar
- 53.V. Serafin, L. Persano, L. Moserle, G. Esposito, M. Ghisi, M. Curtarello, L. Bonanno, M. Masiero, D. Ribatti, M. Stürzl, E. Naschberger, R.S. Croner, A.M. Jubb, A.L. Harris, H.S. Koeppen, A. Amadori, Indraccolo Notch3 signalling promotes tumour growth in colorectal cancer. J. Pathol. 224, 448–460 (2011)CrossRefPubMedGoogle Scholar
- 61.C. Xu, Y. Liu, P. Wang, W. Fan, T.C. Rue, M.P. Upton, J.R. Houck, P. Lohavanichbutr, D.R. Doody, N.D. Futran, L.P. Zhao, S.M. Schwartz, C. Chen, E. Méndez, Integrative analysis of DNA copy number and gene expression in metastatic oral squamous cell carcinoma identifies genes associated with poor survival. Mol. Cancer 9, 143 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
- 62.H.M. Horlings, C. Lai, D.S. Nuyten, H. Halfwerk, P. Kristel, E. van Beers, S.A. Joosse, C. Klijn, P.M. Nederlof, M.J. Reinders, L.F. Wessels, M.J. van de Vijver, Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients. Clin. Cancer Res. 16(2), 651–663 (2010)CrossRefPubMedGoogle Scholar
- 63.E. Yiannakopoulou, Targeting epigenetic mechanisms and microRNAs by aspirin and other non steroidal anti-inflammatory agents--implications for cancer treatment and chemoprevention. Cell. Oncol. 37(3), 167–78 (2014)Google Scholar
- 64.N. Nishida, S. Yamashita, K. Mimori, T. Sudo, F. Tanaka, K. Shibata, H. Yamamoto, H. Ishii, Y. Doki, M. Mori, MicroRNA-10b is a prognostic indicator in colorectal cancer and confers resistance to the chemotherapeutic agent 5-fluorouracil in colorectal cancer cells. Ann. Surg. Oncol. 19(9), 3065–3071 (2012)CrossRefPubMedGoogle Scholar