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Shen MH, Huang CJ, Ho TF, Liu CY, Shih YY, Huang CS, Huang CC. Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations. BMC Cancer 2022; 22:590. [PMID: 35637462 PMCID: PMC9150289 DOI: 10.1186/s12885-022-09627-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature. Methods The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345). Results The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies. Conclusion The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09627-9.
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Affiliation(s)
- Ming-Hung Shen
- Department of Surgery, Fu-Jen Catholic University Hospital, No. 69, Guizi Road, Taishan District, New Taipei City, 243, Taiwan.,Ph. D Program in Nutrition and Food Science, College of Human Ecology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan
| | - Chi-Jung Huang
- Department of Biochemistry, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11490, Taiwan.,Department of Medical Research, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan
| | - Thien-Fiew Ho
- Division of General Surgery, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ying-Yih Shih
- Division of Hematology and Oncology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ching-Shui Huang
- Department of Surgery, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan. .,School of Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei City, 110, Taiwan.
| | - Chi-Cheng Huang
- Department of Surgery, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan, 11217. .,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, No.17, Xuzhou Rd., Taipei City, 100, Taiwan.
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Lopez NE, Weiss AC, Robles J, Fanta P, Ramamoorthy SL. A systematic review of clinically available gene expression profiling assays for stage II colorectal cancer: initial steps toward genetic staging. Am J Surg 2016; 212:700-714. [PMID: 27637150 DOI: 10.1016/j.amjsurg.2016.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/27/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND In recent years, increasingly accessible and novel genetic technologies have spurred keen interest in the application of cancer genetics in predicting prognosis and response to treatment. In particular, investigators have eagerly sought to establish and validate genetic signatures that might improve the identification of patients with stage II colorectal cancer (CRC) who are at highest risk of recurrence. To better understand the evidence for incorporation of genetic assays into clinical practice, we have systematically reviewed those assays that have been validated and are available for clinical use in stage II CRC. METHODS A systematic review was performed using PubMed, Web of Science and Scopus databases. The GRADE system was used to evaluate level of evidence and strength of recommendations. RESULTS After duplicates were removed and exclusion criteria were applied, there were 13 articles for review. CONCLUSION Identifying high-risk patients with stage II CRC using molecular profiling has been the primary aim of many investigators, and the approach is translating into clinical utility.
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Affiliation(s)
- Nicole E Lopez
- Division of Surgical Oncology, University of North Carolina Medical Center, Chapel Hill, NC, USA
| | - Anna C Weiss
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA
| | - Julie Robles
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA
| | - Paul Fanta
- Division of Hematology and Oncology, Department of Medicine, UC San Diego Health System, Moores Cancer Center, La Jolla, CA, USA
| | - Sonia L Ramamoorthy
- Division of Colorectal, Department of Surgery, UC San Diego Health System, Moores Cancer Center, 3855 Health Sciences Drive #0987, La Jolla, CA 92093-0987, USA.
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Johnston PG. Identification of clinically relevant molecular subtypes in colorectal cancer: the dawning of a new era. Oncologist 2014; 19:568-73. [PMID: 24718513 PMCID: PMC4012975 DOI: 10.1634/theoncologist.2014-038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/03/2014] [Indexed: 12/21/2022] Open
Abstract
In recent years, a number of protein and genomic-based biomarkers have begun to refine the prognostic information available for colorectal cancer (CRC) and predict defined patient groups that are likely to benefit from systemic treatment or targeted therapies. Of these, KRAS represents the first biomarker integrated into clinical practice for CRC. Microarray-based gene expression profiling has been used to identify prognostic signatures and, to a lesser extent, predictive signatures in CRC. Despite these advances, a number of major challenges remain. This article, which is based on a lecture delivered as part of the 2013 Bob Pinedo Cancer Care Prize, reviews the impact of molecular biomarkers on the management of CRC, emphasizing changes that have occurred in recent years, and focuses on potential mechanisms of patient stratification and opportunities for novel therapeutic development based on enhanced biological understanding of colorectal cancer.
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Affiliation(s)
- Patrick G Johnston
- Institute of Health Sciences, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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