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Khuntikeo N, Padthaisong S, Loilome W, Klanrit P, Ratchatapusit S, Techasen A, Jareanrat A, Thanasukarn V, Srisuk T, Luvira V, Chindaprasirt J, Sa-ngiamwibool P, Aphivatanasiri C, Intarawichian P, Koonmee S, Prajumwongs P, Titapun A. Mismatch Repair Deficiency Is a Prognostic Factor Predicting Good Survival of Opisthorchis viverrini-Associated Cholangiocarcinoma at Early Cancer Stage. Cancers (Basel) 2023; 15:4831. [PMID: 37835526 PMCID: PMC10572072 DOI: 10.3390/cancers15194831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The mismatch repair (MMR) system prevents DNA mutation; therefore, deficient MMR protein (dMMR) expression causes genetic alterations and microsatellite instability (MSI). dMMR is correlated with a good outcome and treatment response in various cancers; however, the situation remains ambiguous in cholangiocarcinoma (CCA). This study aims to evaluate the prevalence of dMMR and investigate the correlation with clinicopathological features and the survival of CCA patients after resection. MATERIALS AND METHODS Serum and tissues were collected from CCA patients who underwent resection from January 2005 to December 2017. Serum OV IgG was examined using ELISA. The expression of MMR proteins MLH1, MSH2, MSH6 and PMS2 was investigated by immunohistochemistry; subsequently, MMR assessment was evaluated as either proficient or as deficient by pathologists. The clinicopathological features and MMR status were compared using the Chi-square test. Univariate and multivariate analyses were conducted to identify prognostic factors. RESULTS Among the 102 CCA patients, dMMR was detected in 22.5%. Survival analysis revealed that dMMR patients had better survival than pMMR (HR = 0.50, p = 0.008). In multivariate analysis, dMMR was an independent factor for a good prognosis in CCA patients (HR = 0.58, p = 0.041), especially at an early stage (HR = 0.18, p = 0.027). Moreover, subgroup analysis showed dMMR patients who received adjuvant chemotherapy had better survival than surgery alone (HR = 0.28, p = 0.012). CONCLUSION This study showed a high prevalence of dMMR in cholangiocarcinoma with dMMR being the independent prognostic factor for good survival, especially in early-stage CCA and for patients who received adjuvant chemotherapy. dMMR should be the marker for selecting patients to receive a specific adjuvant treatment after resection for CCA.
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Affiliation(s)
- Natcha Khuntikeo
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Sureerat Padthaisong
- Faculty of Allied Health Sciences, Burapha University, Chonburi 20131, Thailand;
| | - Watcharin Loilome
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Poramate Klanrit
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Soontaree Ratchatapusit
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Apiwat Jareanrat
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Vasin Thanasukarn
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Tharatip Srisuk
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Vor Luvira
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Jarin Chindaprasirt
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Medical Oncology Program, Department of Medicine Srinagarind Hospital, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Prakasit Sa-ngiamwibool
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chaiwat Aphivatanasiri
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piyapharom Intarawichian
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Supinda Koonmee
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piya Prajumwongs
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
| | - Attapol Titapun
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (N.K.); (A.J.); (V.T.); (T.S.); (V.L.)
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand; (W.L.); (P.K.); (S.R.); (A.T.); (J.C.); (P.S.-n.); (C.A.); (P.I.); (S.K.); (P.P.)
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Alam MR, Seo KJ, Abdul-Ghafar J, Yim K, Lee SH, Jang HJ, Jung CK, Chong Y. Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers. Brief Bioinform 2023; 24:bbad151. [PMID: 37114657 DOI: 10.1093/bib/bbad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
PURPOSE Evaluation of genetic mutations in cancers is important because distinct mutational profiles help determine individualized drug therapy. However, molecular analyses are not routinely performed in all cancers because they are expensive, time-consuming and not universally available. Artificial intelligence (AI) has shown the potential to determine a wide range of genetic mutations on histologic image analysis. Here, we assessed the status of mutation prediction AI models on histologic images by a systematic review. METHODS A literature search using the MEDLINE, Embase and Cochrane databases was conducted in August 2021. The articles were shortlisted by titles and abstracts. After a full-text review, publication trends, study characteristic analysis and comparison of performance metrics were performed. RESULTS Twenty-four studies were found mostly from developed countries, and their number is increasing. The major targets were gastrointestinal, genitourinary, gynecological, lung and head and neck cancers. Most studies used the Cancer Genome Atlas, with a few using an in-house dataset. The area under the curve of some of the cancer driver gene mutations in particular organs was satisfactory, such as 0.92 of BRAF in thyroid cancers and 0.79 of EGFR in lung cancers, whereas the average of all gene mutations was 0.64, which is still suboptimal. CONCLUSION AI has the potential to predict gene mutations on histologic images with appropriate caution. Further validation with larger datasets is still required before AI models can be used in clinical practice to predict gene mutations.
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Affiliation(s)
- Mohammad Rizwan Alam
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kyung Jin Seo
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jamshid Abdul-Ghafar
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kwangil Yim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sung Hak Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Hyun-Jong Jang
- Catholic Big Data Integration Center, Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yosep Chong
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Targeted Sequencing of Sorted Esophageal Adenocarcinoma Cells Unveils Known and Novel Mutations in the Separated Subpopulations. Clin Transl Gastroenterol 2021; 11:e00202. [PMID: 33094962 PMCID: PMC7508445 DOI: 10.14309/ctg.0000000000000202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Our study aimed at investigating tumor heterogeneity in esophageal adenocarcinoma (EAC) cells regarding clinical outcomes. METHODS Thirty-eight surgical EAC cases who underwent gastroesophageal resection with lymph node dissection in 3 university centers were included. Archival material was analyzed via high-throughput cell sorting technology and targeted sequencing of 63 cancer-related genes. Low-pass sequencing and immunohistochemistry (IHC) were used to validate the results. RESULTS Thirty-five of 38 EACs carried at least one somatic mutation that was absent in the stromal cells; 73.7%, 10.5%, and 10.5% carried mutations in tumor protein 53, cyclin dependent kinase inhibitor 2A, and SMAD family member 4, respectively. In addition, 2 novel mutations were found for hepatocyte nuclear factor-1 alpha in 2 of 38 cases. Tumor protein 53 gene abnormalities were more informative than p53 IHC. Conversely, loss of SMAD4 was more frequently noted with IHC (53%) and was associated with a higher recurrence rate (P = 0.015). Only through cell sorting we were able to detect the presence of hyperdiploid and pseudodiploid subclones in 7 EACs that exhibited different mutational loads and/or additional copy number amplifications, indicating the high genetic heterogeneity of these cancers. DISCUSSION Selective cell sorting allowed the characterization of multiple molecular defects in EAC subclones that were missed in a significant number of cases when whole-tumor samples were analyzed. Therefore, this approach can reveal subtle differences in cancer cell subpopulations. Future studies are required to investigate whether these subclones are responsible for treatment response and disease recurrence.
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Zhang Y, Wu Y, Gong ZY, Ye HD, Zhao XK, Li JY, Zhang XM, Li S, Zhu W, Wang M, Liang GY, Liu Y, Guan X, Zhang DY, Shen B. Distinguishing Rectal Cancer from Colon Cancer Based on the Support Vector Machine Method and RNA-sequencing Data. Curr Med Sci 2021; 41:368-374. [PMID: 33877555 DOI: 10.1007/s11596-021-2356-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/23/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Several studies have indicated that rectal cancer is significantly different from colon cancer in terms of treatment, prognosis, and metastasis. Recently, the differential mRNA expression of colon cancer and rectal cancer has received a great deal of attention. The current study aimed to identify significant differences between colon cancer and rectal cancer based on RNA sequencing (RNA-seq) data via support vector machines (SVM). Here, 393 CRC samples from the The Cancer Genome Atlas (TCGA) database were investigated, including 298 patients with colon cancer and 95 with rectal cancer. Following the random forest (RF) analysis of the mRNA expression data, 96 genes such as HOXB13, PRAC, and BCLAF1 were identified and utilized to build the SVM classification model with the Leave-One-Out Cross-validation (LOOCV) algorithm. In the training (n=196) and the validation cohorts (n=197), the accuracy (82.1 % and 82.2 %, respectively) and the AUC (0.87 and 0.91, respectively) indicated that the established optimal SVM classification model distinguished colon cancer from rectal cancer reasonably. However, additional experiments are required to validate the predicted gene expression levels and functions.
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Affiliation(s)
- Yan Zhang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Yuan Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Zi-Ying Gong
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China
| | - Hai-Dan Ye
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China
| | - Xiao-Kai Zhao
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China
| | - Jie-Yi Li
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China
| | - Xiao-Mei Zhang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Sheng Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Wei Zhu
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Mei Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Ge-Yu Liang
- School of Public Health, Southeast University, Nanjing, 211189, China
| | - Yun Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Xin Guan
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Dao-Yun Zhang
- Shanghai Yunying Medical Technology Co., Ltd., Shanghai, 201612, China.,Jiaxing Yunying Medical Inspection Co., Ltd., Jiaxing, 314000, China
| | - Bo Shen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China.
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Shaib WL, Zakka KM, Jiang R, Yan M, Alese OB, Akce M, Wu C, Behera M, El-Rayes BF. Survival outcome of adjuvant chemotherapy in deficient mismatch repair stage III colon cancer. Cancer 2020; 126:4136-4147. [PMID: 32697360 DOI: 10.1002/cncr.33049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/11/2020] [Accepted: 05/31/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND The prognostic impact of DNA mismatch repair (MMR) status remains controversial in patients with stage III colon cancer who are treated with adjuvant chemotherapy (AC). The aim of this study was to evaluate the survival outcome of AC in deficient mismatch repair (dMMR)/microsatellite instable (MSI) stage III CC. METHODS Patients with pathological stage III CC between 2010 and 2013 were identified from the National Cancer Database using International Classification of Diseases for Oncology (3rd Edition) morphology and topography codes 8140, 8480, and C18.0-18.8. Patients with pathologic stage T3N2, T4N1, or T4N were considered high risk; patients with stage T3N1 were considered low risk. Univariate and multivariable analyses were conducted, and Kaplan-Meier analysis and Cox proportional hazards models were used to identify the association between AC and overall survival (OS). RESULTS A total of 9226 patients with pathological stage III CC were identified, of which 2384 (25.8%) were MSI-high (MSI-H) and met the inclusion criteria of the final analysis. MSI-low (MSI-L) patients (n = 6842) were excluded. There was a preponderance of women (55.0% [n = 1311]), and 76.6% (n = 1825) of patients were non-Hispanic white. The median age was 65 years (range, 19-90 years). The primary sites were the cecum (29.7% [n = 707]), ascending colon (26.0% [n = 620]), sigmoid colon (17.2% [n = 410]), and transverse colon (10.8% [n = 257]). The most common tumor grade was moderately differentiated (n = 50.4% [1202]), followed by poorly differentiated (34.1% [n = 813]) and well differentiated (5.1% [n = 121]). High-risk pathologic stage III CC (T4N1, TxN2) constituted 51.0% (n = 1215) of the study population. High-risk stage III was associated with worse OS compared with low-risk stage III on univariate (P < .001) analysis and displayed a similar trend on multivariable analysis, without a statistically significant difference. Multiagent AC was associated with improved OS compared with no treatment on univariate (P < .001) and multivariable (P < .001) analysis. When stratified by risk status, multiagent AC was associated with improved OS compared with no treatment for high-risk (P < .001) and low-risk (P < .001) stage III disease. CONCLUSION Adjuvant chemotherapy is associated with better OS in stage III dMMR/MSI-H CC. An enhanced benefit was shown for high-risk stage III disease.
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Affiliation(s)
- Walid L Shaib
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Katerina M Zakka
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Renjian Jiang
- Winship Research Informatics, Emory University, Atlanta, Georgia
| | - Ming Yan
- Winship Research Informatics, Emory University, Atlanta, Georgia
| | - Olatunji B Alese
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Mehmet Akce
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Christina Wu
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Madhusmita Behera
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia.,Winship Research Informatics, Emory University, Atlanta, Georgia
| | - Bassel F El-Rayes
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
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Ballestrero A, Bedognetti D, Ferraioli D, Franceschelli P, Labidi-Galy SI, Leo E, Murai J, Pommier Y, Tsantoulis P, Vellone VG, Zoppoli G. Report on the first SLFN11 monothematic workshop: from function to role as a biomarker in cancer. J Transl Med 2017; 15:199. [PMID: 28969705 PMCID: PMC5625715 DOI: 10.1186/s12967-017-1296-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/12/2017] [Indexed: 01/05/2023] Open
Abstract
SLFN11 is a recently discovered protein with a putative DNA/RNA helicase function. First identified in association with the maturation of thymocytes, SLFN11 was later causally associated, by two independent groups, with the resistance to DNA damaging agents such as topoisomerase I and II inhibitors, platinum compounds, and other alkylators, making it an attractive molecule for biomarker development. Later, SLFN11 was linked to antiviral response in human cells and interferon production, establishing a potential bond between immunity and chemotherapy. Recently, we demonstrated the potential role of SLN11 as a biomarker to predict sensitivity to the carboplatin/taxol combination in ovarian cancer. The present manuscript reports on the first international monothematic workshop on SLFN11. Several researchers from around the world, directly and actively involved in the discovery, functional characterization, and study of SLFN11 for its biomarker and medicinal properties gathered to share their views on the current knowledge advances concerning SLFN11. The aim of the manuscript is to summarize the authors’ interventions and the main take-home messages resulting from the workshop.
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Affiliation(s)
- Alberto Ballestrero
- Istituto di Ricovero e Cura a Carattere Scientifico, Policlinico San Martino IST-Istituto Nazionale Tumori, Genoa, Italy.,Università degli Studi di Genova, Viale Benedetto XV, 6, 16132, Genoa, Italy
| | - Davide Bedognetti
- Tumor Biology Immunology and Therapy Branch, Sidra Medical and Research Center, Doah, Qatar
| | - Domenico Ferraioli
- Università degli Studi di Genova, Viale Benedetto XV, 6, 16132, Genoa, Italy.,Centre de Lutte contre le Cancer Léon Bérard, Lyon, France
| | - Paola Franceschelli
- Università degli Studi di Genova, Viale Benedetto XV, 6, 16132, Genoa, Italy
| | | | - Elisabetta Leo
- Oncology, Innovative Medicine Early Development, AstraZeneca, Cambridge, UK
| | - Junko Murai
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Petros Tsantoulis
- Department of Oncology, Hôpitaux Universitaires de Genève, Geneva, Switzerland
| | - Valerio Gaetano Vellone
- Istituto di Ricovero e Cura a Carattere Scientifico, Policlinico San Martino IST-Istituto Nazionale Tumori, Genoa, Italy.,Università degli Studi di Genova, Viale Benedetto XV, 6, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Istituto di Ricovero e Cura a Carattere Scientifico, Policlinico San Martino IST-Istituto Nazionale Tumori, Genoa, Italy. .,Università degli Studi di Genova, Viale Benedetto XV, 6, 16132, Genoa, Italy.
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Yan P, Klingbiel D, Saridaki Z, Ceppa P, Curto M, McKee TA, Roth A, Tejpar S, Delorenzi M, Bosman FT, Fiocca R. Reduced Expression of SMAD4 Is Associated with Poor Survival in Colon Cancer. Clin Cancer Res 2016; 22:3037-47. [PMID: 26861460 DOI: 10.1158/1078-0432.ccr-15-0939] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 01/09/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE SMAD4 loss is associated with the development of metastases and poor prognosis. We evaluated expression of SMAD4 protein and its association with tumor characteristics, including biomarkers and outcome in terms of relapse-free survival and overall survival. EXPERIMENTAL DESIGN We used 1,564 stage II/III colon cancer samples from PETACC-3 to evaluate SMAD4 expression by immunohistochemistry. SMAD4 protein expression was validated by assessing mRNA expression using available expression array data. SMAD4 expression was also studied on 34 adenomas and 10 colon cancer liver metastases with their primaries. Loss of SMAD4 immunoreactivity was defined as focal or diffuse. Cases without SMAD4 loss were subdivided into those with strong and weak expression. RESULTS SMAD4 protein expression was informative in 1,381/1,564 cases. SMAD4 loss was found in 293/1,381 (21%) cases. Of 1,088 cases without SMAD4 loss (79%), 530 showed weak and 558 strong expression. SMAD4 loss occurred also in adenomas, but less extensively than in carcinomas. Liver metastases followed mostly the expression pattern of the primary tumor. SMAD4 loss, including weak expression, identified patients with poor survival in stage II as well as III and in both treatment arms. SMAD4 loss was less frequent in tumors with microsatellite instability and more frequent in those with loss of heterozygosity of 18q. CONCLUSIONS We conclude that clonal loss of SMAD4 expression in adenomas, carcinomas, and liver metastases increases with disease progression. SMAD4 loss, and to a lesser extent weak expression, is strongly associated with poor survival regardless of stage. Clin Cancer Res; 22(12); 3037-47. ©2016 AACR.
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Affiliation(s)
- Pu Yan
- Institute of Pathology, University of Lausanne, Lausanne, Switzerland
| | - Dirk Klingbiel
- Swiss Group for Clinical Cancer Research SAKK, Coordinating Center, Bern, Switzerland. Bioinformatics Core Facility, University of Lausanne, Lausanne, Switzerland
| | - Zenia Saridaki
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Voutes, Heraklion, Greece. Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - Paola Ceppa
- Division of Anatomic Pathology, Department of Surgical and Diagnostic Sciences, University of Genoa and IRCCS S. Martino/IST University Hospital, Genoa, Italy
| | - Monica Curto
- Division of Anatomic Pathology, Department of Surgical and Diagnostic Sciences, University of Genoa and IRCCS S. Martino/IST University Hospital, Genoa, Italy
| | | | - Arnaud Roth
- Oncosurgery Unit, Geneva University Hospital, Geneva, Switzerland
| | - Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - Mauro Delorenzi
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland. Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fredrik T Bosman
- Institute of Pathology, University of Lausanne, Lausanne, Switzerland
| | - Roberto Fiocca
- Division of Anatomic Pathology, Department of Surgical and Diagnostic Sciences, University of Genoa and IRCCS S. Martino/IST University Hospital, Genoa, Italy.
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8
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Nygård SB, Vainer B, Nielsen SL, Bosman F, Tejpar S, Roth A, Delorenzi M, Brünner N, Budinska E. DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer. Clin Cancer Res 2015; 22:1621-31. [PMID: 26542057 DOI: 10.1158/1078-0432.ccr-15-0561] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Prospective-retrospective assessment of the TOP1 gene copy number and TOP1 mRNA expression as predictive biomarkers for adjuvant irinotecan in stage II/III colon cancer. EXPERIMENTAL DESIGN Formalin-fixed, paraffin-embedded tissue microarrays were obtained from an adjuvant colon cancer trial (PETACC3) where patients were randomized to 5-fluorouracil/folinic acid with or without additional irinotecan. TOP1 copy number status was analyzed by fluorescence in situ hybridization (FISH) using a TOP1/CEN20 dual-probe combination. TOP1 mRNA data were available from previous analyses. RESULTS TOP1 FISH and follow-up data were obtained from 534 patients. TOP1 gain was identified in 27% using a single-probe enumeration strategy (≥4 TOP1 signals per cell) and in 31% when defined by a TOP1/CEN20 ratio ≥ 1.5. The effect of additional irinotecan was not dependent on TOP1 FISH status.TOP1 mRNA data were available from 580 patients with stage III disease. Benefit of irinotecan was restricted to patients characterized by TOP1 mRNA expression ≥ third quartile (RFS: HRadjusted, 0.59;P= 0.09; OS: HRadjusted, 0.44;P= 0.03). The treatment by TOP1 mRNA interaction was not statistically significant, but in exploratory multivariable fractional polynomial interaction analysis, increasing TOP1 mRNA values appeared to be associated with increasing benefit of irinotecan. CONCLUSIONS In contrast to the TOP1 copy number, a trend was demonstrated for a predictive property of TOP1 mRNA expression. On the basis of TOP1 mRNA, it might be possible to identify a subgroup of patients where an irinotecan doublet is a clinically relevant option in the adjuvant setting of colon cancer.
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Affiliation(s)
- Sune Boris Nygård
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Ben Vainer
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Signe Lykke Nielsen
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Fred Bosman
- University of Lausanne, University Institute of Pathology, Lausanne, Switzerland
| | - Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium
| | - Arnaud Roth
- Oncosurgery Unit, University Hospital of Geneva, Geneva, Switzerland
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland. University of Lausanne, Ludwig Center for Cancer Research, Lausanne, Switzerland. Oncology Department, University of Lausanne, Lausanne, Switzerland
| | - Nils Brünner
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| | - Eva Budinska
- Masaryk University, Institute of Biostatistics and Analyses, Brno, Czech Republic
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Single Nucleotide Polymorphism (rs4932178) in the P1 Promoter of FURIN Is Not Prognostic to Colon Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:321276. [PMID: 26137475 PMCID: PMC4475562 DOI: 10.1155/2015/321276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/18/2015] [Accepted: 01/26/2015] [Indexed: 01/05/2023]
Abstract
High expression of the proprotein processing enzyme FURIN has been associated with tumor progression and metastasis. A SNP (rs4932178) in the promoter of FURIN has been reported to affect expression in liver, with the T allele resulting in higher expression than the C allele. In this study we have investigated the association of this SNP with prognostic and biological subgroups of colorectal cancer (CRC). In a panel of 1382 patients with CRC, this SNP had no impact on overall survival or on postoperative risk of relapse. This SNP also could not be linked with FURIN expression levels in CRC samples from the patients. Furthermore, we demonstrate in luciferase reporter experiments in the colon cancer cell lines Caco-2 and SW480 and in the hepatocellular carcinoma cell line Huh 7 that expression is not affected by the SNP. Since, FURIN inhibition in human colon cancer cell lines has previously been shown to repress tumor metastases, association between FURIN gene expression levels and postoperative relapse-free survival was also investigated. However, no association could be found. Altogether, we could not confirm an effect of the SNP on FURIN expression in vitro and no correlations could be found in vivo with FURIN expression or outcome.
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Abstract
The discovery of biomarkers that provide information on drug efficacy is recognized as essential for successful and cost-effective treatment of cancer. However, biomarker discovery is difficult, and requires multiple independent studies to identify a target that serves as a suitable predictor of efficacy and to ensure appropriate biomarker validation. Clinical trials that are performed, sometimes sequentially, in Europe, the USA or Asia, are often similar in their design, in part owing to regulatory, marketing, or safety considerations. We believe some of these trials offer additional unique opportunities for biomarker discovery or validation. There are multiple hurdles to overcome, such as homogenous tissue acquisition and analysis, defining and aligning biomarker hypotheses across trials, and the need to adapt sample sizes and trial designs. Nevertheless, we believe that a collaborative engagement of the academic, regulatory and pharmaceutical community can go a long way in addressing these issues and producing more-rapid results in the field of personalized medicine. In this Perspectives, we describe our views on the current fragmented approach to biomarker discovery and validation in relevant trials run within our own regions-that is, Europe, China, and the USA-and hope this article serves as a base for further reflection.
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11
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Klingbiel D, Saridaki Z, Roth AD, Bosman FT, Delorenzi M, Tejpar S. Prognosis of stage II and III colon cancer treated with adjuvant 5-fluorouracil or FOLFIRI in relation to microsatellite status: results of the PETACC-3 trial. Ann Oncol 2015; 26:126-132. [PMID: 25361982 DOI: 10.1093/annonc/mdu499] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Although colon cancer (CC) with microsatellite instability (MSI) has a more favorable prognosis than microsatellite stable (MSS) CC, the impact varies according to clinicopathological parameters. We studied how MSI status affects prognosis in a trial-based cohort of stage II and III CC patients treated with 5-fluorouracil (5-FU)/leucovorin or FOLFIRI. MATERIALS AND METHODS Tissue specimens of 1254 patients were tested for 10 different loci and were classified as MSI-high (MSI-H) when three or more loci were unstable and MSS otherwise. Study end points were overall survival (OS) and relapse-free survival (RFS). RESULTS In stage II, RFS and OS were better for patients with MSI-H than with MSS CC [hazard ratio (HR) 0.26, 95% CI 0.10-0.65, P = 0.004 and 0.16, 95% CI 0.04-0.64, P = 0.01). In stage III, RFS was slightly better for patients with MSI-H CC (HR 0.67, 95% CI 0.46-0.99, P = 0.04), but the difference was not statistically significant for OS (HR 0.70, 95% CI 0.44-1.09, P = 0.11). Outcomes for patients with MSI-H CC were not different between the two treatment arms. RFS was better for patients with MSI-H than with MSS CC in the right and left colon, whereas for OS this was significant only in the right colon. For patients with KRAS- and BRAF-mutated CC, but not for double wild-type patients, RFS and OS were significantly better when the tumors were also MSI-H. An interaction test was statistically significant for KRAS and MSI status (P = 0.005), but not for BRAF status (P = 0.14). CONCLUSIONS Our results confirm that for patients with stage II CC but less so for those with stage III MSI-H is strongly prognostic for RFS and OS. In the presence of 5-FU treatment, stage II patients with MSI-H tumors maintain their survival advantage in comparison with MSS patients and adding irinotecan has no added benefit. CLINICALTRIALS.GOV IDENTIFIER: NCT00026273.
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Affiliation(s)
- D Klingbiel
- SAKK Swiss Group for Clinical Cancer Research, Coordinating Center, Bern; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Z Saridaki
- Laboratory of Tumor Cell Biology School of Medicine, University of Crete, Heraklion, Greece; Center for Human Genetics O&N1, Katholieke Universiteit Leuven, Leuven, Belgium
| | - A D Roth
- Oncosurgery Unit, Geneva University Hospital, Geneva
| | - F T Bosman
- Department of Pathology, Lausanne University, Lausanne
| | - M Delorenzi
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Ludwig Center for Cancer Research; Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - S Tejpar
- Center for Human Genetics O&N1, Katholieke Universiteit Leuven, Leuven, Belgium; Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.
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12
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Di Narzo AF, Tejpar S, Rossi S, Yan P, Popovici V, Wirapati P, Budinska E, Xie T, Estrella H, Pavlicek A, Mao M, Martin E, Scott W, Bosman FT, Roth A, Delorenzi M. Test of Four Colon Cancer Risk-Scores in Formalin Fixed Paraffin Embedded Microarray Gene Expression Data. J Natl Cancer Inst 2014; 106. [DOI: 10.1093/jnci/dju247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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13
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Missiaglia E, Jacobs B, D'Ario G, Di Narzo AF, Soneson C, Budinska E, Popovici V, Vecchione L, Gerster S, Yan P, Roth AD, Klingbiel D, Bosman FT, Delorenzi M, Tejpar S. Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features. Ann Oncol 2014; 25:1995-2001. [PMID: 25057166 DOI: 10.1093/annonc/mdu275] [Citation(s) in RCA: 455] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Differences exist between the proximal and distal colon in terms of developmental origin, exposure to patterning genes, environmental mutagens, and gut flora. Little is known on how these differences may affect mechanisms of tumorigenesis, side-specific therapy response or prognosis. We explored systematic differences in pathway activation and their clinical implications. MATERIALS AND METHODS Detailed clinicopathological data for 3045 colon carcinoma patients enrolled in the PETACC3 adjuvant chemotherapy trial were available for analysis. A subset of 1404 samples had molecular data, including gene expression and DNA copy number profiles for 589 and 199 samples, respectively. In addition, 413 colon adenocarcinoma from TCGA collection were also analyzed. Tumor side-effect on anti-epidermal growth factor receptor (EGFR) therapy was assessed in a cohort of 325 metastatic patients. Outcome variables considered were relapse-free survival and survival after relapse (SAR). RESULTS Proximal carcinomas were more often mucinous, microsatellite instable (MSI)-high, mutated in key tumorigenic pathways, expressed a B-Raf proto-oncogene, serine/threonine kinase (BRAF)-like and a serrated pathway signature, regardless of histological type. Distal carcinomas were more often chromosome instable and EGFR or human epidermal growth factor receptor 2 (HER2) amplified, and more frequently overexpressed epiregulin. While risk of relapse was not different per side, SAR was much poorer for proximal than for distal stage III carcinomas in a multivariable model including BRAF mutation status [N = 285; HR 1.95, 95% CI (1.6-2.4), P < 0.001]. Only patients with metastases from a distal carcinoma responded to anti-EGFR therapy, in line with the predictions of our pathway enrichment analysis. CONCLUSIONS Colorectal carcinoma side is associated with differences in key molecular features, some immediately druggable, with important prognostic effects which are maintained in metastatic lesions. Although within side significant molecular heterogeneity remains, our findings justify stratification of patients by side for retrospective and prospective analyses of drug efficacy and prognosis.
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Affiliation(s)
- E Missiaglia
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - B Jacobs
- Molecular Digestive Oncology Unit, University Hospital Leuven, Leuven, Belgium
| | - G D'Ario
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - A F Di Narzo
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - C Soneson
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - E Budinska
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - V Popovici
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - L Vecchione
- Molecular Digestive Oncology Unit, University Hospital Leuven, Leuven, Belgium
| | - S Gerster
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - P Yan
- Department of Pathology, Lausanne University, Lausanne
| | - A D Roth
- Oncosurgery Unit, Geneva University Hospital, Geneva
| | - D Klingbiel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; The Swiss Group for Clinical Cancer Research (SAKK) Coordinating Center, Bern
| | - F T Bosman
- Department of Pathology, Lausanne University, Lausanne
| | - M Delorenzi
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Ludwig Center for Cancer Research; Oncology Department, University of Lausanne, Lausanne, Switzerland
| | - S Tejpar
- Molecular Digestive Oncology Unit, University Hospital Leuven, Leuven, Belgium.
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Saridaki Z, Souglakos J, Georgoulias V. Prognostic and predictive significance of MSI in stages II/III colon cancer. World J Gastroenterol 2014; 20:6809-6814. [PMID: 24944470 PMCID: PMC4051919 DOI: 10.3748/wjg.v20.i22.6809] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/29/2013] [Accepted: 03/05/2014] [Indexed: 02/07/2023] Open
Abstract
In colon cancer, classic disease staging remains the key prognosis and treatment determinant. Although adjuvant chemotherapy has an established role in stage III colon cancer patients, in stage II it is still a subject of controversy due to its restriction to a small subgroup of patients with high-risk histopathologic features. Patients with stage II tumors form a highly heterogeneous group, with five-year relative overall survival rates ranging from 87.5% (IIA) to 58.4% (IIC). Identifying those for whom adjuvant chemotherapy would be appropriate and necessary has been challenging, and prognostic markers which could serve in the selection of patients more likely to recur or benefit from adjuvant chemotherapy are eagerly needed. The stronger candidate in this category seems to be microsatellite instability (MSI). The recently reported European Society for Medical Oncology guidelines suggest that MSI should be evaluated in stage II colorectal cancer patients in order to contribute in treatment decision-making regarding chemotherapy administration. The hypothetical predictive role of MSI regarding its response to 5-fluorouracil-based adjuvant chemotherapy has proven a much more difficult issue to address. Almost every possible relation between MSI and chemotherapy outcome has been described in the adjuvant colon cancer setting in the international literature, and the matter is far from being settled. In this current report we critically evaluate the prognostic and predictive impact of MSI status in patients with stage II and stage III colon cancer patients.
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15
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Eissa S, Matboli M. Integrated technologies in the post-genomic era for discovery of bladder cancer urinary markers. World J Clin Urol 2013; 2:20-31. [DOI: 10.5410/wjcu.v2.i3.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/10/2013] [Accepted: 11/21/2013] [Indexed: 02/06/2023] Open
Abstract
The incidence of bladder cancer (BC) continues to rise with high recurrence and mortality rate, especially in the past three decades. The development of accurate and successful BC treatment relies mainly on early diagnosis. BC is a heterogeneous disease reflected by the presence of many potential biomarkers associated with different disease phenotypes. Nowadays, cystoscopy and urinary cytology are considered the gold standard diagnostic tools for BC. There are many limitations to cystoscopy including being invasive, labor-intensive and carcinoma in situ of the bladder may easily be missed. Urinary cytology is still a noninvasive technique with high accuracy in high-grade BC with a median sensitivity of 35%. Furthermore, the need for a sensitive, specific, non invasive, easily accessible BC biomarker is a major clinical need. The field of urinary BC biomarkers discovery is still a rapidly evolving discipline in which more recent technologies are evaluated and often optimized if they are not clinically significant to the urologists. Most of the current strategies for BC urinary biomarker detection depend on integration of information gleaned from the fields of genomics, transcriptomics, proteomics, epigenetics, metabolomics and bionanotechnology. Effort is currently being made to identify the most potentially beneficial urinary biomarkers. The purpose of this review is to summarize and explore the efficacy of gathering the information revealed from the cooperation of different omic strategies that paves the way towards various urinary markers discovery for screening, diagnosis and prognosis of human BC.
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Thomas M, Poignée-Heger M, Weisser M, Wessner S, Belousov A. An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples. J Clin Bioinforma 2013; 3:10. [PMID: 23641797 PMCID: PMC3660273 DOI: 10.1186/2043-9113-3-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whole genome microarray gene expression profiling is the 'gold standard' for the discovery of prognostic and predictive genetic markers for human cancers. However, suitable research material is lacking as most diagnostic samples are preserved as formalin-fixed, paraffin-embedded tissue (FFPET). We tested a new workflow and data analysis method optimized for use with FFPET samples. METHODS Sixteen breast tumor samples were split into matched pairs and preserved as FFPET or fresh-frozen (FF). Total RNA was extracted and tested for yield and purity. RNA from FFPET samples was amplified using three different commercially available kits in parallel, and hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays. The array probe set was optimized in silico to exclude misdesigned and misannotated probes. RESULTS FFPET samples processed using the WT-Ovation™ FFPE System V2 (NuGEN) provided 80% specificity and 97% sensitivity compared with FF samples (assuming values of 100%). In addition, in silico probe set redesign improved sequence detection sensitivity and, thus, may rescue potentially significant small-magnitude gene expression changes that could otherwise be diluted by the overall probe set background. CONCLUSION In conclusion, our FFPET-optimized workflow enables the detection of more genes than previous, nonoptimized approaches, opening new possibilities for the discovery, validation, and clinical application of mRNA biomarkers in human diseases.
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Affiliation(s)
- Marlene Thomas
- Pharma Research and Early Development (pRED), Roche Diagnostics GmbH, TR-H, Bldg 231/206a, Nonnenwald 2, 82377 Penzberg, Germany.
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17
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Rossi S, Di Narzo AF, Mestdagh P, Jacobs B, Bosman FT, Gustavsson B, Majoie B, Roth A, Vandesompele J, Rigoutsos I, Delorenzi M, Tejpar S. microRNAs in colon cancer: a roadmap for discovery. FEBS Lett 2012; 586:3000-7. [PMID: 23166923 DOI: 10.1016/j.febslet.2012.07.048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer omics data are exponentially created and associated with clinical variables, and important findings can be extracted based on bioinformatics approaches which can then be experimentally validated. Many of these findings are related to a specific class of non-coding RNA molecules called microRNAs (miRNAs) (post-transcriptional regulators of mRNA expression). The related research field is quite heterogeneous and bioinformaticians, clinicians, statisticians and biologists, as well as data miners and engineers collaborate to cure stored data and on new impulses coming from the output of the latest Next Generation Sequencing technologies. Here we review the main research findings on miRNA of the first 10 years in colon cancer research with an emphasis on possible uses in clinical practice. This review intends to provide a road map in the jungle of publications of miRNA in colorectal cancer, focusing on data availability and new ways to generate biologically relevant information out of these huge amounts of data.
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Affiliation(s)
- Simona Rossi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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18
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Roth AD, Delorenzi M, Tejpar S, Yan P, Klingbiel D, Fiocca R, d'Ario G, Cisar L, Labianca R, Cunningham D, Nordlinger B, Bosman F, Van Cutsem E. Integrated analysis of molecular and clinical prognostic factors in stage II/III colon cancer. J Natl Cancer Inst 2012; 104:1635-46. [PMID: 23104212 DOI: 10.1093/jnci/djs427] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The prognostic potential of individual clinical and molecular parameters in stage II/III colon cancer has been investigated, but a thorough multivariable assessment of their relative impact is missing. METHODS Tumors from patients (N = 1404) in the PETACC3 adjuvant chemotherapy trial were examined for BRAF and KRAS mutations, microsatellite instability (MSI), chromosome 18q loss of heterozygosity (18qLOH), and SMAD4 expression. Their importance in predicting relapse-free survival (RFS) and overall survival (OS) was assessed by Kaplan-Meier analyses, Cox regression models, and recursive partitioning trees. All statistical tests were two-sided. RESULTS MSI-high status and SMAD4 focal loss of expression were identified as independent prognostic factors with better RFS (hazard ratio [HR] of recurrence = 0.54, 95% CI = 0.37 to 0.81, P = .003) and OS (HR of death = 0.43, 95% CI = 0.27 to 0.70, P = .001) for MSI-high status and worse RFS (HR = 1.47, 95% CI = 1.19 to 1.81, P < .001) and OS (HR = 1.58, 95% CI = 1.23 to 2.01, P < .001) for SMAD4 loss. 18qLOH did not have any prognostic value in RFS or OS. Recursive partitioning identified refinements of TNM into new clinically interesting prognostic subgroups. Notably, T3N1 tumors with MSI-high status and retained SMAD4 expression had outcomes similar to stage II disease. CONCLUSIONS Concomitant assessment of molecular and clinical markers in multivariable analysis is essential to confirm or refute their independent prognostic value. Including molecular markers with independent prognostic value might allow more accurate prediction of prognosis than TNM staging alone.
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Affiliation(s)
- Arnaud D Roth
- Oncosurgery Unit, Geneva University Hospital, Geneva, Switzerland.
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Implications for Powering Biomarker Discovery Studies. J Mol Diagn 2012; 14:130-9. [DOI: 10.1016/j.jmoldx.2011.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 10/03/2011] [Accepted: 10/25/2011] [Indexed: 12/18/2022] Open
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Gray RG, Quirke P, Handley K, Lopatin M, Magill L, Baehner FL, Beaumont C, Clark-Langone KM, Yoshizawa CN, Lee M, Watson D, Shak S, Kerr DJ. Validation study of a quantitative multigene reverse transcriptase-polymerase chain reaction assay for assessment of recurrence risk in patients with stage II colon cancer. J Clin Oncol 2011; 29:4611-9. [PMID: 22067390 DOI: 10.1200/jco.2010.32.8732] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE We developed quantitative gene expression assays to assess recurrence risk and benefits from chemotherapy in patients with stage II colon cancer. PATIENTS AND METHODS We sought validation by using RNA extracted from fixed paraffin-embedded primary colon tumor blocks from 1,436 patients with stage II colon cancer in the QUASAR (Quick and Simple and Reliable) study of adjuvant fluoropyrimidine chemotherapy versus surgery alone. A recurrence score (RS) and a treatment score (TS) were calculated from gene expression levels of 13 cancer-related genes (n = 7 recurrence genes and n = 6 treatment benefit genes) and from five reference genes with prespecified algorithms. Cox proportional hazards regression models and log-rank methods were used to analyze the relationship between the RS and risk of recurrence in patients treated with surgery alone and between TS and benefits of chemotherapy. RESULTS Risk of recurrence was significantly associated with RS (hazard ratio [HR] per interquartile range, 1.38; 95% CI, 1.11 to 1.74; P = .004). Recurrence risks at 3 years were 12%, 18%, and 22% for predefined low, intermediate, and high recurrence risk groups, respectively. T stage (HR, 1.94; P < .001) and mismatch repair (MMR) status (HR, 0.31; P < .001) were the strongest histopathologic prognostic factors. The continuous RS was associated with risk of recurrence (P = .006) beyond these and other covariates. There was no trend for increased benefit from chemotherapy at higher TS (P = .95). CONCLUSION The continuous 12-gene RS has been validated in a prospective study for assessment of recurrence risk in patients with stage II colon cancer after surgery and provides prognostic value that complements T stage and MMR. The TS was not predictive of chemotherapy benefit.
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Baraniskin A, Munding J, Schulmann K, Meier D, Porschen R, Arkenau HT, Graeven U, Schmiegel W, Tannapfel A, Reinacher-Schick A. Prognostic value of reduced SMAD4 expression in patients with metastatic colorectal cancer under oxaliplatin-containing chemotherapy: a translational study of the AIO colorectal study group. Clin Colorectal Cancer 2011; 10:24-9. [PMID: 21609932 DOI: 10.3816/ccc.2011.n.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND SMAD4 is a polypeptide with tumor suppressor function being investigated as a prognostic biomarker in Union Internationale Contre le Cancer stages II and III in previous studies, but its role as a prognostic marker in stage IV colorectal cancer (CRC) is still undefined. We investigated the prognostic value of reduced SMAD4 expression in patients with metastatic (mCRC) under first-line oxaliplatin-containing combination chemotherapy. PATIENTS AND METHODS Tumor samples were obtained from patients who took part in a prospective randomized phase III chemotherapy trial of the Arbeitsgemeinschaft Internistische Onkologie of the German Cancer Society colorectal study group, comparing the use of capecitabine plus oxaliplatin with infusional 5-fluorouracil (5-FU) plus oxaliplatin as first-line therapy in mCRC. SMAD4 expression was determined by immunohistochemistry. RESULTS Tumor tissues from 230 patients were obtained. Reduced SMAD4 expression was identified in 34% of samples. Patients with reduced nuclear SMAD4 expression in tumor tissue showed a shorter progression-free survival (PFS; 7.0 months vs. 8.9 months; P = .024) and overall survival (OS; 13.9 months vs. 17.8 months; P = .044) compared with patients retaining SMAD4 expression. The effect of SMAD4 expression on PFS and OS could be demonstrated in univariate and multivariate analyses. CONCLUSION Our data demonstrate the importance of reduced SMAD4 expression in patients with mCRC receiving chemotherapy with oxaliplatin and 5-FU.
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Affiliation(s)
- Alexander Baraniskin
- Department of Internal Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Germany
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Abstract
Colon cancer (CC) therapies have improved patient outcomes significantly over the last decades in both the adjuvant and metastatic settings. With the introduction of a number of novel agents, both traditional chemotherapies and biologically targeted agents, the need to identify subgroups that are likely and not likely to respond to a particular treatment regimen is paramount. This will allow patients who are likely to benefit to receive optimal care, while sparing those unlikely to benefit from unnecessary toxicity and cost. With the identification of several novel biomarkers and a variety of technologies to interrogate the genome, we already are able to rapidly study patient tumor or blood samples and normal tissues to generate a large dataset of aberrations within the cancer. How to digest this complex information to obtain accurate, reliable, and meaningful results that will allow us to provide truly personalized care for CC patients is just starting to be addressed. In this article, we briefly review the history of CC treatment, with an emphasis on current clinical standards that incorporate a "personalized medicine" approach. We then review strategies that will potentially improve our ability to individualize therapy in the future.
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Smith SC, Baras AS, Dancik G, Ru Y, Ding KF, Moskaluk CA, Fradet Y, Lehmann J, Stöckle M, Hartmann A, Lee JK, Theodorescu D. A 20-gene model for molecular nodal staging of bladder cancer: development and prospective assessment. Lancet Oncol 2011; 12:137-43. [PMID: 21256081 DOI: 10.1016/s1470-2045(10)70296-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Neoadjuvant chemotherapy before cystectomy confers a survival benefit in bladder cancer, but it has not been widely adopted since most patients do not benefit and we are at present unable to predict those that do. Since the most important predictor of recurrence after cystectomy is pathologically positive nodes, our aim was to assess techniques that define this stage for the selection of patients for neoadjuvant chemotherapy. METHODS We developed a gene expression model (GEM) to predict the pathological node status in primary tumour tissue from three independent cohorts of patients who were clinically node negative. From a subset of transcripts detected faithfully by microarrays from both paired frozen and formalin-fixed tissues (32 pairs), we developed both the GEM and cutoffs that identified patient strata with raised risk of nodal involvement by use of two separate training cohorts (90 and 66 patients). We then assessed the GEM and cutoffs to predict node-positive disease in tissues from a phase 3 trial cohort (AUO-AB-05/95; 185 patients). FINDINGS We developed a 20-gene GEM with an area under the curve of 0·67 (95% CI 0·60-0·75) for prediction of nodal disease at cystectomy in AUO-AB-05/95. The cutoff system identified patients with high relative risk (1·74, 95% CI 1·03-2·93) and low relative risk (0·70, 95% CI 0·51-0·96) of node-positive disease. Multivariate logistic regression showed the GEM predictor was independent of age, sex, pathological stage, and lymphovascular space invasion (coefficient 9·81, 95% CI 1·64-18·00; p=0·019). INTERPRETATION Selecting patients for neoadjuvant chemotherapy on the basis of risk of node-positive disease has the potential to benefit high-risk patients while sparing other patients toxic effects and delay to cystectomy. FUNDING US National Cancer Institute (R01CA143971).
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Tejpar S, Bertagnolli M, Bosman F, Lenz HJ, Garraway L, Waldman F, Warren R, Bild A, Collins-Brennan D, Hahn H, Harkin DP, Kennedy R, Ilyas M, Morreau H, Proutski V, Swanton C, Tomlinson I, Delorenzi M, Fiocca R, Van Cutsem E, Roth A. Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist 2010; 15:390-404. [PMID: 20350999 PMCID: PMC3227961 DOI: 10.1634/theoncologist.2009-0233] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The number of agents that are potentially effective in the adjuvant treatment of locally advanced resectable colon cancer is increasing. Consequently, it is important to ascertain which subgroups of patients will benefit from a specific treatment. Despite more than two decades of research into the molecular genetics of colon cancer, there is a lack of prognostic and predictive molecular biomarkers with proven utility in this setting. A secondary objective of the Pan European Trials in Adjuvant Colon Cancer-3 trial, which compared irinotecan in combination with 5-fluorouracil and leucovorin in the postoperative treatment of stage III and stage II colon cancer patients, was to undertake a translational research study to assess a panel of putative prognostic and predictive markers in a large colon cancer patient cohort. The Cancer and Leukemia Group B 89803 trial, in a similar design, also investigated the use of prognostic and predictive biomarkers in this setting. In this article, the authors, who are coinvestigators from these trials and performed similar investigations of biomarker discovery in the adjuvant treatment of colon cancer, review the current status of biomarker research in this field, drawing on their experiences and considering future strategies for biomarker discovery in the postgenomic era.
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Affiliation(s)
- Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium.
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Mishra A, Verma M. Cancer biomarkers: are we ready for the prime time? Cancers (Basel) 2010; 2:190-208. [PMID: 24281040 PMCID: PMC3827599 DOI: 10.3390/cancers2010190] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 03/02/2010] [Accepted: 03/19/2010] [Indexed: 12/16/2022] Open
Abstract
A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. In cancer, a biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker might be either a molecule secreted by a tumor or it can be a specific response of the body to the presence of cancer. Genetic, epigenetic, proteomic, glycomic, and imaging biomarkers can be used for cancer diagnosis, prognosis and epidemiology. These markers can be assayed in non-invasively collected biofluids. However, few cancer biomarkers are highly sensitive and specific for cancer detection at the present time. Consequently, biomarkers are not yet ready for routine use due to challenges in their clinical validation for early disease detection, diagnosis and monitoring to improve long-term survival of patients.
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Affiliation(s)
- Alok Mishra
- Institute of Cytology and Preventive Oncology, Division of Molecular Oncology, Noida, 201301, UP, India; E-Mail:
| | - Mukesh Verma
- Methods and Technologies Branch, Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institues of Health (NIH), 6130 Executive Blvd., Suite 5100, Bethesda, MD 20892-7324, USA
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Tanney A, Kennedy RD. Developing mRNA-based biomarkers from formalin-fixed paraffin-embedded tissue. Per Med 2010; 7:205-211. [DOI: 10.2217/pme.10.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cancer is a complex and heterogeneous disease which is one of the leading causes of death in Western civilisations. Thus, oncology is viewed as a primary focus for personalized medicine. It is recognised that cancer treatment needs to be better tailored in order to improve patient outcome. Patient tumor samples will be required to characterize cancer at a molecular level and identify where there may be disease subgroups that should be treated differently. The use of formalin-fixed paraffin-embedded tissue is important for enabling such studies. In this report, we focus on the challenges that have been faced to date along with the technological developments that have now made this possible. We also highlight the impact this may have on drug and diagnostic development.
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Affiliation(s)
- Austin Tanney
- Almac Diagnostics, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
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