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Zuo A, Li J, Weng S, Xu H, Zhang Y, Wang L, Xing Z, Luo P, Cheng Q, Li J, Han X, Liu Z. Integrated Exploration of Epigenetic Dysregulation Reveals a Stemness/EMT Subtype and MMP12 Linked to the Progression and Prognosis in Hepatocellular Carcinoma. J Proteome Res 2024; 23:1821-1833. [PMID: 38652053 DOI: 10.1021/acs.jproteome.4c00036] [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] [Indexed: 04/25/2024]
Abstract
Epigenetic dysregulation drives aberrant transcriptional programs playing a critical role in hepatocellular carcinoma (HCC), which may provide novel insights into the heterogeneity of HCC. This study performed an integrated exploration on the epigenetic dysregulation of miRNA and methylation. We discovered and validated three patterns endowed with gene-related transcriptional traits and clinical outcomes. Specially, a stemness/epithelial-mesenchymal transition (EMT) subtype was featured by immune exhaustion and the worst prognosis. Besides, MMP12, a characteristic gene, was highly expressed in the stemness/EMT subtype, which was verified as a pivotal regulator linked to the unfavorable prognosis and further proven to promote tumor proliferation, invasion, and metastasis in vitro experiments. Proteomic analysis by mass spectrometry sequencing also indicated that the overexpression of MMP12 was significantly associated with cell proliferation and adhesion. Taken together, this study unveils innovative insights into epigenetic dysregulation and identifies a stemness/EMT subtype-specific gene, MMP12, correlated with the progression and prognosis of HCC.
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Affiliation(s)
- Anning Zuo
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinyu Li
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jing Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Sehgal M, Ramu S, Vaz JM, Ganapathy YR, Muralidharan S, Venkatraghavan S, Jolly MK. Characterizing heterogeneity along EMT and metabolic axes in colorectal cancer reveals underlying consensus molecular subtype-specific trends. Transl Oncol 2024; 40:101845. [PMID: 38029508 PMCID: PMC10698572 DOI: 10.1016/j.tranon.2023.101845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
Colorectal cancer (CRC) is highly heterogeneous with variable survival outcomes and therapeutic vulnerabilities. A commonly used classification system in CRC is the Consensus Molecular Subtypes (CMS) based on gene expression patterns. However, how these CMS categories connect to axes of phenotypic plasticity and heterogeneity remains unclear. Here, in our analysis of CMS-specific TCGA data and 101 bulk transcriptomic datasets, we found the epithelial phenotype score to be consistently positively correlated with scores of glycolysis, OXPHOS and FAO pathways, while PD-L1 activity scores positively correlated with mesenchymal phenotype scoring, revealing possible interconnections among plasticity axes. Single-cell RNA-sequencing analysis of patient samples revealed that that CMS2 and CMS3 subtype samples were relatively more epithelial as compared to CMS1 and CMS4. CMS1 revealed two subpopulations: one close to CMS4 (more mesenchymal) and the other closer to CMS2 or CMS3 (more epithelial), indicating a partial EMT-like behavior. Consistent observations were made in single-cell analysis of metabolic axes and PD-L1 activity scores. Together, our results quantify the patterns of two functional interconnected axes of phenotypic heterogeneity - EMT and metabolic reprogramming - in a CMS-specific manner in CRC.
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Affiliation(s)
- Manas Sehgal
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Joel Markus Vaz
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, United States
| | | | - Srinath Muralidharan
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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3
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Zhu Y, Huang C, Zhang C, Zhou Y, Zhao E, Zhang Y, Pan X, Huang H, Liao W, Wang X. LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation. Nat Commun 2023; 14:8141. [PMID: 38065939 PMCID: PMC10709323 DOI: 10.1038/s41467-023-43974-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
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Grants
- 2020N368 Shenzhen Science and Technology Innovation Commission
- C4024-22GF Research Grants Council, University Grants Committee (RGC, UGC)
- 14104223 Research Grants Council, University Grants Committee (RGC, UGC)
- 11103619 Research Grants Council, University Grants Committee (RGC, UGC)
- 14111522 Research Grants Council, University Grants Committee (RGC, UGC)
- R4017-18 Research Grants Council, University Grants Committee (RGC, UGC)
- 82173289 National Natural Science Foundation of China (National Science Foundation of China)
- 81872401 National Natural Science Foundation of China (National Science Foundation of China)
- Guangdong Basic and Applied Basic Research Foundation (Project No.2019B030302012), a startup grant (Project No. 4937084), direct grant (2021.077), Faculty Postdoctoral Fellowship Scheme 2021/22 (Project No. FPFS/2122/32), Shenzhen Bay Scholars Program.
- Guangdong Basic and Applied Basic Research Foundation (2021A1515010425)
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Affiliation(s)
- Yixiao Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chengmei Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yi Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Enen Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yaxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xingyan Pan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Wenting Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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4
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Sun P, Fan S, Li S, Zhao Y, Lu C, Wong KC, Li X. Automated exploitation of deep learning for cancer patient stratification across multiple types. Bioinformatics 2023; 39:btad654. [PMID: 37934154 PMCID: PMC10636288 DOI: 10.1093/bioinformatics/btad654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION Recent frameworks based on deep learning have been developed to identify cancer subtypes from high-throughput gene expression profiles. Unfortunately, the performance of deep learning is highly dependent on its neural network architectures which are often hand-crafted with expertise in deep neural networks, meanwhile, the optimization and adjustment of the network are usually costly and time consuming. RESULTS To address such limitations, we proposed a fully automated deep neural architecture search model for diagnosing consensus molecular subtypes from gene expression data (DNAS). The proposed model uses ant colony algorithm, one of the heuristic swarm intelligence algorithms, to search and optimize neural network architecture, and it can automatically find the optimal deep learning model architecture for cancer diagnosis in its search space. We validated DNAS on eight colorectal cancer datasets, achieving the average accuracy of 95.48%, the average specificity of 98.07%, and the average sensitivity of 96.24%, respectively. Without the loss of generality, we investigated the general applicability of DNAS further on other cancer types from different platforms including lung cancer and breast cancer, and DNAS achieved an area under the curve of 95% and 96%, respectively. In addition, we conducted gene ontology enrichment and pathological analysis to reveal interesting insights into cancer subtype identification and characterization across multiple cancer types. AVAILABILITY AND IMPLEMENTATION The source code and data can be downloaded from https://github.com/userd113/DNAS-main. And the web server of DNAS is publicly accessible at 119.45.145.120:5001.
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Affiliation(s)
- Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Jilin, China
| | - Shijie Fan
- School of Information Science and Technology, Northeast Normal University, Jilin, China
| | - Shaochuan Li
- School of Information Science and Technology, Northeast Normal University, Jilin, China
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Yingwei Zhao
- School of Information Science and Technology, Northeast Normal University, Jilin, China
| | - Chang Lu
- School of Information Science and Technology, Northeast Normal University, Jilin, China
- School of Psychology, Northeast Normal University, Jilin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin, China
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5
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Rejali L, Seifollahi Asl R, Sanjabi F, Fatemi N, Asadzadeh Aghdaei H, Saeedi Niasar M, Ketabi Moghadam P, Nazemalhosseini Mojarad E, Mini E, Nobili S. Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management. Cancers (Basel) 2023; 15:2746. [PMID: 37345083 PMCID: PMC10216373 DOI: 10.3390/cancers15102746] [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: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Romina Seifollahi Asl
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Fatemeh Sanjabi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran P.O. Box 14496-14535, Iran;
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Mahsa Saeedi Niasar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Pardis Ketabi Moghadam
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran; (L.R.); (R.S.A.); (N.F.); (H.A.A.); (M.S.N.); (P.K.M.)
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yaman Street, Chamran Expressway, Tehran P.O. Box 19857-17411, Iran;
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy;
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health—NEUROFARBA—Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
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6
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Yang IP, Yip KL, Chang YT, Chen YC, Huang CW, Tsai HL, Yeh YS, Wang JY. MicroRNAs as Predictive Biomarkers in Patients with Colorectal Cancer Receiving Chemotherapy or Chemoradiotherapy: A Narrative Literature Review. Cancers (Basel) 2023; 15:cancers15051358. [PMID: 36900159 PMCID: PMC10000071 DOI: 10.3390/cancers15051358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is associated with high mortality rates worldwide. The underlying mechanism of tumorigenesis in CRC is complex, involving genetic, lifestyle-related, and environmental factors. Although radical resection with adjuvant FOLFOX (5-fluorouracil, leucovorin, and oxaliplatin) chemotherapy and neoadjuvant chemoradiotherapy have remained mainstays of treatment for patients with stage III CRC and locally advanced rectal cancer, respectively, the oncological outcomes of these treatments are often unsatisfactory. To improve patients' chances of survival, researchers are actively searching for new biomarkers to facilitate the development of more effective treatment strategies for CRC and metastatic CRC (mCRC). MicroRNAs (miRs), small, single-stranded, noncoding RNAs, can post-transcriptionally regulate mRNA translation and trigger mRNA degradation. Recent studies have documented aberrant miR levels in patients with CRC or mCRC, and some miRs are reportedly associated with chemoresistance or radioresistance in CRC. Herein, we present a narrative review of the literature on the roles of oncogenic miRs (oncomiRs) and tumor suppressor miRs (anti-oncomiRs), some of which can be used to predict the responses of patients with CRC to chemotherapy or chemoradiotherapy. Moreover, miRs may serve as potential therapeutic targets because their functions can be manipulated using synthetic antagonists and miR mimics.
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Affiliation(s)
- I-Ping Yang
- Department of Nursing, Shu-Zen College of Medicine and Management, Kaohsiung 82144, Taiwan
| | - Kwan-Ling Yip
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yu-Tang Chang
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Division of Pediatric Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yen-Cheng Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ching-Wen Huang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Hsiang-Lin Tsai
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yung-Sung Yeh
- Division of Trauma and Surgical Critical Care, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Emergency Medicine, Faculty of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Jaw-Yuan Wang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Surgery, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Pingtung Hospital, Ministry of Health and Welfare, Pingtung 90054, Taiwan
- Correspondence:
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7
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Paz-Cabezas M, Calvo-López T, Romera-Lopez A, Tabas-Madrid D, Ogando J, Fernández-Aceñero MJ, Sastre J, Pascual-Montano A, Mañes S, Díaz-Rubio E, Perez-Villamil B. Molecular Classification of Colorectal Cancer by microRNA Profiling: Correlation with the Consensus Molecular Subtypes (CMS) and Validation of miR-30b Targets. Cancers (Basel) 2022; 14:5175. [PMID: 36358609 PMCID: PMC9656292 DOI: 10.3390/cancers14215175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Colorectal cancer is one of the most significant causes of cancer mortality worldwide. Patients stratification is central to improve clinical practice and the Consensus Molecular Subtypes (CMS) have been validated as a useful tool to predict both prognosis and treatment response. This is the first study describing that microRNA profiling can define colorectal cancer CMS subtypes as well as mRNA profiling. MicroRNAs small size facilitates its analysis in serum facilitating a real-time analysis of the disease course. Three microRNA subtypes are identified: miR-LS is associated with the low-stroma/CMS2-subtype; miR-MI with the mucinous-MSI/CMS1-subtype and miR-HS with the high-stroma/CMS4-subtype. MicroRNA novel subtypes and association to the CMS classification were externally validated using TGCA data. Analyzing both mRNAs and miRs in the same population enabled identification of miR target genes and altered biological pathways. A miR-mRNA interaction screening and regulatory network selected major miR targets and was functionally validated for the miR30b/SCL6A4 pair. Abstract Colorectal cancer consensus molecular subtypes (CMSs) are widely accepted and constitutes the basis for patient stratification to improve clinical practice. We aimed to find whether miRNAs could reproduce molecular subtypes, and to identify miRNA targets associated to the High-stroma/CMS4 subtype. The expression of 939 miRNAs was analyzed in tumors classified in CMS. TALASSO was used to find gene-miRNA interactions. A miR-mRNA regulatory network was constructed using Cytoscape. Candidate gene-miR interactions were validated in 293T cells. Hierarchical-Clustering identified three miRNA tumor subtypes (miR-LS; miR-MI; and miR-HS) which were significantly associated (p < 0.001) to the reported mRNA subtypes. miR-LS correlated with the low-stroma/CMS2; miR-MI with the mucinous-MSI/CMS1 and miR-HS with high-stroma/CMS4. MicroRNA tumor subtypes and association to CMSs were validated with TCGA datasets. TALASSO identified 1462 interactions (p < 0.05) out of 21,615 found between 176 miRs and 788 genes. Based on the regulatory network, 88 miR-mRNA interactions were selected as candidates. This network was functionally validated for the pair miR-30b/SLC6A6. We found that miR-30b overexpression silenced 3′-UTR-SLC6A6-driven luciferase expression in 293T-cells; mutation of the target sequence in the 3′-UTR-SLC6A6 prevented the miR-30b inhibitory effect. In conclusion CRC subtype classification using a miR-signature might facilitate a real-time analysis of the disease course and treatment response.
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Affiliation(s)
- Mateo Paz-Cabezas
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Tania Calvo-López
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Alejandro Romera-Lopez
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Daniel Tabas-Madrid
- Immunology and Oncology Department, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Jesus Ogando
- Immunology and Oncology Department, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - María-Jesús Fernández-Aceñero
- Surgical Pathology, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Javier Sastre
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Alberto Pascual-Montano
- Immunology and Oncology Department, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Santos Mañes
- Immunology and Oncology Department, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Eduardo Díaz-Rubio
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Beatriz Perez-Villamil
- Genomics and Microarrays Laboratory, Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdiSSC), Hospital Clinico San Carlos, 28040 Madrid, Spain
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8
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Banias L, Jung I, Chiciudean R, Gurzu S. From Dukes-MAC Staging System to Molecular Classification: Evolving Concepts in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23169455. [PMID: 36012726 PMCID: PMC9409470 DOI: 10.3390/ijms23169455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/12/2022] [Accepted: 08/18/2022] [Indexed: 11/21/2022] Open
Abstract
This historical review aimed to summarize the main changes that colorectal carcinoma (CRC) staging systems suffered over time, starting from the creation of the classical Duke’s classification, modified Astler–Coller staging, internationally used TNM (T—primary tumor, N—regional lymph nodes’ status, M—distant metastases) staging system, and ending with molecular classifications and epithelial–mesenchymal transition (EMT) concept. Besides currently used staging parameters, this paper briefly presents the author’s contribution in creating an immunohistochemical (IHC)-based molecular classification of CRC. It refers to the identification of three molecular groups of CRCs (epithelial, mesenchymal and hybrid) based on the IHC markers E-cadherin, β-catenin, maspin, and vimentin. Maspin is a novel IHC antibody helpful for tumor budding assessment, which role depends on its subcellular localization (cytoplasm vs. nuclei). The long road of updating the staging criteria for CRC has not come to an end. The newest prognostic biomarkers, aimed to be included in the molecular classifications, exert predictive roles, and become more and more important for targeted therapy decisions.
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Affiliation(s)
- Laura Banias
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania
| | - Ioan Jung
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania
| | - Rebeca Chiciudean
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania
- Correspondence: ; Tel.: +40-745-673550; Fax: +40-265-210407
| | - Simona Gurzu
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Science and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania
- Research Center of Oncopathology and Transdisciplinary Research (CCOMT), George Emil Palade University of Medicine, Pharmacy, Science and Technology, 540136 Targu Mures, Romania
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9
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Lenos KJ, Bach S, Ferreira Moreno L, Ten Hoorn S, Sluiter NR, Bootsma S, Vieira Braga FA, Nijman LE, van den Bosch T, Miedema DM, van Dijk E, Ylstra B, Kulicke R, Davis FP, Stransky N, Smolen GA, Coebergh van den Braak RRJ, IJzermans JNM, Martens JWM, Hallam S, Beggs AD, Kops GJPL, Lansu N, Bastiaenen VP, Klaver CEL, Lecca MC, El Makrini K, Elbers CC, Dings MPG, van Noesel CJM, Kranenburg O, Medema JP, Koster J, Koens L, Punt CJA, Tanis PJ, de Hingh IH, Bijlsma MF, Tuynman JB, Vermeulen L. Molecular characterization of colorectal cancer related peritoneal metastatic disease. Nat Commun 2022; 13:4443. [PMID: 35927254 PMCID: PMC9352687 DOI: 10.1038/s41467-022-32198-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/21/2022] [Indexed: 12/11/2022] Open
Abstract
A significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course of their disease. PMs are associated with a poor quality of life, significant morbidity and dismal disease outcome. To improve care for this patient group, a better understanding of the molecular characteristics of CRC-PM is required. Here we present a comprehensive molecular characterization of a cohort of 52 patients. This reveals that CRC-PM represent a distinct CRC molecular subtype, CMS4, but can be further divided in three separate categories, each presenting with unique features. We uncover that the CMS4-associated structural protein Moesin plays a key role in peritoneal dissemination. Finally, we define specific evolutionary features of CRC-PM which indicate that polyclonal metastatic seeding underlies these lesions. Together our results suggest that CRC-PM should be perceived as a distinct disease entity.
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Affiliation(s)
- Kristiaan J Lenos
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
| | - Sander Bach
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Leandro Ferreira Moreno
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Sanne Ten Hoorn
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Nina R Sluiter
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Sanne Bootsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Felipe A Vieira Braga
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Lisanne E Nijman
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Tom van den Bosch
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Daniel M Miedema
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Erik van Dijk
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Ruth Kulicke
- Celsius Therapeutics, 399 Binney Street, Cambridge, MA, 02139, USA
| | - Fred P Davis
- Celsius Therapeutics, 399 Binney Street, Cambridge, MA, 02139, USA
| | - Nicolas Stransky
- Celsius Therapeutics, 399 Binney Street, Cambridge, MA, 02139, USA
| | | | | | - Jan N M IJzermans
- Department of Surgery, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center, Rotterdam, the Netherlands & Cancer Genomics Center, Utrecht, The Netherlands
| | - Sally Hallam
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Geert J P L Kops
- Oncode Institute, Amsterdam, The Netherlands
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nico Lansu
- Oncode Institute, Amsterdam, The Netherlands
- Hubrecht institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vivian P Bastiaenen
- Amsterdam UMC location University of Amsterdam, Department of Surgery, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Charlotte E L Klaver
- Amsterdam UMC location University of Amsterdam, Department of Surgery, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Maria C Lecca
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Khalid El Makrini
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Clara C Elbers
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Mark P G Dings
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Carel J M van Noesel
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Onno Kranenburg
- Department of Surgical Oncology, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan Paul Medema
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Department of Oncogenomics, Meibergdreef 9, Amsterdam, The Netherlands
| | - Lianne Koens
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Cornelis J A Punt
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Pieter J Tanis
- Amsterdam UMC location University of Amsterdam, Department of Surgery, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Ignace H de Hingh
- Department of Surgery, Catharina Hospital, Eindhoven, the Netherlands; GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Jurriaan B Tuynman
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Meibergdreef 9, Amsterdam, The Netherlands.
- Oncode Institute, Amsterdam, The Netherlands.
- Amsterdam UMC location University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
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10
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Adam RS, Poel D, Ferreira Moreno L, Spronck JMA, de Back TR, Torang A, Gomez Barila PM, ten Hoorn S, Markowetz F, Wang X, Verheul HMW, Buffart TE, Vermeulen L. Development of a miRNA-based classifier for detection of colorectal cancer molecular subtypes. Mol Oncol 2022; 16:2693-2709. [PMID: 35298091 PMCID: PMC9297751 DOI: 10.1002/1878-0261.13210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Previously, colorectal cancer (CRC) has been classified into four distinct molecular subtypes based on transcriptome data. These consensus molecular subtypes (CMSs) have implications for our understanding of tumor heterogeneity and the prognosis of patients. So far, this classification has been based on the use of messenger RNAs (mRNAs), although microRNAs (miRNAs) have also been shown to play a role in tumor heterogeneity and biological differences between CMSs. In contrast to mRNAs, miRNAs have a smaller size and increased stability, facilitating their detection. Therefore, we built a miRNA-based CMS classifier by converting the existing mRNA-based CMS classification using machine learning (training dataset of n = 271). The performance of this miRNA-assigned CMS classifier (CMS-miRaCl) was evaluated in several datasets, achieving an overall accuracy of ~ 0.72 (0.6329-0.7987) in the largest dataset (n = 158). To gain insight into the biological relevance of CMS-miRaCl, we evaluated the most important features in the classifier. We found that miRNAs previously reported to be relevant in microsatellite-instable CRCs or Wnt signaling were important features for CMS-miRaCl. Following further studies to validate its robustness, this miRNA-based alternative might simplify the implementation of CMS classification in clinical workflows.
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Affiliation(s)
- Ronja S. Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Dennis Poel
- Department of Medical OncologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Leandro Ferreira Moreno
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Joey M. A. Spronck
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Tim R. de Back
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Arezo Torang
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Patricia M. Gomez Barila
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | - Sanne ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
| | | | - Xin Wang
- Department of Biomedical SciencesCity University of Hong KongKowloon TongHong Kong
- Shenzhen Research InstituteCity University of Hong KongShenzhenChina
| | - Henk M. W. Verheul
- Department of Medical OncologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Tineke E. Buffart
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Department of Gastrointestinal OncologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR)Center for Experimental and Molecular Medicine (CEMM)Cancer Center Amsterdam and Amsterdam Gastroenterology and MetabolismAmsterdam University Medical CentersThe Netherlands
- Oncode InstituteAmsterdamThe Netherlands
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11
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Hisamori S, Mukohyama J, Koul S, Hayashi T, Rothenberg ME, Maeda M, Isobe T, Valencia Salazar LE, Qian X, Johnston DM, Qian D, Lao K, Asai N, Kakeji Y, Gennarino VA, Sahoo D, Dalerba P, Shimono Y. Upregulation of BMI1-suppressor miRNAs (miR-200c, miR-203) during terminal differentiation of colon epithelial cells. J Gastroenterol 2022; 57:407-422. [PMID: 35244768 PMCID: PMC10091510 DOI: 10.1007/s00535-022-01865-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 02/10/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are key regulators of stem cell functions, including self-renewal and differentiation. In this study, we aimed to identify miRNAs that are upregulated during terminal differentiation in the human colon epithelium, and elucidate their role in the mechanistic control of stem cell properties. METHODS "Bottom-of-the-crypt" (EPCAM+/CD44+/CD66alow) and "top-of-the-crypt" (EPCAM+/CD44neg/CD66ahigh) epithelial cells from 8 primary colon specimens (6 human, 2 murine) were purified by flow cytometry and analyzed for differential expression of 335 miRNAs. The miRNAs displaying the highest upregulation in "top-of-the-crypt" (terminally differentiated) epithelial cells were tested for positive correlation and association with survival outcomes in a colon cancer RNA-seq database (n = 439 patients). The two miRNAs with the strongest "top-of-the-crypt" expression profile were evaluated for capacity to downregulate self-renewal effectors and inhibit in vitro proliferation of colon cancer cells, in vitro organoid formation by normal colon epithelial cells and in vivo tumorigenicity by patient-derived xenografts (PDX). RESULTS Six miRNAs (miR-200a, miR-200b, miR-200c, miR-203, miR-210, miR-345) were upregulated in "top-of-the-crypt" cells and positively correlated in expression among colon carcinomas. Overexpression of the three miRNAs with the highest inter-correlation coefficients (miR-200a, miR-200b, miR-200c) associated with improved survival. The top two over-expressed miRNAs (miR-200c, miR-203) cooperated synergistically in suppressing expression of BMI1, a key regulator of self-renewal in stem cell populations, and in inhibiting proliferation, organoid-formation and tumorigenicity of colon epithelial cells. CONCLUSION In the colon epithelium, terminal differentiation associates with the coordinated upregulation of miR-200c and miR-203, which cooperate to suppress BMI1 and disable the expansion capacity of epithelial cells.
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Affiliation(s)
- Shigeo Hisamori
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 6068507, Japan
| | - Junko Mukohyama
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.,Department of Medicine (Division of Digestive and Liver Diseases), Columbia University, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY, 10032, USA.,Digestive and Liver Disease Research Center (DLDRC), Columbia University, New York, NY, 10032, USA.,Columbia Stem Cell Initiative (CSCI), Columbia University, New York, NY, 10032, USA.,Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo, 6500017, Japan.,Department of Hepato-Biliary-Pancreatic and Gastrointestinal Surgery, International University of Health and Welfare (IUHW), Tokyo, 1088329, Japan
| | - Sanjay Koul
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.,Department of Medicine (Division of Digestive and Liver Diseases), Columbia University, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY, 10032, USA.,Digestive and Liver Disease Research Center (DLDRC), Columbia University, New York, NY, 10032, USA.,Columbia Stem Cell Initiative (CSCI), Columbia University, New York, NY, 10032, USA.,Department of Biological Sciences and Geology, Queensboro Community College (QCC), City University of New York (CUNY), New York, NY, 11364, USA
| | - Takanori Hayashi
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, 4701192, Japan
| | - Michael Evan Rothenberg
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Masao Maeda
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, 4701192, Japan.,Department of Pathology, Fujita Health University School of Medicine, Toyoake, Aichi, 4701192, Japan
| | - Taichi Isobe
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Luis Enrique Valencia Salazar
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.,Department of Medicine (Division of Digestive and Liver Diseases), Columbia University, New York, NY, 10032, USA.,Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY, 10032, USA.,Digestive and Liver Disease Research Center (DLDRC), Columbia University, New York, NY, 10032, USA.,Columbia Stem Cell Initiative (CSCI), Columbia University, New York, NY, 10032, USA
| | - Xin Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Darius Michael Johnston
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Kaiqin Lao
- Genetic Sciences Division (GSD), Thermo Fisher Scientific, South San Francisco, CA, 94080, USA
| | - Naoya Asai
- Department of Pathology, Fujita Health University School of Medicine, Toyoake, Aichi, 4701192, Japan
| | - Yoshihiro Kakeji
- Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo, 6500017, Japan
| | - Vincenzo Alessandro Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.,Department of Neurology, Columbia University, New York, NY, 10032, USA.,Department of Pediatrics, Columbia University, New York, NY, 10032, USA.,Initiative for Columbia Ataxia and Tremor (ICAT), Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Debashis Sahoo
- Department of Computer Science and Engineering and Department of Pediatrics, University of California San Diego (UCSD), San Diego, CA, 92123, USA
| | - Piero Dalerba
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA. .,Department of Medicine (Division of Digestive and Liver Diseases), Columbia University, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY, 10032, USA. .,Digestive and Liver Disease Research Center (DLDRC), Columbia University, New York, NY, 10032, USA. .,Columbia Stem Cell Initiative (CSCI), Columbia University, New York, NY, 10032, USA.
| | - Yohei Shimono
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA. .,Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, 4701192, Japan.
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12
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Kandimalla R, Shimura T, Mallik S, Sonohara F, Tsai S, Evans DB, Kim SC, Baba H, Kodera Y, Von Hoff D, Chen X, Goel A. Identification of Serum miRNA Signature and Establishment of a Nomogram for Risk Stratification in Patients With Pancreatic Ductal Adenocarcinoma. Ann Surg 2022; 275:e229-e237. [PMID: 32398486 PMCID: PMC7648727 DOI: 10.1097/sla.0000000000003945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The aim of the study was to perform mRNA-miRNA regulatory network analyses to identify a miRNA panel for molecular subtype identification and stratification of high-risk patients with pancreatic ductal adenocarcinoma (PDAC). BACKGROUND Recent transcriptional profiling effort in PDAC has led to the identification of molecular subtypes that associate with poor survival; however, their clinical significance for risk stratification in patients with PDAC has been challenging. METHODS By performing a systematic analysis in The Cancer Genome Atlas and International Cancer Genome Consortium cohorts, we discovered a panel of miRNAs that associated with squamous and other poor molecular subtypes in PDAC. Subsequently, we used logistic regression analysis to develop models for risk stratification and Cox proportional hazard analysis to determine survival prediction probability of this signature in multiple cohorts of 433 patients with PDAC, including a tissue cohort (n = 199) and a preoperative serum cohort (n = 51). RESULTS We identified a panel of 9 miRNAs that were significantly upregulated (miR-205-5p and -934) or downregulated (miR-192-5p, 194-5p, 194-3p, 215-5p, 375-3p, 552-3p, and 1251-5p) in PDAC molecular subtypes with poor survival [squamous, area under the receiver operating characteristic curve (AUC) = 0.90; basal, AUC = 0.89; and quasimesenchymal, AUC = 0.83]. The validation of this miRNA panel in a tissue clinical cohort was a significant predictor of overall survival (hazard ratio = 2.48, P < 0.0001), and this predictive accuracy improved further in a risk nomogram which included key clinicopathological factors. Finally, we were able to successfully translate this miRNA predictive signature into a liquid biopsy-based assay in preoperative serum specimens from PDAC patients (hazard ratio: 2.85, P = 0.02). CONCLUSION We report a novel miRNA risk-stratification signature that can be used as a noninvasive assay for the identification of high-risk patients and potential disease monitoring in patients with PDAC.
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Affiliation(s)
- Raju Kandimalla
- Center for Gastrointestinal Research; Center from Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Tadanobu Shimura
- Center for Gastrointestinal Research; Center from Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Saurav Mallik
- Division of Biostatistics and Bioinformatics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Fuminori Sonohara
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Susan Tsai
- Department of Surgery, Division of Surgical Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Douglas B Evans
- Department of Surgery, Division of Surgical Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Song Cheol Kim
- Department of Hepatic and Pancreatobiliary Surgery, Asan Medical Center, Seoul, Korea
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Science, Kumamoto University, Kumamoto, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Xi Chen
- Division of Biostatistics and Bioinformatics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Ajay Goel
- Center for Gastrointestinal Research; Center from Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
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13
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Adipose stem cell niche reprograms the colorectal cancer stem cell metastatic machinery. Nat Commun 2021; 12:5006. [PMID: 34408135 PMCID: PMC8373975 DOI: 10.1038/s41467-021-25333-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 08/03/2021] [Indexed: 12/30/2022] Open
Abstract
Obesity is a strong risk factor for cancer progression, posing obesity-related cancer as one of the leading causes of death. Nevertheless, the molecular mechanisms that endow cancer cells with metastatic properties in patients affected by obesity remain unexplored. Here, we show that IL-6 and HGF, secreted by tumor neighboring visceral adipose stromal cells (V-ASCs), expand the metastatic colorectal (CR) cancer cell compartment (CD44v6 + ), which in turn secretes neurotrophins such as NGF and NT-3, and recruits adipose stem cells within tumor mass. Visceral adipose-derived factors promote vasculogenesis and the onset of metastatic dissemination by activation of STAT3, which inhibits miR-200a and enhances ZEB2 expression, effectively reprogramming CRC cells into a highly metastatic phenotype. Notably, obesity-associated tumor microenvironment provokes a transition in the transcriptomic expression profile of cells derived from the epithelial consensus molecular subtype (CMS2) CRC patients towards a mesenchymal subtype (CMS4). STAT3 pathway inhibition reduces ZEB2 expression and abrogates the metastatic growth sustained by adipose-released proteins. Together, our data suggest that targeting adipose factors in colorectal cancer patients with obesity may represent a therapeutic strategy for preventing metastatic disease. Obesity is a major risk factor for cancer related death. Here, the authors show that visceral adipose-derived factors promote vasculogenesis and metastatic dissemination by activation of STAT3, which inhibits miR-200a and enhances ZEB2 expression, effectively reprogramming colorectal cancer cells into a highly metastatic phenotype.
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14
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Adam RS, Blomberg I, Ten Hoorn S, Bijlsma MF, Vermeulen L. The recurring features of molecular subtypes in distinct gastrointestinal malignancies-A systematic review. Crit Rev Oncol Hematol 2021; 164:103428. [PMID: 34284100 DOI: 10.1016/j.critrevonc.2021.103428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022] Open
Abstract
In colorectal cancer (CRC), pancreatic ductal adenocarcinoma (PDAC) and gastric cancer (GC) multiple studies of inter-tumor heterogeneity have identified molecular subtypes, which correlate with clinical features. Our aim was to investigate the attributes of molecular subtypes across three different gastrointestinal cancer types. We performed a systematic search for publications on molecular subtypes or classifications in PDAC and GC and compared the described subtypes with the established consensus molecular subtypes of CRC. Examining the characteristics of subtypes across CRC, PDAC and GC resulted in four categories of subtypes. We describe uniting and distinguishing features within a mesenchymal, an epithelial, an immunogenic and a metabolic and digestive subtype category. We conclude that molecular subtypes of CRC, PDAC and GC display relevant overlap in molecular features and clinical outcomes. This finding encourages quantitative studies on subtypes across different cancer types and could lead to a paradigm shift in future treatment strategies.
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Affiliation(s)
- Ronja S Adam
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Ilse Blomberg
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Sanne Ten Hoorn
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental and Molecular Medicine (CEMM), Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands; Oncode Institute, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands.
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15
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The Clinical Assessment of MicroRNA Diagnostic, Prognostic, and Theranostic Value in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13122916. [PMID: 34208056 PMCID: PMC8230660 DOI: 10.3390/cancers13122916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary MiRNAs are of great interest within colorectal cancers in diagnosis, prognosis, and within the field of personalized treatments; they are present within different biological fluids such as blood and can lead to specific information for daily clinical use. Herein, we review the current literature focusing on miRNAs as potential diagnostic and prognostic biomarkers in patients treated for colorectal cancers. Detection and analysis of miRNA expression are cost-effective and lead to high sensitivity and specificity rates. However, it is now necessary to highlight the most sensitive and specific miRNAs for each goal, either diagnostic, prognostic, or theranostic, thanks to multicentric prospective studies. Abstract MiRNAs have recently become a subject of great interest within cancers and especially colorectal cancers in diagnosis, prognosis, and therapy decisions; herein we review the current literature focusing on miRNAs in colorectal cancers, and we discuss future challenges to use this tool on a daily clinical basis. In liquid biopsies, miRNAs seem easily accessible and can give important information toward each step of the management of colorectal cancers. However, it is now necessary to highlight the most sensitive and specific miRNAs for each goal thanks to multicentric prospective studies. Conclusions: by their diversity and the feasibility of their use, miRNAs are getting part of the armamentarium of healthcare management of colorectal cancers.
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16
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Ten Hoorn S, de Back TR, Sommeijer DW, Vermeulen L. Clinical Value of Consensus Molecular Subtypes in Colorectal Cancer: A Systematic Review and Meta-Analysis. J Natl Cancer Inst 2021; 114:503-516. [PMID: 34077519 PMCID: PMC9002278 DOI: 10.1093/jnci/djab106] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background The consensus molecular subtypes (CMSs) of colorectal cancer (CRC) capture tumor heterogeneity at the gene-expression level. Currently, a restricted number of molecular features are used to guide treatment for CRC. We summarize the evidence on the clinical value of the CMSs. Methods We systematically identified studies in Medline and Embase that evaluated the prognostic and predictive value of CMSs in CRC patients. A random-effect meta-analysis was performed on prognostic data. Predictive data were summarized. Results In local disease, CMS4 tumors were associated with worse overall survival (OS) compared with CMS1 (hazard ratio [HR] = 3.28, 95% confidence interval = 1.27 to 8.47) and CMS2 cancers (HR = 2.60, 95% confidence interval = 1.93 to 3.50). In metastatic disease, CMS1 consistently had worse survival than CMS2-4 (OS HR range = 0.33-0.55; progression-free survival HR range = 0.53-0.89). Adjuvant chemotherapy in stage II and III CRC was most beneficial for OS in CMS2 and CMS3 (HR range = 0.16-0.45) and not effective in CMS4 tumors. In metastatic CMS4 cancers, an irinotecan-based regimen improved outcome compared with oxaliplatin (HR range = 0.31-0.72). The addition of bevacizumab seemed beneficial in CMS1, and anti-epidermal growth factor receptor therapy improved outcome for KRAS wild-type CMS2 patients. Conclusions The CMS classification holds clear potential for clinical use in predicting both prognosis and response to systemic therapy, which seems to be independent of the classifier used. Prospective studies are warranted to support implementation of the CMS taxonomy in clinical practice.
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Affiliation(s)
- Sanne Ten Hoorn
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Tim R de Back
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands
| | - Dirkje W Sommeijer
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Flevohospital, Department of Internal Medicine, Hospitaalweg 1, 1315 RA, Almere, The Netherlands
| | - Louis Vermeulen
- Amsterdam UMC, University of Amsterdam, LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.,Oncode Institute, Amsterdam UMC, Meibergdreef 9, 1105 AZ Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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17
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Zhang Y, Zhu L, Wang X. NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data. Front Genet 2021; 12:608042. [PMID: 33968127 PMCID: PMC8100334 DOI: 10.3389/fgene.2021.608042] [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: 09/18/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Targeted therapy has been widely adopted as an effective treatment strategy to battle against cancer. However, cancers are not single disease entities, but comprising multiple molecularly distinct subtypes, and the heterogeneity nature prevents precise selection of patients for optimized therapy. Dissecting cancer subtype-specific signaling pathways is crucial to pinpointing dysregulated genes for the prioritization of novel therapeutic targets. Nested effects models (NEMs) are a group of graphical models that encode subset relations between observed downstream effects under perturbations to upstream signaling genes, providing a prototype for mapping the inner workings of the cell. In this study, we developed NEM-Tar, which extends the original NEMs to predict drug targets by incorporating causal information of (epi)genetic aberrations for signaling pathway inference. An information theory-based score, weighted information gain (WIG), was proposed to assess the impact of signaling genes on a specific downstream biological process of interest. Subsequently, we conducted simulation studies to compare three inference methods and found that the greedy hill-climbing algorithm demonstrated the highest accuracy and robustness to noise. Furthermore, two case studies were conducted using multi-omics data for colorectal cancer (CRC) and gastric cancer (GC) in the TCGA database. Using NEM-Tar, we inferred signaling networks driving the poor-prognosis subtypes of CRC and GC, respectively. Our model prioritized not only potential individual drug targets such as HER2, for which FDA-approved inhibitors are available but also the combinations of multiple targets potentially useful for the design of combination therapies.
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Affiliation(s)
- Yuchen Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Lina Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
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18
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Chen Y, Wu T, Zhu Z, Huang H, Zhang L, Goel A, Yang M, Wang X. An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Semin Cancer Biol 2021; 74:134-155. [PMID: 33766650 DOI: 10.1016/j.semcancer.2021.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
EV-miRNAs are microRNA (miRNA) molecules encapsulated in extracellular vesicles (EVs), which play crucial roles in tumor pathogenesis, progression, and metastasis. Recent studies about EV-miRNAs have gained novel insights into cancer biology and have demonstrated a great potential to develop novel liquid biopsy assays for various applications. Notably, compared to conventional liquid biomarkers, EV-miRNAs are more advantageous in representing host-cell molecular architecture and exhibiting higher stability and specificity. Despite various available techniques for EV-miRNA separation, concentration, profiling, and data analysis, a standardized approach for EV-miRNA biomarker development is yet lacking. In this review, we performed a substantial literature review and distilled an integrated workflow encompassing important steps for EV-miRNA biomarker development, including sample collection and EV isolation, EV-miRNA extraction and quantification, high-throughput data preprocessing, biomarker prioritization and model construction, functional analysis, as well as validation. With the rapid growth of "big data", we highlight the importance of efficient mining of high-throughput data for the discovery of EV-miRNA biomarkers and integrating multiple independent datasets for in silico and experimental validations to increase the robustness and reproducibility. Furthermore, as an efficient strategy in systems biology, network inference provides insights into the regulatory mechanisms and can be used to select functionally important EV-miRNAs to refine the biomarker candidates. Despite the encouraging development in the field, a number of challenges still hinder the clinical translation. We finally summarize several common challenges in various biomarker studies and discuss potential opportunities emerging in the related fields.
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Affiliation(s)
- Yu Chen
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Tan Wu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Zhongxu Zhu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Hao Huang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China.
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19
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Plowman PN, Plowman CE. Onco-ontogeny recapitulates phylogeny - a consideration. Oncogene 2021; 40:1542-1550. [PMID: 33452457 DOI: 10.1038/s41388-020-01624-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/09/2022]
Affiliation(s)
- P N Plowman
- Department of Clinical Oncology, St. Bartholomew's Hospital, West Smithfield, London, UK.
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20
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Wang X, Liu J, Wang D, Feng M, Wu X. Epigenetically regulated gene expression profiles reveal four molecular subtypes with prognostic and therapeutic implications in colorectal cancer. Brief Bioinform 2020; 22:6029313. [PMID: 33300554 DOI: 10.1093/bib/bbaa309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Transcriptomic deregulation by epigenetic mechanisms plays a crucial role in the heterogeneous progression of colorectal cancer (CRC). Herein, we first demonstrated that the frequencies of the aberrancies of DNA methylation-correlated (METcor) and microRNA (miRNA)-correlated (MIRcor) genes were significantly co-regulated. Next, through integrative clustering of the expression profiles of METcor and MIRcor genes, four molecular subtypes were identified in CRC patients from The Cancer Genome Atlas and then validated in four independent datasets. More importantly, the four subtypes were well characterized and showed distinct clinical and molecular features: (i) S-I: high metabolic activity, sensitive to 5-fluorouracil-based chemotherapy and good prognosis; (ii) S-II: moderate metabolic activity, marked proliferation, frequent KRAS mutation and intermediate prognosis; (iii) S-III: moderate metabolic activity, marked proliferation, promoter DNA hypermethylation, high mutation burden, frequent BRAF and EGFR mutations, moderate levels of epithelial-mesenchymal transition (EMT) and transforming growth factor β (TGFβ) signals, immune-inflamed phenotype, sensitive to cetuximab and death protein-1 inhibitor treatment and relatively poor prognosis and (iv) S-IV: miRNA overexpression, stem/serrated/mesenchymal-like properties, hypoxia, high levels of EMT and TGFβ signals, immune-excluded phenotype and poor prognosis. Overall, this study established a molecular classification based on epigenetically regulated gene expression profiles, thereby providing a better understanding of the epigenetic mechanisms underlying CRC heterogeneity.
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Affiliation(s)
- Xiaokang Wang
- Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, National Clinical Research Center for Cancer, China
| | - Jinfeng Liu
- Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, National Clinical Research Center for Cancer, China
| | - Danwen Wang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Key Laboratory of Tumor Biological Behavior of Hubei Province, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, China
| | - Maohui Feng
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Key Laboratory of Tumor Biological Behavior of Hubei Province, Clinical Medical Research Center of Peritoneal Cancer of Wuhan, Clinical Cancer Study Center of Hubei Province, China
| | - Xiongzhi Wu
- Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin Clinical Research Center for Cancer, National Clinical Research Center for Cancer, China
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21
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Wielandt AM, Hurtado C, Moreno C M, Villarroel C, Castro M, Estay M, Simian D, Martinez M, Vial MT, Kronberg U, López-Köstner F. Characterization of Chilean patients with sporadic colorectal cancer according to the three main carcinogenic pathways: Microsatellite instability, CpG island methylator phenotype and Chromosomal instability. Tumour Biol 2020; 42:1010428320938492. [PMID: 32635826 DOI: 10.1177/1010428320938492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Molecular classification of colorectal cancer is difficult to implement in clinical settings where hundreds of genes are involved, and resources are limited. This study aims to characterize the molecular subtypes of patients with sporadic colorectal cancer based on the three main carcinogenic pathways microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and chromosomal instability (CIN) in a Chilean population. Although several reports have characterized colorectal cancer, most do not represent Latin-American populations. Our study includes 103 colorectal cancer patients who underwent surgery, without neoadjuvant treatment, in a private hospital between 2008 and 2017. MSI, CIN, and CIMP status were assessed. Frequent mutations in KRAS, BRAF, and PIK3CA genes were analyzed by Sanger sequencing, and statistical analysis was performed by Fisher's exact and/or chi-square test. Survival curves were estimated with Kaplan-Meier and log-rank test. Based on our observations, we can classify the tumors in four subgroups, Group 1: MSI-high tumors (15%) are located in the right colon, occur at older age, and 60% show a BRAF mutation; Group 2: CIN-high tumors (38%) are in the left colon, and 26% have KRAS mutations. Group 3: [MSI/CIN/CIMP]-low/negative tumors (30%) are left-sided, and 39% have KRAS mutations; Group 4: CIMP-high tumors (15%) were more frequent in men and left side colon, with 27% KRAS and 7% presented BRAF mutations. Three percent of patients could not be classified. We found that CIMP-high was associated with a worse prognosis, both in MSI-high and MSI stable patients (p = 0.0452). Group 3 (Low/negative tumors) tend to have better overall survival compared with MSI-high, CIMP-high, and CIN-high tumors. This study contributes to understanding the heterogeneity of tumors in the Chilean population being one of the few characterizations performed in Latin-America. Given the limited resources of these countries, these results allow to improve molecular characterization in Latin-American colorectal cancer populations and confirm the possibility of using the three main carcinogenic pathways to define therapeutic strategies.
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Affiliation(s)
- Ana María Wielandt
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Claudia Hurtado
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Mauricio Moreno C
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile.,Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Cynthia Villarroel
- Oncology and Molecular Genetics Laboratory, Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Magdalena Castro
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | - Marlene Estay
- Coloproctology Unit, Clínica Las Condes, Santiago, Chile
| | - Daniela Simian
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | - Maripaz Martinez
- Academic Department Research Unit, Clínica Las Condes, Santiago, Chile
| | | | - Udo Kronberg
- Coloproctology Unit, Clínica Las Condes, Santiago, Chile
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22
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Zhang B, Wang L, Liu Z, Shao B, Jiang W, Shu P. Integrated analysis identifies an immune-based prognostic signature for the mesenchymal identity in colorectal cancer. Medicine (Baltimore) 2020; 99:e20617. [PMID: 32569190 PMCID: PMC7310905 DOI: 10.1097/md.0000000000020617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) has been divided into 4 consensus molecular subtypes (CMSs), of which CMS4 has the mesenchymal identity and the highest relapse rate. Our goal is to develop a prognostic signature by integrating the immune system and mesenchymal modalities involved in CMS4. METHODS The gene expression profiles collected from 5 public datasets were applied to this study, including 1280 samples totally. Network analysis was applied to integrate the mesenchymal modalities and immune signature to establish an immune-based prognostic signature for CRC (IPSCRC). RESULTS We identified 6 immune genes as key factors of CMS4 and established the IPSCRC. The IPSCRC could significantly divide patients into high- and low- risk groups in terms of relapse-free survival (RFS) and overall survival (OS) and in discovery (RFS: P < .0001) and 4 independent validation sets (RFS range: P = .01 to <.0001; OS range: P = .02-.0004). After stage stratification, the IPSCRC could still distinguish poor prognosis patients in discovery (RFS: P = .04) and validation cohorts (RFS range: P = .04-.007) within stage II in terms of RFS. Further, in multivariate analysis, the IPSCRC remained an independent predictor of prognosis. Moreover, Macrophage M2 was significantly enriched in the high-risk group, while plasma cells enriched in the low-risk group. CONCLUSION We propose an immune-based signature identified by network analysis, which is a promising prognostic biomarker and help for the selection of CRC patients who might benefit from more rigorous therapies. Further prospective studies are warranted to test and validate its efficiency for clinical application.
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Affiliation(s)
| | | | | | | | | | - Peng Shu
- Molecular Laboratory, Beilun People's Hospital, Ningbo, China
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23
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Zhang Y, Zhu L, Wang X. A Network-Based Approach for Identification of Subtype-Specific Master Regulators in Pancreatic Ductal Adenocarcinoma. Genes (Basel) 2020; 11:genes11020155. [PMID: 32024063 PMCID: PMC7074188 DOI: 10.3390/genes11020155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the predominant subtype of pancreatic cancer, has been reported with equal mortality and incidence for decades. The lethality of PDAC is largely due to its late presentation, when surgical resection is no longer an option. Similar to other major malignancies, it is now clear that PDAC is not a single disease, posing a great challenge to precise selection of patients for optimized adjuvant therapy. A representative study found that PDAC comprises four distinct molecular subtypes: squamous, pancreatic progenitor, immunogenic, and aberrantly differentiated endocrine exocrine (ADEX). However, little is known about the molecular mechanisms underlying specific PDAC subtypes, hampering the design of novel targeted agents. In this study we performed network inference that integrates miRNA expression and gene expression profiles to dissect the miRNA regulatory mechanism specific to the most aggressive squamous subtype of PDAC. Master regulatory analysis revealed that the particular subtype of PDAC is predominantly influenced by miR-29c and miR-192. Further integrative analysis found miR-29c target genes LOXL2, ADAM12 and SERPINH1, which all showed strong association with prognosis. Furthermore, we have preliminarily revealed that the PDAC cell lines with high expression of these miRNA target genes showed significantly lower sensitivities to multiple anti-tumor drugs. Together, our integrative analysis elucidated the squamous subtype-specific regulatory mechanism, and identified master regulatory miRNAs and their downstream genes, which are potential prognostic and predictive biomarkers.
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Affiliation(s)
- Yuchen Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; (Y.Z.); (L.Z.)
| | - Lina Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; (Y.Z.); (L.Z.)
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; (Y.Z.); (L.Z.)
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Correspondence: ; Tel.: +852-3442-2367
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24
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Francescangeli F, Contavalli P, De Angelis ML, Careccia S, Signore M, Haas TL, Salaris F, Baiocchi M, Boe A, Giuliani A, Tcheremenskaia O, Pagliuca A, Guardiola O, Minchiotti G, Colace L, Ciardi A, D'Andrea V, La Torre F, Medema J, De Maria R, Zeuner A. A pre-existing population of ZEB2 + quiescent cells with stemness and mesenchymal features dictate chemoresistance in colorectal cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:2. [PMID: 31910865 PMCID: PMC6947904 DOI: 10.1186/s13046-019-1505-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 12/28/2022]
Abstract
Background Quiescent/slow cycling cells have been identified in several tumors and correlated with therapy resistance. However, the features of chemoresistant populations and the molecular factors linking quiescence to chemoresistance are largely unknown. Methods A population of chemoresistant quiescent/slow cycling cells was isolated through PKH26 staining (which allows to separate cells on the basis of their proliferation rate) from colorectal cancer (CRC) xenografts and subjected to global gene expression and pathway activation analyses. Factors expressed by the quiescent/slow cycling population were analyzed through lentiviral overexpression approaches for their ability to induce a dormant chemoresistant state both in vitro and in mouse xenografts. The correlation between quiescence-associated factors, CRC consensus molecular subtype and cancer prognosis was analyzed in large patient datasets. Results Untreated colorectal tumors contain a population of quiescent/slow cycling cells with stem cell features (quiescent cancer stem cells, QCSCs) characterized by a predetermined mesenchymal-like chemoresistant phenotype. QCSCs expressed increased levels of ZEB2, a transcription factor involved in stem cell plasticity and epithelial-mesenchymal transition (EMT), and of antiapototic factors pCRAF and pASK1. ZEB2 overexpression upregulated pCRAF/pASK1 levels resulting in increased chemoresistance, enrichment of cells with stemness/EMT traits and proliferative slowdown of tumor xenografts. In parallel, chemotherapy treatment of tumor xenografts induced the prevalence of QCSCs with a stemness/EMT phenotype and activation of the ZEB2/pCRAF/pASK1 axis, resulting in a chemotherapy-unresponsive state. In CRC patients, increased ZEB2 levels correlated with worse relapse-free survival and were strongly associated to the consensus molecular subtype 4 (CMS4) characterized by dismal prognosis, decreased proliferative rates and upregulation of EMT genes. Conclusions These results show that chemotherapy-naive tumors contain a cell population characterized by a coordinated program of chemoresistance, quiescence, stemness and EMT. Such population becomes prevalent upon drug treatment and is responsible for chemotherapy resistance, thus representing a key target for more effective therapeutic approaches.
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Affiliation(s)
- Federica Francescangeli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Paola Contavalli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Maria Laura De Angelis
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Silvia Careccia
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Michele Signore
- RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Tobias Longin Haas
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy
| | - Federico Salaris
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Marta Baiocchi
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Boe
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161, Rome, Italy
| | - Olga Tcheremenskaia
- Environment and Health Department, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alfredo Pagliuca
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Ombretta Guardiola
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR,Via Pietro Castellino 111, 80131, Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR,Via Pietro Castellino 111, 80131, Naples, Italy
| | - Lidia Colace
- Department of Surgical Sciences, Policlinico Umberto I/Sapienza University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - Antonio Ciardi
- Department of Surgery "Pietro Valdoni", Policlinico Umberto I/Sapienza University of Rome, via Lancisi 2, 00161, Rome, Italy
| | - Vito D'Andrea
- Department of Surgical Sciences, Policlinico Umberto I/Sapienza University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - Filippo La Torre
- Surgical Sciences and Emergency Department, Policlinico Umberto I/Sapienza University of Rome, Viale del Policlinico 155, 00161, Rome, Italy
| | - JanPaul Medema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 9, 1105, AZ, Amsterdam, The Netherlands
| | - Ruggero De Maria
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy. .,Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168, Rome, Italy.
| | - Ann Zeuner
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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DeepCC: a novel deep learning-based framework for cancer molecular subtype classification. Oncogenesis 2019; 8:44. [PMID: 31420533 PMCID: PMC6697729 DOI: 10.1038/s41389-019-0157-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/13/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Molecular subtyping of cancer is a critical step towards more individualized therapy and provides important biological insights into cancer heterogeneity. Although gene expression signature-based classification has been widely demonstrated to be an effective approach in the last decade, the widespread implementation has long been limited by platform differences, batch effects, and the difficulty to classify individual patient samples. Here, we describe a novel supervised cancer classification framework, deep cancer subtype classification (DeepCC), based on deep learning of functional spectra quantifying activities of biological pathways. In two case studies about colorectal and breast cancer classification, DeepCC classifiers and DeepCC single sample predictors both achieved overall higher sensitivity, specificity, and accuracy compared with other widely used classification methods such as random forests (RF), support vector machine (SVM), gradient boosting machine (GBM), and multinomial logistic regression algorithms. Simulation analysis based on random subsampling of genes demonstrated the robustness of DeepCC to missing data. Moreover, deep features learned by DeepCC captured biological characteristics associated with distinct molecular subtypes, enabling more compact within-subtype distribution and between-subtype separation of patient samples, and therefore greatly reduce the number of unclassifiable samples previously. In summary, DeepCC provides a novel cancer classification framework that is platform independent, robust to missing data, and can be used for single sample prediction facilitating clinical implementation of cancer molecular subtyping.
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Integrative Network Analysis Reveals a MicroRNA-Based Signature for Prognosis Prediction of Epithelial Ovarian Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:1056431. [PMID: 31275959 PMCID: PMC6582839 DOI: 10.1155/2019/1056431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Background Epithelial ovarian cancer (EOC) is a heterogeneous disease, which has been recently classified into four molecular subtypes, of which the mesenchymal subtype exhibited the worst prognosis. We aimed to identify a microRNA- (miRNA-) based signature by incorporating the molecular modalities involved in the mesenchymal subtype for risk stratification, which would allow the identification of patients who might benefit from more rigorous treatments. Method We characterized the regulatory mechanisms underlying the mesenchymal subtype using network analyses integrating gene and miRNA expression profiles from The Cancer Genome Atlas (TCGA) cohort to identify a miRNA signature for prognosis prediction. Results We identified four miRNAs as the master regulators of the mesenchymal subtype and developed a risk score model. The 4-miRNA signature significantly predicted overall survival (OS) and progression-free survival (PFS) in discovery (p=0.004 and p=0.04) and two independent public datasets (GSE73582: OS, HR: 2.26 (1.26-4.05), p=0.005, PFS, HR: 2.03 (1.34-3.09), p<0.001; GSE25204: OS, HR: 3.07 (1.73-5.46), p<0.001, PFS, HR: 2.59 (1.72-3.88), p<0.001). Moreover, in multivariate analyses, the miRNA signature maintained as an independent prognostic predictor and achieved superior efficiency compared to the currently used clinical factors. Conclusions In conclusion, our network analysis identified a 4-miRNA signature which has prognostic value superior to currently reported clinical covariates. This signature warrants further testing and validation for use in clinical practice.
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High Expression of LTBP2 Contributes to Poor Prognosis in Colorectal Cancer Patients and Correlates with the Mesenchymal Colorectal Cancer Subtype. DISEASE MARKERS 2019; 2019:5231269. [PMID: 30956730 PMCID: PMC6431450 DOI: 10.1155/2019/5231269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 02/07/2019] [Indexed: 01/12/2023]
Abstract
Colorectal cancer (CRC) is a complex and heterogeneous disease with four consensus molecular subtypes (CMS1-4). LTBP2 is a member of the fibrillin/LTBP super family and plays a critical role in tumorigenesis by activating TGF-β in the CMS4 CRC subtype. So far, the expression and prognostic significance of LTBP2 in CRC remains obscure. In this study, we aimed to analyze the mRNA and protein expression levels of LTBP2 in CRC tissues and then estimate their values as a potential prognostic biomarker. We detected the mRNA expression of LTBP2 in 28 cases of fresh CRC tissues and 4 CRC cell lines and the protein expression of LTBP2 in 483 samples of CRC tissues, matched tumor-adjacent tissues, and benign colorectal diseases. LTBP2 protein expression was then correlated to patients' clinical features and overall survival. Both LTBP2 mRNA and protein expression levels in CRC tissues were remarkably superior to those in adjacent normal colorectal tissues (P = 0.0071 and P < 0.001, respectively), according to TCGA dataset of CRC. High LTBP2 protein expression was correlated with TNM stage (P < 0.001), T stage (P < 0.001), N stage (P < 0.001), and M stage (P < 0.001). High LTBP2 protein expression was related to poor overall survival in CRC patients and was an independent prognostic factor for CRC. LTBP2 mRNA expression was especially higher in the CMS4 subtype (P < 0.001), which was confirmed in CRC cell lines. Our data suggested that LTBP2 may act as an oncogene in the development of colorectal cancer and have important significance in predicting CRC prognosis. LTBP2 could be a novel biomarker and potential therapeutic target for mesenchymal colorectal cancer and can improve the outcome of high-risk CRC.
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Wang W, Kandimalla R, Huang H, Zhu L, Li Y, Gao F, Goel A, Wang X. Molecular subtyping of colorectal cancer: Recent progress, new challenges and emerging opportunities. Semin Cancer Biol 2019; 55:37-52. [PMID: 29775690 PMCID: PMC6240404 DOI: 10.1016/j.semcancer.2018.05.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Similar to many other malignancies, CRC is a heterogeneous disease, making it a clinical challenge for optimization of treatment modalities in reducing the morbidity and mortality associated with this disease. A more precise understanding of the biological properties that distinguish patients with colorectal tumors, especially in terms of their clinical features, is a key requirement towards a more robust, targeted-drug design, and implementation of individualized therapies. In the recent decades, extensive studies have reported distinct CRC subtypes, with a mutation-centered view of tumor heterogeneity. However, more recently, the paradigm has shifted towards transcriptome-based classifications, represented by six independent CRC taxonomies. In 2015, the colorectal cancer subtyping consortium reported the identification of four consensus molecular subtypes (CMSs), providing thus far the most robust classification system for CRC. In this review, we summarize the historical timeline of CRC classification approaches; discuss their salient features and potential limitations that may require further refinement in near future. In other words, in spite of the recent encouraging progress, several major challenges prevent translation of molecular knowledge gleaned from CMSs into the clinic. Herein, we summarize some of these potential challenges and discuss exciting new opportunities currently emerging in related fields. We believe, close collaborations between basic researchers, bioinformaticians and clinicians are imperative for addressing these challenges, and eventually paving the path for CRC subtyping into routine clinical practice as we usher into the era of personalized medicine.
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Affiliation(s)
- Wei Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | - Raju Kandimalla
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, 3410 Worth Street, Suite 610, Dallas, TX 75246, USA
| | - Hao Huang
- College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Lina Zhu
- College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Ying Li
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | - Feng Gao
- College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, 3410 Worth Street, Suite 610, Dallas, TX 75246, USA.
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong.
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Low miR200c expression in tumor budding of invasive front predicts worse survival in patients with localized colon cancer and is related to PD-L1 overexpression. Mod Pathol 2019; 32:306-313. [PMID: 30206410 DOI: 10.1038/s41379-018-0124-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/22/2018] [Accepted: 07/23/2018] [Indexed: 12/13/2022]
Abstract
At the histological level, tumor budding in colon cancer is the result of cells undergoing at least partial epithelial-to-mesenchymal transition. The microRNA 200 family is an important epigenetic driver of this process, mainly by downregulating zinc-finger E-box binding homeobox (ZEB) and transforming growth factor beta (TGF-β) expression. We retrospectively explored the expression of the miR200 family, and ZEB1 and ZEB2, and their relationship with immune resistance mediated through PD-L1 overexpression. For this purpose, we analyzed a series of 125 colon cancer cases and took samples from two different tumor sites: the area of tumor budding at the invasive front and from the tumor center. We found significant ZEB overexpression and a reduction in miR200 in budding areas, a profile compatible with epithelial-to-mesenchymal transition. In multivariate analysis of the cases with localized disease, low miR200c expression in budding areas, but not at the tumor center, was an adverse tumor-specific survival factor (hazard ratio: 0.12; 95% confidence interval: 0.03-0.81; p = 0.02) independent of the clinical stage of the disease. PD-L1 was significantly overexpressed in the budding areas and its levels correlated with a mesenchymal transition profile. These results highlight the importance of including budding areas among the samples used for biomarker evaluation and provides relevant data on the influence of mesenchymal transition in the immune resistance mediated by PD-L1 overexpression.
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Varkaris A, Katsiampoura A, Davis JS, Shah N, Lam M, Frias RL, Ivan C, Shimizu M, Morris J, Menter D, Overman M, Tran H, Heymach J, Chun YS, Vauthey JN, Calin G, Kopetz S. Circulating inflammation signature predicts overall survival and relapse-free survival in metastatic colorectal cancer. Br J Cancer 2019; 120:340-345. [PMID: 30636774 PMCID: PMC6353894 DOI: 10.1038/s41416-018-0360-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 10/03/2018] [Accepted: 11/27/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Metastatic colorectal cancer (mCRC) is a highly heterogeneous disease from a clinical, molecular, and immunological perspective. Current predictive models rely primarily in tissue based genetic analysis, which not always correlate with inflammatory response. Here we evaluated the role of a circulating inflammatory signature as a prognostic marker in mCRC. METHODS Two hundred eleven newly diagnosed patients with mCRC were enrolled in the study. One hundred twenty-one patients had unresectable metastases, whereas ninety patients had potentially resectable liver metastases at presentation. Analysis of miR-21, IL-6, and IL-8 in the plasma of peripheral blood was performed at baseline. Patients with high circulating levels of ≥2 of the three inflammation markers (miR-21, IL-6, and IL-8) were considered to have the "Inflammation phenotype-positive CISIG". RESULTS Positive CISIG was found in 39/90 (43%) and 50/121 (45%) patients in the resectable and unresectable cohort, respectively. In the resectable population the median relapse-free survival was 18.4 compared to 31.4 months (p = 0.001 HR 2.09, 95% CI 1.2-3.67) for positive vs. negative CISIG. In contrast, the individual components were not significant. In the same population the median overall survival was 46.2 compared to 66.0 months (p = 0.0003, HR 2.57, 95% CI 1.26-5.27) for positive vs. negative CISIG, but not significant for the individual components. In the unresectable population, the median overall survival was 13.5 compared to 25.0 months (p = 0.0008, HR 2.49, 95% CI 1.46-4.22) for positive vs. negative CISIG. IL-6 was independently prognostic with overall survival of 16.2 compared to 27.0 months (p = 0.004, HR 1.96, 95% CI 1.24-3.11) for high vs. low IL-6, but not the other components. Using a Cox regression model, we demonstrated that CISIG is an independent predictive marker of survival in patients with unresectable disease (HR 1.8, 95% CI 1.2, 2.8, p < 0.01). CONCLUSION In two different cohorts, we demonstrated that CISIG is a strong prognostic factor of relapse-free and overall survival of patients with mCRC. Based on these data, analysis of circulating inflammatory signaling can be complimentary to traditional molecular testing.
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Affiliation(s)
- Andreas Varkaris
- Department of Hematology Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Anastasia Katsiampoura
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- St. Elizabeth's Medical Center, Boston, MA, USA
| | - Jennifer S Davis
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neeraj Shah
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Lam
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosa Lizeth Frias
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristina Ivan
- Department of Experimental Therapeutics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey Morris
- Department of Biostatistics, Division of Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Overman
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hai Tran
- Department of Thoracic/Head and Neck Medical Oncology - Research, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yun Shin Chun
- Hepato-Pancreato-Biliary Section, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jean-Nicolas Vauthey
- Hepato-Pancreato-Biliary Section, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Calin
- Department of Experimental Therapeutics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Menter DG, Davis JS, Broom BM, Overman MJ, Morris J, Kopetz S. Back to the Colorectal Cancer Consensus Molecular Subtype Future. Curr Gastroenterol Rep 2019; 21:5. [PMID: 30701321 PMCID: PMC6622456 DOI: 10.1007/s11894-019-0674-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW This review seeks to provide an informed prospective on the advances in molecular profiling and analysis of colorectal cancer (CRC). The goal is to provide a historical context and current summary on how advances in gene and protein sequencing technology along with computer capabilities led to our current bioinformatic advances in the field. RECENT FINDINGS An explosion of knowledge has occurred regarding genetic, epigenetic, and biochemical alterations associated with the evolution of colorectal cancer. This has led to the realization that CRC is a heterogeneous disease with molecular alterations often dictating natural history, response to treatment, and outcome. The consensus molecular subtypes (CMS) classification classifies CRC into four molecular subtypes with distinct biological characteristics, which may form the basis for clinical stratification and subtype-based targeted intervention. This review summarizes new developments of a field moving "Back to the Future." CRC molecular subtyping will better identify key subtype specific therapeutic targets and responses to therapy.
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Affiliation(s)
- David G Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA.
| | - Jennifer S Davis
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bradley M Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA
| | - Jeffrey Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard--Unit 0426, Houston, TX, 77030, USA
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Genetic dissection of the miR-200-Zeb1 axis reveals its importance in tumor differentiation and invasion. Nat Commun 2018; 9:4671. [PMID: 30405106 PMCID: PMC6220299 DOI: 10.1038/s41467-018-07130-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022] Open
Abstract
The epithelial-to-mesenchymal transition (EMT) is an important mechanism for cancer progression and metastasis. Numerous in vitro and tumor-profiling studies point to the miR-200-Zeb1 axis as crucial in regulating this process, yet in vivo studies involving its regulation within a physiological context are lacking. Here, we show that miR-200 ablation in the Rip-Tag2 insulinoma mouse model induces beta-cell dedifferentiation, initiates an EMT expression program, and promotes tumor invasion. Strikingly, disrupting the miR-200 sites of the endogenous Zeb1 locus causes a similar phenotype. Reexpressing members of the miR-200 superfamily in vitro reveals that the miR-200c family and not the co-expressed and closely related miR-141 family is responsible for regulation of Zeb1 and EMT. Our results thus show that disrupting the in vivo regulation of Zeb1 by miR-200c is sufficient to drive EMT, thus highlighting the importance of this axis in tumor progression and invasion and its potential as a therapeutic target.
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Kandimalla R, Gao F, Matsuyama T, Ishikawa T, Uetake H, Takahashi N, Yamada Y, Becerra C, Kopetz S, Wang X, Goel A. Genome-wide Discovery and Identification of a Novel miRNA Signature for Recurrence Prediction in Stage II and III Colorectal Cancer. Clin Cancer Res 2018. [PMID: 29514841 DOI: 10.1158/1078-0432.ccr-17-3236] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose: The current tumor-node-metastasis (TNM) staging system is inadequate at identifying patients with high-risk colorectal cancer. Using a systematic and comprehensive biomarker discovery and validation approach, we aimed to identify an miRNA recurrence classifier (MRC) that can improve upon the current TNM staging as well as is superior to currently offered molecular assays.Experimental Design: Three independent genome-wide miRNA expression profiling datasets were used for biomarker discovery (N = 158) and in silico validation (N = 109 and N = 40) to identify an miRNA signature for predicting tumor recurrence in patients with colorectal cancer. Subsequently, this signature was analytically trained and validated in retrospectively collected independent patient cohorts of fresh-frozen (N = 127, cohort 1) and formalin-fixed paraffin-embedded (FFPE; N = 165, cohort 2 and N = 139, cohort 3) specimens.Results: We identified an 8-miRNA signature that significantly predicted recurrence-free interval (RFI) in the discovery (P = 0.002) and two independent publicly available datasets (P = 0.00006 and P = 0.002). The RT-PCR-based validation in independent clinical cohorts revealed that MRC-derived high-risk patients succumb to significantly poor RFI in patients with stage II and III colorectal cancer [cohort 1: hazard ratio (HR), 3.44 (1.56-7.45), P = 0.001; cohort 2: HR, 6.15 (3.33-11.35), P = 0.001; and cohort 3: HR, 4.23 (2.26-7.92), P = 0.0003]. In multivariate analyses, MRC emerged as an independent predictor of tumor recurrence and achieved superior predictive accuracy over the currently available molecular assays. The RT-PCR-based MRC risk score = (-0.1218 × miR-744) + (-3.7142 × miR-429) + (-2.2051 × miR-362) + (3.0564 × miR-200b) + (2.4997 × miR-191) + (-0.0065 × miR-30c2) + (2.2224 × miR-30b) + (-1.1162 × miR-33a).Conclusions: This novel MRC is superior to currently used clinicopathologic features, as well as National Comprehensive Cancer Network (NCCN) criteria, and works regardless of adjuvant chemotherapy status in identifying patients with high-risk stage II and III colorectal cancer. This can be readily deployed in clinical practice with FFPE specimens for decision-making pending further model testing and validation. Clin Cancer Res; 24(16); 3867-77. ©2018 AACRSee related commentary by Rodriguez et al., p. 3787.
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Affiliation(s)
- Raju Kandimalla
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Feng Gao
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Takatoshi Matsuyama
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.,Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Toshiaki Ishikawa
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Naoki Takahashi
- Department of Gastroenterology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhide Yamada
- Department of Gastroenterology, National Cancer Center Hospital, Tokyo, Japan
| | - Carlos Becerra
- Texas Oncology, Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.
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O'Brien SJ, Carter JV, Burton JF, Oxford BG, Schmidt MN, Hallion JC, Galandiuk S. The role of the miR-200 family in epithelial-mesenchymal transition in colorectal cancer: a systematic review. Int J Cancer 2018; 142:2501-2511. [DOI: 10.1002/ijc.31282] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/16/2018] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Stephen J. O'Brien
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
| | - Jane V. Carter
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
- Department of Surgery; North Cumbria University Hospitals NHS Trust; Whitehaven Cumbria United Kingdom
| | - James F. Burton
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
| | - Brent G. Oxford
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
| | - Miranda N. Schmidt
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
| | - Jacob C. Hallion
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
| | - Susan Galandiuk
- Price Institute of Surgical Research, The Hiram C. Polk Jr., M.D. Department of Surgery, University of Louisville; Louisville KY
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Linnekamp JF, Hooff SRV, Prasetyanti PR, Kandimalla R, Buikhuisen JY, Fessler E, Ramesh P, Lee KAST, Bochove GGW, de Jong JH, Cameron K, Leersum RV, Rodermond HM, Franitza M, Nürnberg P, Mangiapane LR, Wang X, Clevers H, Vermeulen L, Stassi G, Medema JP. Consensus molecular subtypes of colorectal cancer are recapitulated in in vitro and in vivo models. Cell Death Differ 2018; 25:616-633. [PMID: 29305587 DOI: 10.1038/s41418-017-0011-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is a highly heterogeneous disease both from a molecular and clinical perspective. Several distinct molecular entities, such as microsatellite instability (MSI), have been defined that make up biologically distinct subgroups with their own clinical course. Recent data indicated that CRC can be best segregated into four groups called consensus molecular subtypes (CMS1-4), each of which has a unique biology and gene expression pattern. In order to develop improved, subtype-specific therapies and to gain insight into the molecular wiring and origin of these subtypes, reliable models are needed. This study was designed to determine the heterogeneity and identify the presence of CMSs in a large panel of CRC cell lines, primary cultures and patient-derived xenografts (PDX). We provide a repository encompassing this heterogeneity and moreover describe that a large part of the models can be robustly assigned to one of the four CMSs, independent of the stromal contribution. We subsequently validate our CMS stratification by functional analysis which for instance shows mesenchymal enrichment in CMS4 and metabolic dysregulation in CMS3. Finally, we observe a clear difference in sensitivity to chemotherapy-induced apoptosis, specifically between CMS2 and CMS4. This relates to the in vivo efficacy of chemotherapy, which delays outgrowth of CMS2, but not CMS4 xenografts. Combined our data indicate that molecular subtypes are faithfully modelled in CRC cell cultures and PDXs, representing tumour cell intrinsic and stable features. This repository provides researchers with a platform to study CRC using the existing heterogeneity.
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Affiliation(s)
- Janneke F Linnekamp
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Sander R van Hooff
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Pramudita R Prasetyanti
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Raju Kandimalla
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Joyce Y Buikhuisen
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Evelyn Fessler
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands.,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Prashanthi Ramesh
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Kelly A S T Lee
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Grehor G W Bochove
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Johan H de Jong
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Kate Cameron
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Ronald van Leersum
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Hans M Rodermond
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Marek Franitza
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Laura R Mangiapane
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical and Oncological Sciences, University of Palermo, Via del Vespro 131, Palermo, 90134, Italy
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Hans Clevers
- Cancer Genomics Netherlands, Utrecht, The Netherlands.,Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC), 3584 CT, Utrecht, The Netherlands.,Princess Máxima Centre for Pediatric Oncology, Utrecht, 3584 CT, The Netherlands
| | - Louis Vermeulen
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Giorgio Stassi
- Cellular and Molecular Pathophysiology Laboratory, Department of Surgical and Oncological Sciences, University of Palermo, Via del Vespro 131, Palermo, 90134, Italy
| | - Jan Paul Medema
- Cancer Center Amsterdam, Laboratory of Experimental Oncology and Radiobiology (LEXOR), CEMM, Academic Medical Center, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. .,Cancer Genomics Netherlands, Utrecht, The Netherlands.
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Sveen A, Bruun J, Eide PW, Eilertsen IA, Ramirez L, Murumägi A, Arjama M, Danielsen SA, Kryeziu K, Elez E, Tabernero J, Guinney J, Palmer HG, Nesbakken A, Kallioniemi O, Dienstmann R, Lothe RA. Colorectal Cancer Consensus Molecular Subtypes Translated to Preclinical Models Uncover Potentially Targetable Cancer Cell Dependencies. Clin Cancer Res 2017; 24:794-806. [PMID: 29242316 DOI: 10.1158/1078-0432.ccr-17-1234] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/26/2017] [Accepted: 12/06/2017] [Indexed: 01/27/2023]
Abstract
Purpose: Response to standard oncologic treatment is limited in colorectal cancer. The gene expression-based consensus molecular subtypes (CMS) provide a new paradigm for stratified treatment and drug repurposing; however, drug discovery is currently limited by the lack of translation of CMS to preclinical models.Experimental Design: We analyzed CMS in primary colorectal cancers, cell lines, and patient-derived xenografts (PDX). For classification of preclinical models, we developed an optimized classifier enriched for cancer cell-intrinsic gene expression signals, and performed high-throughput in vitro drug screening (n = 459 drugs) to analyze subtype-specific drug sensitivities.Results: The distinct molecular and clinicopathologic characteristics of each CMS group were validated in a single-hospital series of 409 primary colorectal cancers. The new, cancer cell-adapted classifier was found to perform well in primary tumors, and applied to a panel of 148 cell lines and 32 PDXs, these colorectal cancer models were shown to recapitulate the biology of the CMS groups. Drug screening of 33 cell lines demonstrated subtype-dependent response profiles, confirming strong response to EGFR and HER2 inhibitors in the CMS2 epithelial/canonical group, and revealing strong sensitivity to HSP90 inhibitors in cells with the CMS1 microsatellite instability/immune and CMS4 mesenchymal phenotypes. This association was validated in vitro in additional CMS-predicted cell lines. Combination treatment with 5-fluorouracil and luminespib showed potential to alleviate chemoresistance in a CMS4 PDX model, an effect not seen in a chemosensitive CMS2 PDX model.Conclusions: We provide translation of CMS classification to preclinical models and uncover a potential for targeted treatment repurposing in the chemoresistant CMS4 group. Clin Cancer Res; 24(4); 794-806. ©2017 AACR.
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Affiliation(s)
- Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Lorena Ramirez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mariliina Arjama
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Kushtrim Kryeziu
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Elena Elez
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Josep Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Justin Guinney
- SAGE Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Hector G Palmer
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Arild Nesbakken
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Rodrigo Dienstmann
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.,SAGE Bionetworks, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. .,K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Institute for Clinical Medicine, University of Oslo, Oslo, Norway
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CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Sci Rep 2017; 7:16618. [PMID: 29192179 PMCID: PMC5709354 DOI: 10.1038/s41598-017-16747-x] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/15/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancers (CRCs) can be divided into four gene expression-based biologically distinct consensus molecular subtypes (CMS). This classification provides a potential framework for stratified treatment, but to identify novel CMS-drug associations, translation of the subtypes to pre-clinical models is essential. The currently available classifier is dependent on gene expression signals from the immune and stromal compartments of tumors and fails to identify the poor-prognostic CMS4-mesenchymal group in immortalized cell lines, patient-derived organoids and xenografts. To address this, we present a novel CMS classifier based on a filtered set of cancer cell-intrinsic, subtype-enriched gene expression markers. This new classifier, referred to as CMScaller, recapitulated the subtypes in both in vitro and in vivo models (551 in total). Importantly, by analyzing public drug response data from patient-derived xenografts and cell lines, we show that the subtypes are predictive of response to standard CRC drugs. CMScaller is available as an R package.
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38
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Purcell RV, Visnovska M, Biggs PJ, Schmeier S, Frizelle FA. Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Sci Rep 2017; 7:11590. [PMID: 28912574 PMCID: PMC5599497 DOI: 10.1038/s41598-017-11237-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.
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Affiliation(s)
- Rachel V Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand.
| | - Martina Visnovska
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Patrick J Biggs
- Hopkirk Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Frank A Frizelle
- Department of Surgery, University of Otago, Christchurch, New Zealand
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39
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Markopoulos GS, Roupakia E, Tokamani M, Chavdoula E, Hatziapostolou M, Polytarchou C, Marcu KB, Papavassiliou AG, Sandaltzopoulos R, Kolettas E. A step-by-step microRNA guide to cancer development and metastasis. Cell Oncol (Dordr) 2017; 40:303-339. [DOI: 10.1007/s13402-017-0341-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2017] [Indexed: 01/17/2023] Open
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40
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The potential role of platelets in the consensus molecular subtypes of colorectal cancer. Cancer Metastasis Rev 2017; 36:273-288. [DOI: 10.1007/s10555-017-9678-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Berg KCG, Eide PW, Eilertsen IA, Johannessen B, Bruun J, Danielsen SA, Bjørnslett M, Meza-Zepeda LA, Eknæs M, Lind GE, Myklebost O, Skotheim RI, Sveen A, Lothe RA. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol Cancer 2017; 16:116. [PMID: 28683746 PMCID: PMC5498998 DOI: 10.1186/s12943-017-0691-y] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Colorectal cancer (CRC) cell lines are widely used pre-clinical model systems. Comprehensive insights into their molecular characteristics may improve model selection for biomedical studies. Methods We have performed DNA, RNA and protein profiling of 34 cell lines, including (i) targeted deep sequencing (n = 612 genes) to detect single nucleotide variants and insertions/deletions; (ii) high resolution DNA copy number profiling; (iii) gene expression profiling at exon resolution; (iv) small RNA expression profiling by deep sequencing; and (v) protein expression analysis (n = 297 proteins) by reverse phase protein microarrays. Results The cell lines were stratified according to the key molecular subtypes of CRC and data were integrated at two or more levels by computational analyses. We confirm that the frequencies and patterns of DNA aberrations are associated with genomic instability phenotypes and that the cell lines recapitulate the genomic profiles of primary carcinomas. Intrinsic expression subgroups are distinct from genomic subtypes, but consistent at the gene-, microRNA- and protein-level and dominated by two distinct clusters; colon-like cell lines characterized by expression of gastro-intestinal differentiation markers and undifferentiated cell lines showing upregulation of epithelial-mesenchymal transition and TGFβ signatures. This sample split was concordant with the gene expression-based consensus molecular subtypes of primary tumors. Approximately ¼ of the genes had consistent regulation at the DNA copy number and gene expression level, while expression of gene-protein pairs in general was strongly correlated. Consistent high-level DNA copy number amplification and outlier gene- and protein- expression was found for several oncogenes in individual cell lines, including MYC and ERBB2. Conclusions This study expands the view of CRC cell lines as accurate molecular models of primary carcinomas, and we present integrated multi-level molecular data of 34 widely used cell lines in easily accessible formats, providing a resource for preclinical studies in CRC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0691-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Merete Bjørnslett
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mette Eknæs
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ola Myklebost
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway. .,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.
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Colorectal cancer subtypes: Translation to routine clinical pathology. Cancer Treat Rev 2017; 57:1-7. [DOI: 10.1016/j.ctrv.2017.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023]
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43
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Li Y, Cai B, Shen L, Dong Y, Lu Q, Sun S, Liu S, Ma S, Ma PX, Chen J. MiRNA-29b suppresses tumor growth through simultaneously inhibiting angiogenesis and tumorigenesis by targeting Akt3. Cancer Lett 2017; 397:111-119. [PMID: 28365400 DOI: 10.1016/j.canlet.2017.03.032] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 12/31/2022]
Abstract
The traditional anti-angiogenic cancer therapy could trigger hypoxia induced factor (HIF) response, leading to "reactive resistance" to chemotherapy. Simultaneously inhibiting both angiogenesis and tumorigenesis would be ideal to overcome this limitation. MicroRNAs (miRNAs) are increasingly explored as new agents for cancer therapy. In the present study, we identified a microRNA (miR-29b) with the ability of simultaneously inhibiting angiogenesis and tumorigenesis. Ectopic expression of miR-29b inhibits HUVECs formed three-dimensional capillary-like tubular structures, tumor cell proliferation, migration and tumor formation. Systemic administration of miR-29b potently suppressed tumor vascularization and cancer cell activity in vivo, resulting in dramatic suppression of tumor growth without toxicity. Moreover, we demonstrated the role of miR-29b in anti-angiogenesis and anti-tumorigenesis is through targeting Akt3 and inducing VEGF and C-myc arrest in breast cancer cells. These findings indicate that this single miRNA could be used as an efficient anti-cancer therapeutic agent to address a critical challenge in cancer therapy.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Bolei Cai
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Liangliang Shen
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Yan Dong
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Qun Lu
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Endodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Shukai Sun
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Endodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Shiyu Liu
- State Key Laboratory of Military Stomatology, Center for Tissue Engineering, School of Stomatology, The Forth Military Medical University, China
| | - Shufang Ma
- Jia-Yi Dentistry and Cosmetic Surgery Clinic, Xi'an, 710032, China
| | - Peter X Ma
- Department of Biologic and Materials Science, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Jihua Chen
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Oral Diseases, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China.
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44
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Fessler E, Medema JP. Colorectal Cancer Subtypes: Developmental Origin and Microenvironmental Regulation. Trends Cancer 2016; 2:505-518. [DOI: 10.1016/j.trecan.2016.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022]
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