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EGFR Protein Expression in KRAS Wild-Type Metastatic Colorectal Cancer Is Another Negative Predictive Factor of the Cetuximab Therapy. Cancers (Basel) 2020; 12:cancers12030614. [PMID: 32155907 PMCID: PMC7139947 DOI: 10.3390/cancers12030614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/15/2022] Open
Abstract
The selection of colorectal cancer patients for anti-epidermal growth factor receptor (EGFR) antibody therapy is based on the determination of their RAS mutation status—a strongly negative predictive factor—since the protein target, EGFR, is not a reliable predictor of therapeutic response. In this study, we revisited the EGFR protein issue using a cohort of 90 patients with KRAS exon2 wild-type colorectal cancer who have been treated with cetuximab therapy. Twenty-nine of these patients had metastatic tissue available for analysis. The level of EGFR protein expression in the patients was determined by immunohistochemistry and evaluated by H-score (HS) methodology. Progression-free survival (PFS) and overall survival (OS) of the patients were determined according to the EGFR-HS ranges of both the primary and metastatic tissues using Kaplan–Meyer statistics. In the case of primary tumors, EGFR scores lower than HS = 200 were associated with significantly longer OS. In the case of metastatic tissues, all levels lower than the EGFR-HS range chosen were associated with significantly longer OS. These results are explained by the fact that metastatic tissues rarely maintained the expression levels of the primary tumors. On the other hand, high EGFR expression levels in either primary tumors or metastatic tissues were associated with multiple metastatic disease. This suggests a negative prognostic role of EGFR expression. However, in a multivariate analysis, one-sidedness remained a strong independent predictive factor of survival. Previous studies demonstrated that the EGFR expression level depends on sidedness. Therefore, a subgroup analysis of the left- and right-sided cases was performed on both primary and metastatic tissues. In the case of metastic tissues, an analysis confirmed a better OS in low EGFR protein-expressing cases than in high EGFR protein-expressing cases. Collectively, these data suggest that EGFR protein expression is another negative predictive factor of the efficacy of cetuximab therapy of KRAS exon2 wild-type colorectal cancer.
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Jing C, Wang T, Ma R, Cao H, Wang Z, Liu S, Chen D, Zhang J, Wu Y, Zhang Y, Wu J, Feng J. New genetic variations discovered in KRAS wild-type cetuximab resistant chinese colorectal cancer patients. Mol Carcinog 2020; 59:478-491. [PMID: 32141150 DOI: 10.1002/mc.23172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022]
Abstract
To perform a comprehensive genomic analysis of colorectal cancer (CRC) tumor to detect genetic variants and identify novel resistant mutations associated with cetuximab-resistance in CRC patients. A retrospective study was performed using whole exome sequencing (WES) to identify common genetic factors from 22 cetuximab-sensitive and 10 cetuximab-resistant patients. In all 10 cetuximab-resistant patients, we discovered there are 37 significantly mutated genes (SMGs). CYP4A11 was the most frequently mutated gene in cetuximab-resistant patients. BCAS1 and GOLGA6L1 were found to be among the second group of frequently mutated genes with a frequency of 60%. After cosine similarity analysis, three mutational signatures (signature a, b, and c) were found in all CRC tumors, similar to signature 1, 5, and 6 in COSMIC, respectively. Gene ontology analysis was performed on SMGs and found 12 enriched GO terms. Four genes are enriched in six specific Kyoto Encyclopedia of Genes and Genomes pathway groups, including the metabolism of xenobiotics by cytochrome P450, steroid hormone biosynthesis, retinol metabolism, and drug metabolism. Our data supports a network composed of SMGs and cellular signaling pathways that have been positively linked to the mechanisms of cetuximab resistance. These involve DNA damage repair, angiogenesis, invasion, drug metabolism, and the CRC tumor microenvironment. There is a SMG, OR9G1 correlated with survival rates of KRAS wild-type colon adenocarcinoma patients. These findings support further investigation using WES in a prospective clinical study of cetuximab resistance CRC, to further identify, confirm, and extend the clinical significance of these and other potentially important new candidate predictive biomarkers of cetuximab response.
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Affiliation(s)
- Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Cell Biology, Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Siwen Liu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dan Chen
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Junying Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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153
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Sato H, Schoenfeld AJ, Siau E, Lu YC, Tai H, Suzawa K, Kubota D, Lui AJW, Qeriqi B, Mattar M, Offin M, Sakaguchi M, Toyooka S, Drilon A, Rosen NX, Kris MG, Solit D, De Stanchina E, Davare MA, Riely GJ, Ladanyi M, Somwar R. MAPK Pathway Alterations Correlate with Poor Survival and Drive Resistance to Therapy in Patients with Lung Cancers Driven by ROS1 Fusions. Clin Cancer Res 2020; 26:2932-2945. [PMID: 32122926 DOI: 10.1158/1078-0432.ccr-19-3321] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/21/2020] [Accepted: 02/25/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE ROS1 tyrosine kinase inhibitors (TKI) provide significant benefit in lung adenocarcinoma patients with ROS1 fusions. However, as observed with all targeted therapies, resistance arises. Detecting mechanisms of acquired resistance (AR) is crucial to finding novel therapies and improve patient outcomes. EXPERIMENTAL DESIGN ROS1 fusions were expressed in HBEC and NIH-3T3 cells either by cDNA overexpression (CD74/ROS1, SLC34A2/ROS1) or CRISPR-Cas9-mediated genomic engineering (EZR/ROS1). We reviewed targeted large-panel sequencing data (using the MSK-IMPACT assay) patients treated with ROS1 TKIs, and genetic alterations hypothesized to confer AR were modeled in these cell lines. RESULTS Eight of the 75 patients with a ROS1 fusion had a concurrent MAPK pathway alteration and this correlated with shorter overall survival. In addition, the induction of ROS1 fusions stimulated activation of MEK/ERK signaling with minimal effects on AKT signaling, suggesting the importance of the MAPK pathway in driving ROS1 fusion-positive cancers. Of 8 patients, 2 patients harbored novel in-frame deletions in MEK1 (MEK1delE41_L54) and MEKK1 (MEKK1delH907_C916) that were acquired after ROS1 TKIs, and 2 patients harbored NF1 loss-of-function mutations. Expression of MEK1del or MEKK1del, and knockdown of NF1 in ROS1 fusion-positive cells activated MEK/ERK signaling and conferred resistance to ROS1 TKIs. Combined targeting of ROS1 and MEK inhibited growth of cells expressing both ROS1 fusion and MEK1del. CONCLUSIONS We demonstrate that downstream activation of the MAPK pathway can mediate of innate acquired resistance to ROS1 TKIs and that patients harboring ROS1 fusion and concurrent downstream MAPK pathway alterations have worse survival. Our findings suggest a treatment strategy to target both aberrations.
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Affiliation(s)
- Hiroki Sato
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Evan Siau
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yue Christine Lu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Huichun Tai
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ken Suzawa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daisuke Kubota
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allan J W Lui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Besnik Qeriqi
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marissa Mattar
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Masakiyo Sakaguchi
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shinichi Toyooka
- Department of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Alexander Drilon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal X Rosen
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark G Kris
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Solit
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa De Stanchina
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Monika A Davare
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Gregory J Riely
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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154
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Kim SY, Kim TW. Current challenges in the implementation of precision oncology for the management of metastatic colorectal cancer. ESMO Open 2020; 5:e000634. [PMID: 32188714 PMCID: PMC7078672 DOI: 10.1136/esmoopen-2019-000634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/28/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
Over the last few decades, molecularly targeted agents have been used for the treatment of metastatic colorectal cancer. They have made remarkable contributions to prolonging the lives of patients. The emergence of several biomarkers and their introduction to the clinic have also aided in guiding such treatment. Recently, next-generation sequencing (NGS) has enabled clinicians to identify these biomarkers more easily and reliably. However, there is considerable uncertainty in interpreting and implementing the vast amount of information from NGS. The clinical relevance of biomarkers other than NGS are also subjects of debate. This review covers controversial issues and recent findings on such therapeutics and their molecular targets, including VEGF, EGFR, BRAF, HER2, RAS, actionable fusions, Wnt pathway and microsatellite instability for comprehensive understanding of obstacles on the road to precision oncology in metastatic colorectal cancer.
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Affiliation(s)
- Sun Young Kim
- Department of Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Songpa-gu, Seoul, Republic of Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan, College of Medicine, Songpa-gu, Seoul, Republic of Korea
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155
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Yegodayev KM, Novoplansky O, Golden A, Prasad M, Levin L, Jagadeeshan S, Zorea J, Dimitstein O, Joshua BZ, Cohen L, Khrameeva E, Elkabets M. TGF-Beta-Activated Cancer-Associated Fibroblasts Limit Cetuximab Efficacy in Preclinical Models of Head and Neck Cancer. Cancers (Basel) 2020; 12:cancers12020339. [PMID: 32028632 PMCID: PMC7073231 DOI: 10.3390/cancers12020339] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/22/2022] Open
Abstract
Most head and neck cancer (HNC) patients are resistant to cetuximab, an antibody against the epidermal growth factor receptor. Such therapy resistance is known to be mediated, in part, by stromal cells surrounding the tumor cells; however, the mechanisms underlying such a resistance phenotype remain unclear. To identify the mechanisms of cetuximab resistance in an unbiased manner, RNA-sequencing (RNA-seq) of HNC patient-derived xenografts (PDXs) was performed. Comparing the gene expression of HNC-PDXs before and after treatment with cetuximab indicated that the transforming growth factor-beta (TGF-beta) signaling pathway was upregulated in the stromal cells of PDXs that progressed on cetuximab treatment (CetuximabProg-PDX). However, in PDXs that were extremely sensitive to cetuximab (CetuximabSen-PDX), the TGF-beta pathway was downregulated in the stromal compartment. Histopathological analysis of PDXs showed that TGF-beta-activation was detected in cancer-associated fibroblasts (CAFs) of CetuximabProg-PDX. These TGF-beta-activated CAFs were sufficient to limit cetuximab efficacy in vitro and in vivo. Moreover, blocking the TGF-beta pathway using the SMAD3 inhibitor, SIS3, enhanced cetuximab efficacy and prevented the progression of CetuximabProg-PDX. Altogether, our findings indicate that TGF-beta-activated CAFs play a role in limiting cetuximab efficacy in HNC.
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Affiliation(s)
- Ksenia M. Yegodayev
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Ofra Novoplansky
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Artemiy Golden
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Manu Prasad
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Liron Levin
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel;
| | - Sankar Jagadeeshan
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Jonathan Zorea
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Orr Dimitstein
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
- Department of Otolaryngology-Head & Neck Surgery, Soroka University Medical Center, 84105 Beer-Sheva, Israel
| | - Ben-Zion Joshua
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
- Department of Otolaryngology-Head & Neck Surgery, Soroka University Medical Center, 84105 Beer-Sheva, Israel
| | - Limor Cohen
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
| | - Ekaterina Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
- Correspondence: (E.K.); (M.E.); Tel.: +7-495-280-14-81 (E.K.); +972-8642-8846 (M.E.)
| | - Moshe Elkabets
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, 84105 Beer-Sheva, Israel (O.N.); (M.P.); (S.J.); (J.Z.); (L.C.)
- Faculty of Health Sciences, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel; (O.D.); (B.-Z.J.)
- Correspondence: (E.K.); (M.E.); Tel.: +7-495-280-14-81 (E.K.); +972-8642-8846 (M.E.)
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156
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Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular Biology and Evolution of Cancer: From Discovery to Action. Mol Biol Evol 2020; 37:320-326. [PMID: 31642480 PMCID: PMC6993850 DOI: 10.1093/molbev/msz242] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understanding of the underlying molecular evolutionary processes. Herein we discuss a suite of concepts and tools from evolutionary and ecological theory that can inform cancer biology in new and meaningful ways. We also highlight current challenges to applying these concepts, and propose ways in which incorporating these concepts could identify new therapeutic modes and vulnerabilities in cancer.
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Affiliation(s)
- Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Heather Gardner
- Sackler School of Graduate Biomedical Sciences, Tufts University, Medford, MA
| | | | - Ella F Gunady
- Department of Medicine, Duke University Medical Center, Durham, NC
| | - Amy M Boddy
- Department of Anthropology, University of California, Santa Barbara, CA
| | | | | | - Stephen G Gaffney
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | | | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, United Kingdom
- King’s College London, London, United Kingdom
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Kate Megquier
- Broad Institute, Massachusettes Institute of Technology and Harvard University
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, and Department of Biology, Temple University, Philadelphia, PA
| | - Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
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157
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von Loga K, Woolston A, Punta M, Barber LJ, Griffiths B, Semiannikova M, Spain G, Challoner B, Fenwick K, Simon R, Marx A, Sauter G, Lise S, Matthews N, Gerlinger M. Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer. Nat Commun 2020; 11:139. [PMID: 31949146 PMCID: PMC6965135 DOI: 10.1038/s41467-019-13915-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/05/2019] [Indexed: 01/09/2023] Open
Abstract
Mismatch repair deficient (dMMR) gastro-oesophageal adenocarcinomas (GOAs) show better outcomes than their MMR-proficient counterparts and high immunotherapy sensitivity. The hypermutator-phenotype of dMMR tumours theoretically enables high evolvability but their evolution has not been investigated. Here we apply multi-region exome sequencing (MSeq) to four treatment-naive dMMR GOAs. This reveals extreme intratumour heterogeneity (ITH), exceeding ITH in other cancer types >20-fold, but also long phylogenetic trunks which may explain the exquisite immunotherapy sensitivity of dMMR tumours. Subclonal driver mutations are common and parallel evolution occurs in RAS, PIK3CA, SWI/SNF-complex genes and in immune evasion regulators. MSeq data and evolution analysis of single region-data from 64 MSI GOAs show that chromosome 8 gains are early genetic events and that the hypermutator-phenotype remains active during progression. MSeq may be necessary for biomarker development in these heterogeneous cancers. Comparison with other MSeq-analysed tumour types reveals mutation rates and their timing to determine phylogenetic tree morphologies.
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Affiliation(s)
- Katharina von Loga
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
- Biomedical Research Centre, The Royal Marsden Hospital, London, SM2 5PT, United Kingdom
| | - Andrew Woolston
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Marco Punta
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
| | - Louise J Barber
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Beatrice Griffiths
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Maria Semiannikova
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Georgia Spain
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Benjamin Challoner
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Andreas Marx
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Institute of Pathology, University Hospital Fuerth, 90766, Fuerth, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stefano Lise
- Bioinformatics Core, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Marco Gerlinger
- Translational Oncogenomics Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, SW3 6JB, United Kingdom.
- Gastrointestinal Cancer Unit, The Royal Marsden Hospital, London, SW3 6JJ, United Kingdom.
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158
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Abstract
Drug-induced mutagenesis may accelerate cancer evolution and resistance
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Affiliation(s)
- Marco Gerlinger
- Translational Oncogenomics Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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159
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Chen CH, Lu TP. Utilizing gene expression profiles to characterize tumor infiltrating lymphocytes in cancers. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:S289. [PMID: 32016008 DOI: 10.21037/atm.2019.11.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ching-Hsuan Chen
- Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taipei
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taipei
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160
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Sundar R, Tan IBH, Chee CE. Negative Predictive Biomarkers in Colorectal Cancer: PRESSING Ahead. J Clin Oncol 2019; 37:3066-3068. [DOI: 10.1200/jco.19.01977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Raghav Sundar
- National University Health System, Singapore
- Duke-National University of Singapore Medical School, Singapore
- National University of Singapore, Singapore
| | - Iain Bee Huat Tan
- Duke-National University of Singapore Medical School, Singapore
- National Cancer Centre Singapore, Singapore
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore
| | - Cheng E. Chee
- National University Health System, Singapore
- National University of Singapore, Singapore
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161
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Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M. Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment. J Immunother Cancer 2019; 7:309. [PMID: 31735170 PMCID: PMC6859637 DOI: 10.1186/s40425-019-0769-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Patient derived organoids (PDOs) can be established from colorectal cancers (CRCs) as in vitro models to interrogate cancer biology and its clinical relevance. We applied mass spectrometry (MS) immunopeptidomics to investigate neoantigen presentation and whether this can be augmented through interferon gamma (IFNγ) or MEK-inhibitor treatment. METHODS Four microsatellite stable PDOs from chemotherapy refractory and one from a treatment naïve CRC were expanded to replicates with 100 million cells each, and HLA class I and class II peptide ligands were analyzed by MS. RESULTS We identified an average of 9936 unique peptides per PDO which compares favorably against published immunopeptidomics studies, suggesting high sensitivity. Loss of heterozygosity of the HLA locus was associated with low peptide diversity in one PDO. Peptides from genes without detectable expression by RNA-sequencing were rarely identified by MS. Only 3 out of 612 non-silent mutations encoded for neoantigens that were detected by MS. In contrast, computational HLA binding prediction estimated that 304 mutations could generate neoantigens. One hundred ninety-six of these were located in expressed genes, still exceeding the number of MS-detected neoantigens 65-fold. Treatment of four PDOs with IFNγ upregulated HLA class I expression and qualitatively changed the immunopeptidome, with increased presentation of IFNγ-inducible genes. HLA class II presented peptides increased dramatically with IFNγ treatment. MEK-inhibitor treatment showed no consistent effect on HLA class I or II expression or the peptidome. Importantly, no additional HLA class I or II presented neoantigens became detectable with any treatment. CONCLUSIONS Only 3 out of 612 non-silent mutations encoded for neoantigens that were detectable by MS. Although MS has sensitivity limits and biases, and likely underestimated the true neoantigen burden, this established a lower bound of the percentage of non-silent mutations that encode for presented neoantigens, which may be as low as 0.5%. This could be a reason for the poor responses of non-hypermutated CRCs to immune checkpoint inhibitors. MEK-inhibitors recently failed to improve checkpoint-inhibitor efficacy in CRC and the observed lack of HLA upregulation or improved peptide presentation may explain this.
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Affiliation(s)
- Alice Newey
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Beatrice Griffiths
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Justine Michaux
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Hui Song Pak
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Andrew Woolston
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Maria Semiannikova
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Georgia Spain
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Louise J. Barber
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Sheela Rao
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - David Watkins
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - Ian Chau
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - George Coukos
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Naureen Starling
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - David Cunningham
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - Michal Bassani-Sternberg
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Marco Gerlinger
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
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162
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Catalano I, Grassi E, Bertotti A, Trusolino L. Immunogenomics of Colorectal Tumors: Facts and Hypotheses on an Evolving Saga. Trends Cancer 2019; 5:779-788. [PMID: 31813455 DOI: 10.1016/j.trecan.2019.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 01/10/2023]
Abstract
Immunotherapy with immune checkpoint inhibitors is an approved treatment option for a subpopulation of patients with colorectal cancers that display microsatellite instability. However, not all individuals within this subgroup respond to immunotherapy, and molecular biomarkers for effective patient stratification are still lacking. In this opinion article, we provide an overview of the different biological parameters that contribute to rendering colorectal cancers with microsatellite instability potentially sensitive to immunotherapy. We critically discuss the reasons why such parameters have limited predictive value and the implications therein. We also consider that a more informed knowledge of response determinants in this tumor subtype could help understand the mechanisms of immunotherapy resistance in microsatellite stable tumors. We conclude that the dynamic nature of the interactions between cancer and immune cells complicates conventional biomarker development and argue that a new generation of adaptive metrics, borrowed from evolutionary genetics, may improve the effectiveness and reliability of clinical decision making.
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Affiliation(s)
- Irene Catalano
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Elena Grassi
- Candiolo Cancer Institute - FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO IRCCS, 10060 Candiolo, Torino, Italy.
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163
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Sveen A, Cremolini C, Dienstmann R. Predictive modeling in colorectal cancer: time to move beyond consensus molecular subtypes. Ann Oncol 2019; 30:1682-1685. [PMID: 31868904 DOI: 10.1093/annonc/mdz412] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- A Sveen
- Division for Cancer Medicine, Department of Molecular Oncology, Institute for Cancer Research & K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - C Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - R Dienstmann
- Oncology Data Science, Vall d'Hebron Institute of Oncology, Barcelona, Spain.
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164
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Khan K, Valeri N, Dearman C, Rao S, Watkins D, Starling N, Chau I, Cunningham D. Targeting EGFR pathway in metastatic colorectal cancer- tumour heterogeniety and convergent evolution. Crit Rev Oncol Hematol 2019; 143:153-163. [PMID: 31678702 DOI: 10.1016/j.critrevonc.2019.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/30/2022] Open
Abstract
Despite significant progress in management of metastatic colorectal cancer (mCRC) pertaining to better screening procedures and amelioration of the therapeutic armamentarium with targeted therapies, prognosis remains poor. Targeting epidermal growth factor receptor (EGFR) has been of particular interest owing to favourable efficacy benefits demonstrated by monoclonal antibodies (cetuximab and panitumumab) in various clinical settings and development of predictive biomarkers informing treatment decisions respectively. In spite of optimal patient selection based on RAS mutation status, primary and secondary resistance to monoclonal antibodies is higher than desired. Further research into predictive biomarkers is therefore essential, but has, to date, been conducted with considerable limitations. Whilst molecular heterogeneity has been demonstrated by several studies in mCRC, for incomprehensible reasons, multiple resistant genetic alterations that emerge under the selective pressure of EGFR-targeted therapies are somehow able to influence the biological and clinical behaviour of cancer cells, despite being detectable at extremely low frequencies. Intriguingly, these subclonal events largely seem to converge on RAS/RAF/MAPK pathway in patients treated with EGFR-targeted monoclonal antibodies. This review describes the clinical and biological evolution and development of EGFR targeted therapies in mCRC, the challenges in the presence of molecular complexities, the role of cell free (cf)-DNA and future strategies that could lead to further optimal discovery of clinically meaningful biomarkers and application of precision medicine.
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Affiliation(s)
- Khurum Khan
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK; Gastrointestinal Unit, University College London Hospitals, 250 Euston Road London, NW1 2AF, UK
| | - Nicola Valeri
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Charles Dearman
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Sheela Rao
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - David Watkins
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Naureen Starling
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - Ian Chau
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, Sutton SM2 5PT, UK.
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166
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Abstract
In this issue of Cancer Cell, Woolston et al. show that colorectal cancers that become refractory to initially effective anti-EGFR therapy contain an abundance of stromal and immune cells, irrespective of the contextual presence of resistance-conferring mutations. This reconfiguration puts forward therapeutic opportunities for patients who relapse on EGFR-targeting treatment.
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Affiliation(s)
- Irene Catalano
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy.
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