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García-Ruano D, Jain A, Heins ZJ, Wong BG, Yimer Wolle E, Khalil AS, Coudreuse D. Long-term evolution of proliferating cells using the eVOLVER platform. Open Biol 2023; 13:230118. [PMID: 37491941 PMCID: PMC10369027 DOI: 10.1098/rsob.230118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/28/2023] [Indexed: 07/27/2023] Open
Abstract
Experimental evolution using fast-growing unicellular organisms is a unique strategy for deciphering the principles and mechanisms underlying evolutionary processes as well as the architecture and wiring of basic biological functions. Over the past decade, this approach has benefited from the development of powerful systems for the continuous control of the growth of independently evolving cultures. While the first devices compatible with multiplexed experimental evolution remained challenging to implement and required constant user intervention, the recently developed eVOLVER framework represents a fully automated closed-loop system for laboratory evolution assays. However, it remained difficult to maintain and compare parallel evolving cultures in tightly controlled environments over long periods of time using eVOLVER. Furthermore, a number of tools were lacking to cope with the various issues that inevitably occur when conducting such long-term assays. Here we present a significant upgrade of the eVOLVER framework, providing major modifications of the experimental methodology, hardware and software as well as a new stand-alone protocol. Altogether, these adaptations and improvements make the eVOLVER a versatile and unparalleled set-up for long-term experimental evolution.
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Affiliation(s)
- Daniel García-Ruano
- Institute of Genetics and Development of Rennes, CNRS UMR 6290 – University of Rennes 1, Rennes, France
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
| | - Akanksha Jain
- Institute of Genetics and Development of Rennes, CNRS UMR 6290 – University of Rennes 1, Rennes, France
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
| | - Zachary J. Heins
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Brandon G. Wong
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Ezira Yimer Wolle
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Ahmad S. Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA
| | - Damien Coudreuse
- Institute of Genetics and Development of Rennes, CNRS UMR 6290 – University of Rennes 1, Rennes, France
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
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2
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Garc A-Ruano D, Jain A, Heins ZJ, Wong BG, Wolle EY, Khalil AS, Coudreuse D. Long-term evolution of proliferating cells using the eVOLVER platform. bioRxiv 2023:2023.03.28.534552. [PMID: 37034650 PMCID: PMC10081182 DOI: 10.1101/2023.03.28.534552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Experimental evolution using fast-growing unicellular organisms is a unique strategy for deciphering the principles and mechanisms underlying evolutionary processes as well as the architecture and wiring of basic biological functions. Over the past decade, this approach has benefited from the development of powerful systems for the continuous control of the growth of independently evolving cultures. While the first devices compatible with multiplexed experimental evolution remained challenging to implement and required constant user intervention, the recently-developed eVOLVER framework represents a fully automated closed-loop system for laboratory evolution assays. However, it remained difficult to maintain and compare parallel evolving cultures in tightly controlled environments over long periods of time using eVOLVER. Furthermore, a number of tools were lacking to cope with the various issues that inevitably occur when conducting such long-term assays. Here we present a significant upgrade of the eVOLVER framework, providing major modifications of the experimental methodology, hardware and software as well as a new standalone protocol. Altogether, these adaptations and improvements make the eVOLVER a versatile and unparalleled setup for long-term experimental evolution.
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Huang TP, Heins ZJ, Miller SM, Wong BG, Balivada PA, Wang T, Khalil AS, Liu DR. High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Nat Biotechnol 2023; 41:96-107. [PMID: 36076084 PMCID: PMC9849140 DOI: 10.1038/s41587-022-01410-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/30/2022] [Indexed: 01/25/2023]
Abstract
Despite the availability of Cas9 variants with varied protospacer-adjacent motif (PAM) compatibilities, some genomic loci-especially those with pyrimidine-rich PAM sequences-remain inaccessible by high-activity Cas9 proteins. Moreover, broadening PAM sequence compatibility through engineering can increase off-target activity. With directed evolution, we generated four Cas9 variants that together enable targeting of most pyrimidine-rich PAM sequences in the human genome. Using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution, we evolved Nme2Cas9, a compact Cas9 variant, into variants that recognize single-nucleotide pyrimidine-PAM sequences. We developed a general selection strategy that requires functional editing with fully specified target protospacers and PAMs. We applied this selection to evolve high-activity variants eNme2-T.1, eNme2-T.2, eNme2-C and eNme2-C.NR. Variants eNme2-T.1 and eNme2-T.2 offer access to N4TN PAM sequences with comparable editing efficiencies as existing variants, while eNme2-C and eNme2-C.NR offer less restrictive PAM requirements, comparable or higher activity in a variety of human cell types and lower off-target activity at N4CN PAM sequences.
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Affiliation(s)
- Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zachary J Heins
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Brandon G Wong
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Pallavi A Balivada
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. Nat Rev Methods Primers 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
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5
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Wu P, Heins ZJ, Muller JT, Katsnelson L, de Bruijn I, Abeshouse AA, Schultz N, Fenyö D, Gao J. Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal. Mol Cell Proteomics 2019; 18:1893-1898. [PMID: 31308250 PMCID: PMC6731080 DOI: 10.1074/mcp.tir119.001673] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 07/14/2019] [Indexed: 11/06/2022] Open
Abstract
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced extensive mass spectrometry-based proteomics data for selected breast, colon, and ovarian tumors from The Cancer Genome Atlas (TCGA). We have incorporated the CPTAC proteomics data into the cBioPortal to support easy exploration and integrative analysis of these proteomic datasets in the context of the clinical and genomics data from the same tumors. cBioPortal is an open source platform for exploring, visualizing, and analyzing multidimensional cancer genomics and clinical data. The public instance of the cBioPortal (http://cbioportal.org/) hosts more than 200 cancer genomics studies, including all of the data from TCGA. Its biologist-friendly interface provides many rich analysis features, including a graphical summary of gene-level data across multiple platforms, correlation analysis between genes or other data types, survival analysis, and per-patient data visualization. Here, we present the integration of the CPTAC mass spectrometry-based proteomics data into the cBioPortal, consisting of 77 breast, 95 colorectal, and 174 ovarian tumors that already have been profiled by TCGA for mutations, copy number alterations, gene expression, and DNA methylation. As a result, the CPTAC data can now be easily explored and analyzed in the cBioPortal in the context of clinical and genomics data. By integrating CPTAC data into cBioPortal, limitations of TCGA proteomics array data can be overcome while also providing a user-friendly web interface, a web API, and an R client to query the mass spectrometry data together with genomic, epigenomic, and clinical data.
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Affiliation(s)
- Pamela Wu
- ‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; §Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016; ¶Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016
| | - Zachary J Heins
- ‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - James T Muller
- ¶Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016
| | - Lizabeth Katsnelson
- ¶Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016
| | - Ino de Bruijn
- ‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Adam A Abeshouse
- ‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Nikolaus Schultz
- ‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065; **Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - David Fenyö
- ‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; §Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016.
| | - Jianjiong Gao
- ‖Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065; **Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
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6
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Heins ZJ, Mancuso CP, Kiriakov S, Wong BG, Bashor CJ, Khalil AS. Designing Automated, High-throughput, Continuous Cell Growth Experiments Using eVOLVER. J Vis Exp 2019. [PMID: 31157778 DOI: 10.3791/59652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Continuous culture methods enable cells to be grown under quantitatively controlled environmental conditions, and are thus broadly useful for measuring fitness phenotypes and improving our understanding of how genotypes are shaped by selection. Extensive recent efforts to develop and apply niche continuous culture devices have revealed the benefits of conducting new forms of cell culture control. This includes defining custom selection pressures and increasing throughput for studies ranging from long-term experimental evolution to genome-wide library selections and synthetic gene circuit characterization. The eVOLVER platform was recently developed to meet this growing demand: a continuous culture platform with a high degree of scalability, flexibility, and automation. eVOLVER provides a single standardizing platform that can be (re)-configured and scaled with minimal effort to perform many different types of high-throughput or multi-dimensional growth selection experiments. Here, a protocol is presented to provide users of the eVOLVER framework a description for configuring the system to conduct a custom, large-scale continuous growth experiment. Specifically, the protocol guides users on how to program the system to multiplex two selection pressures - temperature and osmolarity - across many eVOLVER vials in order to quantify fitness landscapes of Saccharomyces cerevisiae mutants at fine resolution. We show how the device can be configured both programmatically, through its open-source web-based software, and physically, by arranging fluidic and hardware layouts. The process of physically setting up the device, programming the culture routine, monitoring and interacting with the experiment in real-time over the internet, sampling vials for subsequent offline analysis, and post experiment data analysis are detailed. This should serve as a starting point for researchers across diverse disciplines to apply eVOLVER in the design of their own complex and high-throughput cell growth experiments to study and manipulate biological systems.
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Affiliation(s)
- Zachary J Heins
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | - Christopher P Mancuso
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | - Szilvia Kiriakov
- Biological Design Center, Boston University; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University
| | - Brandon G Wong
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University
| | | | - Ahmad S Khalil
- Biological Design Center, Boston University; Department of Biomedical Engineering, Boston University; Wyss Institute for Biologically Inspired Engineering, Harvard University;
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7
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Janjigian YY, Sanchez-Vega F, Jonsson P, Chatila WK, Hechtman JF, Ku GY, Riches JC, Tuvy Y, Kundra R, Bouvier N, Vakiani E, Gao J, Heins ZJ, Gross BE, Kelsen DP, Zhang L, Strong VE, Schattner M, Gerdes H, Coit DG, Bains M, Stadler ZK, Rusch VW, Jones DR, Molena D, Shia J, Robson ME, Capanu M, Middha S, Zehir A, Hyman DM, Scaltriti M, Ladanyi M, Rosen N, Ilson DH, Berger MF, Tang L, Taylor BS, Solit DB, Schultz N. Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer. Cancer Discov 2018; 8:49-58. [PMID: 29122777 PMCID: PMC5813492 DOI: 10.1158/2159-8290.cd-17-0787] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
The incidence of esophagogastric cancer is rapidly rising, but only a minority of patients derive durable benefit from current therapies. Chemotherapy as well as anti-HER2 and PD-1 antibodies are standard treatments. To identify predictive biomarkers of drug sensitivity and mechanisms of resistance, we implemented prospective tumor sequencing of patients with metastatic esophagogastric cancer. There was no association between homologous recombination deficiency defects and response to platinum-based chemotherapy. Patients with microsatellite instability-high tumors were intrinsically resistant to chemotherapy but more likely to achieve durable responses to immunotherapy. The single Epstein-Barr virus-positive patient achieved a durable, complete response to immunotherapy. The level of ERBB2 amplification as determined by sequencing was predictive of trastuzumab benefit. Selection for a tumor subclone lacking ERBB2 amplification, deletion of ERBB2 exon 16, and comutations in the receptor tyrosine kinase, RAS, and PI3K pathways were associated with intrinsic and/or acquired trastuzumab resistance. Prospective genomic profiling can identify patients most likely to derive durable benefit to immunotherapy and trastuzumab and guide strategies to overcome drug resistance.Significance: Clinical application of multiplex sequencing can identify biomarkers of treatment response to contemporary systemic therapies in metastatic esophagogastric cancer. This large prospective analysis sheds light on the biological complexity and the dynamic nature of therapeutic resistance in metastatic esophagogastric cancers. Cancer Discov; 8(1); 49-58. ©2017 AACR.See related commentary by Sundar and Tan, p. 14See related article by Pectasides et al., p. 37This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
| | - Francisco Sanchez-Vega
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Jamie C Riches
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Ritika Kundra
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jianjiong Gao
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zachary J Heins
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin E Gross
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Schattner
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Hans Gerdes
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manjit Bains
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Valerie W Rusch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Michael F Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
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8
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:1004. [PMID: 28777785 DOI: 10.1038/nm0817-1004c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Abida W, Armenia J, Gopalan A, Brennan R, Walsh M, Barron D, Danila D, Rathkopf D, Morris M, Slovin S, McLaughlin B, Curtis K, Hyman DM, Durack JC, Solomon SB, Arcila ME, Zehir A, Syed A, Gao J, Chakravarty D, Vargas HA, Robson ME, Vijai J, Offit K, Donoghue MT, Abeshouse AA, Kundra R, Heins ZJ, Penson AV, Harris C, Taylor BS, Ladanyi M, Mandelker D, Zhang L, Reuter VE, Kantoff PW, Solit DB, Berger MF, Sawyers CL, Schultz N, Scher HI. Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making. JCO Precis Oncol 2017; 2017:PO.17.00029. [PMID: 28825054 PMCID: PMC5558263 DOI: 10.1200/po.17.00029] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE A long natural history and a predominant osseous pattern of metastatic spread are impediments to the adoption of precision medicine in patients with prostate cancer. To establish the feasibility of clinical genomic profiling in the disease, we performed targeted deep sequencing of tumor and normal DNA from patients with locoregional, metastatic non-castrate, and metastatic castration-resistant prostate cancer (CRPC). METHODS Patients consented to genomic analysis of their tumor and germline DNA. A hybridization capture-based clinical assay was employed to identify single nucleotide variations, small insertions and deletions, copy number alterations and structural rearrangements in over 300 cancer-related genes in tumors and matched normal blood. RESULTS We successfully sequenced 504 tumors from 451 patients with prostate cancer. Potentially actionable alterations were identified in DNA damage repair (DDR), PI3K, and MAP kinase pathways. 27% of patients harbored a germline or a somatic alteration in a DDR gene that may predict for response to PARP inhibition. Profiling of matched tumors from individual patients revealed that somatic TP53 and BRCA2 alterations arose early in tumors from patients who eventually developed metastatic disease. In contrast, comparative analysis across disease states revealed that APC alterations were enriched in metastatic tumors, while ATM alterations were specifically enriched in CRPC. CONCLUSION Through genomic profiling of prostate tumors representing the disease clinical spectrum, we identified a high frequency of potentially actionable alterations and possible drivers of disease initiation, metastasis and castration-resistance. Our findings support the routine use of tumor and germline DNA profiling for patients with advanced prostate cancer, for the purpose of guiding enrollment in targeted clinical trials and counseling families at increased risk of malignancy.
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Affiliation(s)
- Wassim Abida
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Armenia
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anuradha Gopalan
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Brennan
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Walsh
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Barron
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Danila
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana Rathkopf
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Morris
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Susan Slovin
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kristen Curtis
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M. Hyman
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeremy C. Durack
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Maria E. Arcila
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aijazuddin Syed
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjiong Gao
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Mark E. Robson
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joseph Vijai
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ritika Kundra
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zachary J. Heins
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Barry S. Taylor
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liying Zhang
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Victor E. Reuter
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David B. Solit
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Nikolaus Schultz
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
| | - Howard I. Scher
- All authors: Memorial Sloan Kettering Cancer Center, New York, NY
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10
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Ku GY, Sanchez-Vega F, Chatila W, Margolis M, Fein C, Ilson DH, Hechtman JF, Tuvy Y, Bouvier N, Kundra R, Shia J, Heins ZJ, Middha S, Zehir A, Ladanyi M, Berger MF, Tang LH, Solit DB, Schultz N, Janjigian YY. Correlation of benefit from immune checkpoint inhibitors with next gen sequencing (NGS) profiles in esophagogastric cancer (EGC) patients. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.4025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
4025 Background: Immuno-oncology (IO) with anti-PD-1 and –PD-L1 antibodies (Abs) is active in EGC but only benefits a minority of Pts. Biomarkers are needed to identify responders. Methods: We reviewed our experience of Pts treated with anti-PD-1/PD-L1 Abs and correlated their outcomes with PD-L1 and mismatch repair protein (MMR) status by immunohistochemistry (IHC), as well as MSK-IMPACT (≥340-gene) NGS profile. MSIsensor from IMPACT assesses microsatellite instability phenotype, while ≥20 mutations (or 17 mutations/Mb) strongly correlates with MMR-deficiency (dMMR) by IHC (J Clin Oncol 2016;34:2141). Progression-free (PFS) and overall survival (OS) were analyzed from the start of IO. Results: 71 Pts were identified, with 3 Pts receiving 2 IO regimens. 66 had adenoCAs and 5 had squamous CAs. Median age 58, 77% male, 96% had received ≥2 prior chemo regimens. 39 (55%), 18 (25%) and 17 Pts (24%) respectively received anti-PD-1, anti-PD-L1 and anti-CTLA-4 plus anti-PD-1/PD-L1 Abs. 6 Pts (8%) had objective response (2 complete responses or CRs) and the median PFS and OS are 1.6 and 4.7 mos; 2-yr OS is 17%. PD-L1 IHC was performed in 16 Pts (23%; 7 +ve), MMR was tested in 20 Pts (28%; 4 dMMR) and IMPACT was obtained in 44 Pts (62%). All 4 dMMR tumors were also MSI by MSIsensor and had a median of 46 mutations (range, 29-63) or, equivalently, 33 mutations/Mb (range, 21-46); 2 of 2 dMMR tumors tested PD-L1 +ve. 3 of the 4 Pts with dMMR/MSI tumors had a response (including 1 CR) and the median OS of these 4 Pts is not reached with 23+ months of follow-up. Finally, a patient whose tumor is MMR-proficient, not MSI but has 15 mutations (including in POLD1), achieved an ongoing CR at 37+ mos. For the 44 Pts with IMPACT testing, there appeared to be improved OS for tumors with ≥10 vs. <10 mutations/Mb (2-yr OS 80% vs. 12%, p=0.03). Conclusions: Pts with tumors that are MSI or have ≥10 mutations/Mb on MSK-IMPACT appear to derive significant benefit from IO. MSK-IMPACT can offer novel information, identify novel mutations (e.g. POLD1) and may be used to help select Pts for IO. We are seeking to define a mutation no. cut-off that can serve as a biomarker and updated data will be presented.
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Affiliation(s)
| | | | - Walid Chatila
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Carly Fein
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Yaelle Tuvy
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Sumit Middha
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Laura H. Tang
- Memorial Sloan-Kettering Cancer Center, New York, NY
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11
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:703-713. [PMID: 28481359 PMCID: PMC5461196 DOI: 10.1038/nm.4333] [Citation(s) in RCA: 2144] [Impact Index Per Article: 306.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.
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Affiliation(s)
- Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronak H Shah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hyunjae R Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Barron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Abhinita S Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mustafa H Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Zhen Y Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iwona J Kiecka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie B Son
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lisa Stewart
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kerry A Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam A Abeshouse
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander V Penson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Niedzica Camacho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew T Chang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin E Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zachary J Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hsiao-Wei Chen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sarah Phillips
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jiaojiao Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Wills
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael Eubank
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stacy B Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stuart M Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dalicia N Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jesse Galle
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert Durany
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roy Cambria
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emmet J Jordan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maeve A Lowery
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio M Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tara E Soumerai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Coleman
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bernard Bochner
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul J Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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12
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Yaeger R, Shah MA, Miller VA, Kelsen JR, Wang K, Heins ZJ, Ross JS, He Y, Sanford E, Yantiss RK, Balasubramanian S, Stephens PJ, Schultz N, Oren M, Tang L, Kelsen D. Genomic Alterations Observed in Colitis-Associated Cancers Are Distinct From Those Found in Sporadic Colorectal Cancers and Vary by Type of Inflammatory Bowel Disease. Gastroenterology 2016; 151:278-287.e6. [PMID: 27063727 PMCID: PMC5472377 DOI: 10.1053/j.gastro.2016.04.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/25/2016] [Accepted: 04/02/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel diseases, such as Crohn's disease (CD) and ulcerative colitis (UC), are at increased risk for small bowel or colorectal cancers (colitis-associated cancers [CACs]). We compared the spectrum of genomic alterations in CACs with those of sporadic colorectal cancers (CRCs) and investigated differences between CACs from patients with CD vs UC. METHODS We studied tumor tissues from patients with CACs treated at Memorial Sloan Kettering Cancer Center or Weill Cornell Medical College from 2003 through 2015. We performed hybrid capture-based next-generation sequencing analysis of >300 cancer-related genes to comprehensively characterize genomic alterations. RESULTS We performed genomic analyses of 47 CACs (from 29 patients with UC and 18 with CD; 43 primary tumors and 4 metastases). Primary tumors developed in the ileum (n = 2), right colon (n = 18), left colon (n = 6), and rectosigmoid or rectum (n = 21). We found genomic alterations in TP53, IDH1, and MYC to be significantly more frequent, and mutations in APC to be significantly less frequent, than those reported in sporadic CRCs by The Cancer Genome Atlas or Foundation Medicine. We identified genomic alterations that might be targeted by a therapeutic agent in 17 of 47 (36%) CACs. These included the mutation encoding IDH1 R132; amplification of FGFR1, FGFR2, and ERBB2; and mutations encoding BRAF V600E and an EML4-ALK fusion protein. Alterations in IDH1 and APC were significantly more common in CACs from patients with CD than UC. CONCLUSIONS In an analysis of CACs from 47 patients, we found significant differences in the spectrum of genomic alterations in CACs compared with sporadic CRCs. We observed a high frequency of IDH1 R132 mutations in patients with CD but not UC, as well as a high frequency of MYC amplification in CACs. Many genetic alterations observed in CACs could serve as therapeutic targets.
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Affiliation(s)
- Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manish A. Shah
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Judith R. Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kai Wang
- Foundation Medicine Inc., Cambridge, MA,Department of Pathology & Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zachary J. Heins
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Yuting He
- Foundation Medicine Inc., Cambridge, MA
| | | | - Rhonda K. Yantiss
- Department of Pathology, Weill Cornell Medical College, New York, NY
| | | | | | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute, Israel
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York.
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13
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Harding JJ, Heins ZJ, Connell LC, Soumerai T, Kemeny NE, Jarnagin WR, O'Reilly EM, DeMatteo RP, D'Angelica MI, Lowery MA, Kingham TP, Gambarin M, Hyman DM, LY M, Hamilton CR, Berger MF, Solit DB, Saltz L, Schultz N, Abou-Alfa GK. Identification of potentially actionable molecular alterations in advanced hepatocellular carcinoma (HCC). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e15635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- James J. Harding
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | - Tara Soumerai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Maeve Aine Lowery
- Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY
| | | | - Maya Gambarin
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Michele LY
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Leonard Saltz
- Memorial Sloan Kettering Cancer Center, New York, NY
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