1
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Hynds RE, Huebner A, Pearce DR, Hill MS, Akarca AU, Moore DA, Ward S, Gowers KHC, Karasaki T, Al Bakir M, Wilson GA, Pich O, Martínez-Ruiz C, Hossain ASMM, Pearce SP, Sivakumar M, Ben Aissa A, Grönroos E, Chandrasekharan D, Kolluri KK, Towns R, Wang K, Cook DE, Bosshard-Carter L, Naceur-Lombardelli C, Rowan AJ, Veeriah S, Litchfield K, Crosbie PAJ, Dive C, Quezada SA, Janes SM, Jamal-Hanjani M, Marafioti T, McGranahan N, Swanton C. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models. Nat Commun 2024; 15:4653. [PMID: 38821942 PMCID: PMC11143323 DOI: 10.1038/s41467-024-47547-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/28/2024] [Indexed: 06/02/2024] Open
Abstract
Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor. Whole-exome sequencing enabled comparison of tumors and PDX models and we provide an adapted mouse reference genome for improved removal of NOD scid gamma (NSG) mouse-derived reads from sequencing data. PDX model establishment caused a genomic bottleneck, with models often representing a single tumor subclone. While distinct tumor subclones were represented in independent models from the same tumor, individual PDX models did not fully recapitulate intratumor heterogeneity. On-going genomic evolution in mice contributed modestly to the genomic distance between tumors and PDX models. Our study highlights the importance of considering primary tumor heterogeneity when using PDX models and emphasizes the benefit of comprehensive tumor sampling.
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Affiliation(s)
- Robert E Hynds
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Epithelial Cell Biology in ENT Research Group (EpiCENTR), Developmental Biology and Cancer, Great Ormond Street University College London Institute of Child Health, London, UK.
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David R Pearce
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ayse U Akarca
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Kate H C Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - A S Md Mukarram Hossain
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Simon P Pearce
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Deepak Chandrasekharan
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Krishna K Kolluri
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Rebecca Towns
- Biological Services Unit, University College London, London, UK
| | - Kaiwen Wang
- School of Medicine, University of Leeds, Leeds, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Leticia Bosshard-Carter
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Andrew J Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Philip A J Crosbie
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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2
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Chen X, Cheng G, Zhu L, Liu T, Yang X, Liu R, Ou Z, Zhang S, Tan W, Lin D, Wu C. Alarmin S100A8 imparts chemoresistance of esophageal cancer by reprogramming cancer-associated fibroblasts. Cell Rep Med 2024:101576. [PMID: 38776909 DOI: 10.1016/j.xcrm.2024.101576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Chemotherapy remains the first-line treatment for advanced esophageal cancer. However, durable benefits are achieved by only a limited subset of individuals due to the elusive chemoresistance. Here, we utilize patient-derived xenografts (PDXs) from esophageal squamous-cell carcinoma to investigate chemoresistance mechanisms in preclinical settings. We observe that activated cancer-associated fibroblasts (CAFs) are enriched in the tumor microenvironment of PDXs resistant to chemotherapy. Mechanistically, we reveal that cancer-cell-derived S100A8 triggers the intracellular RhoA-ROCK-MLC2-MRTF-A pathway by binding to the CD147 receptor of CAFs, inducing CAF polarization and leading to chemoresistance. Therapeutically, we demonstrate that blocking the S100A8-CD147 pathway can improve chemotherapy efficiency. Prognostically, we found the S100A8 levels in peripheral blood can serve as an indicator of chemotherapy responsiveness. Collectively, our study offers a comprehensive understanding of the molecular mechanisms underlying chemoresistance in esophageal cancer and highlights the potential value of S100A8 in the clinical management of esophageal cancer.
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Affiliation(s)
- Xinjie Chen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Guoyu Cheng
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Liang Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Tianyuan Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Xinyu Yang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Rucheng Liu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Zhengjie Ou
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Wen Tan
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100021, China; Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; CAMS Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100006, China.
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3
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Wu Y, Chen S, Yang X, Sato K, Lal P, Wang Y, Shinkle AT, Wendl MC, Primeau TM, Zhao Y, Gould A, Sun H, Mudd JL, Hoog J, Mashl RJ, Wyczalkowski MA, Mo CK, Liu R, Herndon JM, Davies SR, Liu D, Ding X, Evrard YA, Welm BE, Lum D, Koh MY, Welm AL, Chuang JH, Moscow JA, Meric-Bernstam F, Govindan R, Li S, Hsieh J, Fields RC, Lim KH, Ma CX, Zhang H, Ding L, Chen F. Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma. Cancer Res 2023; 83:4161-4178. [PMID: 38098449 PMCID: PMC10722140 DOI: 10.1158/0008-5472.can-23-0604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/17/2023] [Accepted: 09/25/2023] [Indexed: 12/18/2023]
Abstract
Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug resistance. Combination therapies that leverage tumor molecular profiles could offer an avenue for enhancing treatment efficacy and addressing the limitations of current therapies. To identify effective strategies for treating RCC, we selected ten drugs guided by tumor biology to test in six RCC patient-derived xenograft (PDX) models. The multitargeted tyrosine kinase inhibitor (TKI) cabozantinib and mTORC1/2 inhibitor sapanisertib emerged as the most effective drugs, particularly when combined. The combination demonstrated favorable tolerability and inhibited tumor growth or induced tumor regression in all models, including two from patients who experienced treatment failure with FDA-approved TKI and immunotherapy combinations. In cabozantinib-treated samples, imaging analysis revealed a significant reduction in vascular density, and single-nucleus RNA sequencing (snRNA-seq) analysis indicated a decreased proportion of endothelial cells in the tumors. SnRNA-seq data further identified a tumor subpopulation enriched with cell-cycle activity that exhibited heightened sensitivity to the cabozantinib and sapanisertib combination. Conversely, activation of the epithelial-mesenchymal transition pathway, detected at the protein level, was associated with drug resistance in residual tumors following combination treatment. The combination effectively restrained ERK phosphorylation and reduced expression of ERK downstream transcription factors and their target genes implicated in cell-cycle control and apoptosis. This study highlights the potential of the cabozantinib plus sapanisertib combination as a promising treatment approach for patients with RCC, particularly those whose tumors progressed on immune checkpoint inhibitors and other TKIs. SIGNIFICANCE The molecular-guided therapeutic strategy of combining cabozantinib and sapanisertib restrains ERK activity to effectively suppress growth of renal cell carcinomas, including those unresponsive to immune checkpoint inhibitors.
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Affiliation(s)
- Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Xiaolu Yang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Kazuhito Sato
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Preet Lal
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yuefan Wang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Andrew T. Shinkle
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Michael C. Wendl
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
- McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tina M. Primeau
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Alanna Gould
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Hua Sun
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Jacqueline L. Mudd
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Jeremy Hoog
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - R. Jay Mashl
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Matthew A. Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Chia-Kuei Mo
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - Ruiyang Liu
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| | - John M. Herndon
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
- Department of Surgery, Washington University in St. Louis, St. Louis, Missouri
| | - Sherri R. Davies
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Di Liu
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Xi Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yvonne A. Evrard
- Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Bryan E. Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - David Lum
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Mei Yee Koh
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Alana L. Welm
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Jeffrey A. Moscow
- Investigational Drug Branch, National Cancer Institute, Bethesda, Maryland
| | | | - Ramaswamy Govindan
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Shunqiang Li
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - James Hsieh
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ryan C. Fields
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Kian-Huat Lim
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Cynthia X. Ma
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
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4
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He F, Bandyopadhyay AM, Klesse LJ, Rogojina A, Chun SH, Butler E, Hartshorne T, Holland T, Garcia D, Weldon K, Prado LNP, Langevin AM, Grimes AC, Sugalski A, Shah S, Assanasen C, Lai Z, Zou Y, Kurmashev D, Xu L, Xie Y, Chen Y, Wang X, Tomlinson GE, Skapek SX, Houghton PJ, Kurmasheva RT, Zheng S. Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer. Nat Commun 2023; 14:7600. [PMID: 37990009 PMCID: PMC10663468 DOI: 10.1038/s41467-023-43373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Subcutaneous patient-derived xenografts (PDXs) are an important tool for childhood cancer research. Here, we describe a resource of 68 early passage PDXs established from 65 pediatric solid tumor patients. Through genomic profiling of paired PDXs and patient tumors (PTs), we observe low mutational similarity in about 30% of the PT/PDX pairs. Clonal analysis in these pairs show an aggressive PT minor subclone seeds the major clone in the PDX. We show evidence that this subclone is more immunogenic and is likely suppressed by immune responses in the PT. These results suggest interplay between intratumoral heterogeneity and antitumor immunity may underlie the genetic disparity between PTs and PDXs. We further show that PDXs generally recapitulate PTs in copy number and transcriptomic profiles. Finally, we report a gene fusion LRPAP1-PDGFRA. In summary, we report a childhood cancer PDX resource and our study highlights the role of immune constraints on tumor evolution.
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Affiliation(s)
- Funan He
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
| | - Abhik M Bandyopadhyay
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Laura J Klesse
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Anna Rogojina
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sang H Chun
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Erin Butler
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Taylor Hartshorne
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Trevor Holland
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dawn Garcia
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Luz-Nereida Perez Prado
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Anne-Marie Langevin
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Allison C Grimes
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Aaron Sugalski
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Shafqat Shah
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
| | - Chatchawin Assanasen
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Dias Kurmashev
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Lin Xu
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Xiaojing Wang
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Gail E Tomlinson
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Pediatrics, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Stephen X Skapek
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Gill Center for Cancer and Blood Disorders, Children's Health Children's Medical Center, Dallas, TX, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX, USA.
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA.
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5
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Goodstal SM, Lin J, Crandall T, Crowley L, Bender AT, Pereira A, Soloviev M, Wesolowski JS, Iadevaia R, Schelhorn SE, Ross E, Morandi F, Ma J, Clark A. Preclinical evidence for the effective use of TL-895, a highly selective and potent second-generation BTK inhibitor, for the treatment of B-cell malignancies. Sci Rep 2023; 13:20412. [PMID: 37989777 PMCID: PMC10663516 DOI: 10.1038/s41598-023-47735-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
TL-895 (formerly known as M7583) is a potent, highly selective, adenosine triphosphate (ATP)-competitive, second-generation, irreversible inhibitor of Bruton's tyrosine kinase (BTK). We characterized its biochemical and cellular effects in in vitro and in vivo models. TL-895 was evaluated preclinically for potency against BTK using IC50 concentration-response curves; selectivity using a 270-kinase panel; BTK phosphorylation in Ramos Burkitt's lymphoma cells by ProteinSimple Wes analysis of one study; anti-proliferative effects in primary chronic lymphocytic leukemia (CLL) blasts; cell viability effects in diffuse large B-cell lymphoma (DLBCL) and mantle-cell lymphoma (MCL) cell lines; effects on antibody-dependent cell-mediated cytotoxicity (ADCC) from Daudi cells and chromium-51 release from human tumor cell lines; and efficacy in vivo using four MCL xenograft model and 21 DLBCL patient-derived xenograft (PDX) models (subtypes: 9 ABC, 11 GCB, 1 Unclassified). TL-895 was active against recombinant BTK (average IC50 1.5 nM) and inhibited only three additional kinases with IC50 within tenfold of BTK activity. TL-895 inhibited BTK auto-phosphorylation at the Y223 phosphorylation site (IC50 1-10 nM). TL-895 inhibited the proliferation of primary CLL blasts in vitro and inhibited growth in a subset of activated DLBCL and MCL cell lines. TL-895 inhibited the ADCC mechanism of therapeutic antibodies only at supra-clinical exposure levels. TL-895 significantly inhibited tumor growth in the Mino MCL xenograft model and in 5/21 DLBCL PDX models relative to vehicle controls. These findings demonstrate the potency of TL-895 for BTK and its efficacy in models of B-cell lymphoma despite its refined selectivity.
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Affiliation(s)
- Samantha M Goodstal
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA.
| | - Jing Lin
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Timothy Crandall
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Lindsey Crowley
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Andrew T Bender
- Research Unit Immunology, EMD Serono Research and Development Institute, Inc., Billerica, MA, 01821, USA
| | - Albertina Pereira
- Research Unit Immunology, EMD Serono Research and Development Institute, Inc., Billerica, MA, 01821, USA
| | - Maria Soloviev
- Protein Engineering Antibody Technologies, EMD Serono Research and Development Institute, Inc., Billerica, MA, 01821, USA
| | - John S Wesolowski
- Protein Engineering Antibody Technologies, EMD Serono Research and Development Institute, Inc., Billerica, MA, 01821, USA
| | - Riham Iadevaia
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Sven-Eric Schelhorn
- Oncology Bioinformatics Quantitative Pharmacology and Drug Disposition (QPD) Biopharma, Merck KGaA, 64293, Darmstadt, Germany
| | - Edith Ross
- Oncology Bioinformatics Quantitative Pharmacology and Drug Disposition (QPD) Biopharma, Merck KGaA, 64293, Darmstadt, Germany
| | - Federica Morandi
- Discovery and Development Technologies, EMD Serono Research and Development Institute, Inc., Billerica, MA, 01821, USA
| | - Jianguo Ma
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
| | - Anderson Clark
- Research Unit Oncology, EMD Serono Research and Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA, 01821, USA
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6
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Oien DB, Sharma S, Hattersley MM, DuPont M, Criscione SW, Prickett L, Goeppert AU, Drew L, Yao Y, Zhang J, Chan HM. BET inhibition targets ABC-DLBCL constitutive B-cell receptor signaling through PAX5. Blood Adv 2023; 7:5108-5121. [PMID: 37184294 PMCID: PMC10477446 DOI: 10.1182/bloodadvances.2022009257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023] Open
Abstract
B-cell receptor (BCR) signaling is essential for the diffuse large B-cell lymphoma (DLBCL) subtype that originates from activated B-cells (ABCs). ABC-DLBCL cells are sensitive to Bruton tyrosine kinase intervention. However, patients with relapsed or refractory ABC-DLBCL had overall response rates from 33% to 37% for Bruton tyrosine kinase inhibitors, suggesting the evaluation of combination-based treatment for improved efficacy. We investigated the efficacy and mechanism of the bromodomain and extraterminal motif (BET) inhibitor AZD5153 combined with the Bruton tyrosine kinase inhibitor acalabrutinib in ABC-DLBCL preclinical models. AZD5153 is a bivalent BET inhibitor that simultaneously engages the 2 bromodomains of BRD4. Adding AZD5153 to acalabrutinib demonstrated combination benefits in ABC-DLBCL cell line and patient-derived xenograft models. Differential expression analyses revealed PAX5 transcriptional activity as a novel downstream effector of this drug combination. PAX5 is a transcription factor for BCR signaling genes and may be critical for perpetually active BCR signaling in ABC-DLBCL. Our analyses further indicated significant alterations in BCR, RELB/alternative NF-κB, and toll-like receptor/interferon signaling. Validation of these results mapped a positive-feedback signaling loop regulated by PAX5. We demonstrated that AZD5153 decreased PAX5 expression, whereas acalabrutinib disruption of BCR signaling inhibited PAX5 activation. Furthermore, several interferon levels were decreased by AZD5153 and acalabrutinib in tumors. Adding interferon-beta1 (IFNβ1) to cells treated with acalabrutinib partially rescued PAX5 activation. Our results demonstrate that AZD5153 enhances the efficacy of acalabrutinib through PAX5 and BCR mechanisms that are critical for ABC-DLBCL.
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Affiliation(s)
- Derek B. Oien
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Samanta Sharma
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | | | - Michelle DuPont
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | | | - Laura Prickett
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Anne U. Goeppert
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Lisa Drew
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Yi Yao
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Jingwen Zhang
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
| | - Ho Man Chan
- Research and Early Development, Oncology R&D, AstraZeneca, Boston, MA
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7
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Fiumara M, Ferrari S, Omer-Javed A, Beretta S, Albano L, Canarutto D, Varesi A, Gaddoni C, Brombin C, Cugnata F, Zonari E, Naldini MM, Barcella M, Gentner B, Merelli I, Naldini L. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat Biotechnol 2023:10.1038/s41587-023-01915-4. [PMID: 37679541 DOI: 10.1038/s41587-023-01915-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
Abstract
Base and prime editors (BEs and PEs) may provide more precise genetic engineering than nuclease-based approaches because they bypass the dependence on DNA double-strand breaks. However, little is known about their cellular responses and genotoxicity. Here, we compared state-of-the-art BEs and PEs and Cas9 in human hematopoietic stem and progenitor cells with respect to editing efficiency, cytotoxicity, transcriptomic changes and on-target and genome-wide genotoxicity. BEs and PEs induced detrimental transcriptional responses that reduced editing efficiency and hematopoietic repopulation in xenotransplants and also generated DNA double-strand breaks and genotoxic byproducts, including deletions and translocations, at a lower frequency than Cas9. These effects were strongest for cytidine BEs due to suboptimal inhibition of base excision repair and were mitigated by tailoring delivery timing and editor expression through optimized mRNA design. However, BEs altered the mutational landscape of hematopoietic stem and progenitor cells across the genome by increasing the load and relative proportions of nucleotide variants. These findings raise concerns about the genotoxicity of BEs and PEs and warrant further investigation in view of their clinical application.
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Affiliation(s)
- Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Attya Omer-Javed
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Gaddoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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8
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Alkim E, Dowst H, DiCarlo J, Dobrolecki LE, Hernández-Herrera A, Hormuth DA, Liao Y, McOwiti A, Pautler R, Rimawi M, Roark A, Srinivasan RR, Virostko J, Zhang B, Zheng F, Rubin DL, Yankeelov TE, Lewis MT. Toward Practical Integration of Omic and Imaging Data in Co-Clinical Trials. Tomography 2023; 9:810-828. [PMID: 37104137 PMCID: PMC10144684 DOI: 10.3390/tomography9020066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023] Open
Abstract
Co-clinical trials are the concurrent or sequential evaluation of therapeutics in both patients clinically and patient-derived xenografts (PDX) pre-clinically, in a manner designed to match the pharmacokinetics and pharmacodynamics of the agent(s) used. The primary goal is to determine the degree to which PDX cohort responses recapitulate patient cohort responses at the phenotypic and molecular levels, such that pre-clinical and clinical trials can inform one another. A major issue is how to manage, integrate, and analyze the abundance of data generated across both spatial and temporal scales, as well as across species. To address this issue, we are developing MIRACCL (molecular and imaging response analysis of co-clinical trials), a web-based analytical tool. For prototyping, we simulated data for a co-clinical trial in "triple-negative" breast cancer (TNBC) by pairing pre- (T0) and on-treatment (T1) magnetic resonance imaging (MRI) from the I-SPY2 trial, as well as PDX-based T0 and T1 MRI. Baseline (T0) and on-treatment (T1) RNA expression data were also simulated for TNBC and PDX. Image features derived from both datasets were cross-referenced to omic data to evaluate MIRACCL functionality for correlating and displaying MRI-based changes in tumor size, vascularity, and cellularity with changes in mRNA expression as a function of treatment.
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Affiliation(s)
- Emel Alkim
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heidi Dowst
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julie DiCarlo
- Oden Institute for Computational Engineering and Sciences, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Austin, TX 78712, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology and Radiology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - David A Hormuth
- Oden Institute for Computational Engineering and Sciences, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Austin, TX 78712, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Apollo McOwiti
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robia Pautler
- Department of Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mothaffar Rimawi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ashley Roark
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jack Virostko
- Oden Institute for Computational Engineering and Sciences, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Austin, TX 78712, USA
- Department of Oncology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fei Zheng
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel L Rubin
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas E Yankeelov
- Oden Institute for Computational Engineering and Sciences, Austin, TX 78712, USA
- Livestrong Cancer Institutes, Austin, TX 78712, USA
- Department of Oncology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T Lewis
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology and Radiology, Baylor College of Medicine, Houston, TX 77030, USA
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9
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Ter Brugge P, Moser SC, Bièche I, Kristel P, Ibadioune S, Eeckhoutte A, de Bruijn R, van der Burg E, Lutz C, Annunziato S, de Ruiter J, Masliah Planchon J, Vacher S, Courtois L, El-Botty R, Dahmani A, Montaudon E, Morisset L, Sourd L, Huguet L, Derrien H, Nemati F, Chateau-Joubert S, Larcher T, Salomon A, Decaudin D, Reyal F, Coussy F, Popova T, Wesseling J, Stern MH, Jonkers J, Marangoni E. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers. Nat Commun 2023; 14:1958. [PMID: 37029129 PMCID: PMC10082194 DOI: 10.1038/s41467-023-37537-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.
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Affiliation(s)
- Petra Ter Brugge
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sarah C Moser
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Petra Kristel
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabrina Ibadioune
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Alexandre Eeckhoutte
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Julian de Ruiter
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Courtois
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Rania El-Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Elodie Montaudon
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ludivine Morisset
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Sourd
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Léa Huguet
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Heloise Derrien
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | | | | | - Anne Salomon
- Department of Pathology, Institut Curie, PSL University, 75005, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fabien Reyal
- Department of Surgery, Institut Curie, PSL University, 75005, Paris, France
| | - Florence Coussy
- Department of Medical Oncology, Institut Curie, PSL University, 75005, Paris, France
| | - Tatiana Popova
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jelle Wesseling
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marc-Henri Stern
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France.
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10
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Lee RH, Roy R, Li H, Hechmer A, Zhu TR, Izgutdina A, Olshen AB, Johnson DE, Grandis JR. Therapeutic implications of transcriptomics in head and neck cancer patient-derived xenografts. PLoS One 2023; 18:e0282177. [PMID: 36857322 PMCID: PMC9977000 DOI: 10.1371/journal.pone.0282177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/08/2023] [Indexed: 03/02/2023] Open
Abstract
There are currently no clinical strategies utilizing tumor gene expression to inform therapeutic selection for patients with head and neck squamous cell carcinoma (HNSCC). One of the challenges in developing predictive biomarkers is the limited characterization of preclinical HNSCC models. Patient-derived xenografts (PDXs) are increasingly recognized as translationally relevant preclinical avatars for human tumors; however, the overall transcriptomic concordance of HNSCC PDXs with primary human HNSCC is understudied, especially in human papillomavirus-associated (HPV+) disease. Here, we characterized 64 HNSCC PDXs (16 HPV+ and 48 HPV-) at the transcriptomic level using RNA-sequencing. The range of human-specific reads per PDX varied from 64.6%-96.5%, with a comparison of the most differentially expressed genes before and after removal of mouse transcripts revealing no significant benefit to filtering out mouse mRNA reads in this cohort. We demonstrate that four previously established HNSCC molecular subtypes found in The Cancer Genome Atlas (TCGA) are also clearly recapitulated in HNSCC PDXs. Unsupervised hierarchical clustering yielded a striking natural division of HNSCC PDXs by HPV status, with C19orf57 (BRME1), a gene previously correlated with positive response to cisplatin in cervical cancer, among the most significantly differentially expressed genes between HPV+ and HPV- PDXs. In vivo experiments demonstrated a possible relationship between increased C19orf57 expression and superior anti-tumor responses of PDXs to cisplatin, which should be investigated further. These findings highlight the value of PDXs as models for HPV+ and HPV- HNSCC, providing a resource for future discovery of predictive biomarkers to guide treatment selection in HNSCC.
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Affiliation(s)
- Rex H. Lee
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Hua Li
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Aaron Hechmer
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Tian Ran Zhu
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adila Izgutdina
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Adam B. Olshen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Daniel E. Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
| | - Jennifer R. Grandis
- Department of Otolaryngology, Head and Neck Surgery, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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11
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Van Hemelryk A, Tomljanovic I, de Ridder CMA, Stuurman DC, Teubel WJ, Erkens-Schulze S, Verhoef EI, Remmers S, Mahes AJ, van Leenders GJLH, van Royen ME, van de Werken HJG, Grudniewska M, Jenster GW, van Weerden WM. Patient-Derived Xenografts and Organoids Recapitulate Castration-Resistant Prostate Cancer with Sustained Androgen Receptor Signaling. Cells 2022; 11:cells11223632. [PMID: 36429059 PMCID: PMC9688335 DOI: 10.3390/cells11223632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Castration-resistant prostate cancer (CRPC) remains an incurable and lethal malignancy. The development of new CRPC treatment strategies is strongly impeded by the scarcity of representative, scalable and transferable preclinical models of advanced, androgen receptor (AR)-driven CRPC. Here, we present contemporary patient-derived xenografts (PDXs) and matching PDX-derived organoids (PDXOs) from CRPC patients who had undergone multiple lines of treatment. These models were comprehensively profiled at the morphologic, genomic (n = 8) and transcriptomic levels (n = 81). All are high-grade adenocarcinomas that exhibit copy number alterations and transcriptomic features representative of CRPC patient cohorts. We identified losses of PTEN and RB1, MYC amplifications, as well as genomic alterations in TP53 and in members of clinically actionable pathways such as AR, PI3K and DNA repair pathways. Importantly, the clinically observed continued reliance of CRPC tumors on AR signaling is preserved across the entire set of models, with AR amplification identified in four PDXs. We demonstrate that PDXs and PDXOs faithfully reflect donor tumors and mimic matching patient drug responses. In particular, our models predicted patient responses to subsequent treatments and captured sensitivities to previously received therapies. Collectively, these PDX-PDXO pairs constitute a reliable new resource for in-depth studies of treatment-induced, AR-driven resistance mechanisms. Moreover, PDXOs can be leveraged for large-scale tumor-specific drug response profiling critical for accelerating therapeutic advances in CRPC.
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Affiliation(s)
- Annelies Van Hemelryk
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Ingrid Tomljanovic
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Corrina M. A. de Ridder
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Debra C. Stuurman
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Wilma J. Teubel
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sigrun Erkens-Schulze
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Esther I. Verhoef
- Department of Pathology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sebastiaan Remmers
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Amrish J. Mahes
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Geert J. L. H. van Leenders
- Department of Pathology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Harmen J. G. van de Werken
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Cancer Computational Biology Center, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Department of Immunology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | | | - Guido W. Jenster
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Wytske M. van Weerden
- Department of Urology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
- Correspondence: ; Tel.: +31-107-043-674
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12
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Wang H, Chan KYY, Cheng CK, Ng MH, Lee PY, Cheng FWT, Lam GKS, Chow TW, Ha SY, Chiang AK, Leung WH, Leung AY, Wang CC, Zhang T, Zhang XB, So CC, Yuen YP, Sun Q, Zhang C, Xu Y, Cheung JTK, Ng WH, Tang PMK, Kang W, To KF, Lee WYW, Wong RS, Poon ENY, Zhao Q, Huang J, Chen C, Yuen PMP, Li CK, Leung AWK, Leung KT. Pharmacogenomic Profiling of Pediatric Acute Myeloid Leukemia to Identify Therapeutic Vulnerabilities and Inform Functional Precision Medicine. Blood Cancer Discov 2022; 3:516-535. [PMID: 35960210 PMCID: PMC9894568 DOI: 10.1158/2643-3230.bcd-22-0011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/31/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the expanding portfolio of targeted therapies for adults with acute myeloid leukemia (AML), direct implementation in children is challenging due to inherent differences in underlying genetics. Here we established the pharmacologic profile of pediatric AML by screening myeloblast sensitivity to approved and investigational agents, revealing candidates of immediate clinical relevance. Drug responses ex vivo correlated with patient characteristics, exhibited age-specific alterations, and concorded with activities in xenograft models. Integration with genomic data uncovered new gene-drug associations, suggesting actionable therapeutic vulnerabilities. Transcriptome profiling further identified gene-expression signatures associated with on- and off-target drug responses. We also demonstrated the feasibility of drug screening-guided treatment for children with high-risk AML, with two evaluable cases achieving remission. Collectively, this study offers a high-dimensional gene-drug clinical data set that could be leveraged to research the unique biology of pediatric AML and sets the stage for realizing functional precision medicine for the clinical management of the disease. SIGNIFICANCE We conducted integrated drug and genomic profiling of patient biopsies to build the functional genomic landscape of pediatric AML. Age-specific differences in drug response and new gene-drug interactions were identified. The feasibility of functional precision medicine-guided management of children with high-risk AML was successfully demonstrated in two evaluable clinical cases. This article is highlighted in the In This Issue feature, p. 476.
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Affiliation(s)
- Han Wang
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kathy Yuen Yee Chan
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Keung Cheng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Margaret H.L. Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Po Yi Lee
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Frankie Wai Tsoi Cheng
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon, Hong Kong
| | - Grace Kee See Lam
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon, Hong Kong
| | - Tin Wai Chow
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Kowloon, Hong Kong
| | - Shau Yin Ha
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Alan K.S. Chiang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wing Hang Leung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Anskar Y.H. Leung
- Department of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tao Zhang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiao-Bing Zhang
- Department of Medicine, Loma Linda University, Loma Linda, California
| | - Chi Chiu So
- Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong
| | - Yuet Ping Yuen
- Department of Pathology, Hong Kong Children's Hospital, Kowloon, Hong Kong
| | - Qiwei Sun
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Zhang
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yaqun Xu
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - John Tak Kit Cheung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wing Hei Ng
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Patrick Ming-Kuen Tang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wayne Yuk Wai Lee
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Raymond S.M. Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ellen Ngar Yun Poon
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Qi Zhao
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Junbin Huang
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Patrick Man Pan Yuen
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi-kong Li
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong.,Corresponding Authors: Kam Tong Leung, E-mail: ; Chi-kong Li, Hong Kong Children's Hospital, 1 Shing Cheong Road, Kowloon Bay, Kowloon, Hong Kong. Phone: 852-3513-3176; Fax: 852-2636-0020; E-mail: ; and Alex Wing Kwan Leung, E-mail:
| | - Alex Wing Kwan Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong.,Corresponding Authors: Kam Tong Leung, E-mail: ; Chi-kong Li, Hong Kong Children's Hospital, 1 Shing Cheong Road, Kowloon Bay, Kowloon, Hong Kong. Phone: 852-3513-3176; Fax: 852-2636-0020; E-mail: ; and Alex Wing Kwan Leung, E-mail:
| | - Kam Tong Leung
- Department of Paediatrics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong.,Corresponding Authors: Kam Tong Leung, E-mail: ; Chi-kong Li, Hong Kong Children's Hospital, 1 Shing Cheong Road, Kowloon Bay, Kowloon, Hong Kong. Phone: 852-3513-3176; Fax: 852-2636-0020; E-mail: ; and Alex Wing Kwan Leung, E-mail:
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13
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Yen WC, Chang IYF, Chang K, Ouyang C, Liu CR, Tsai TL, Zhang YC, Wang CI, Wang YH, Yu AL, Liu H, Wu CC, Chang YS, Yu JS, Yang CY. Genomic and Molecular Signatures of Successful Patient-Derived Xenografts for Oral Cavity Squamous Cell Carcinoma. Front Oncol 2022; 12:792297. [PMID: 35444950 PMCID: PMC9013835 DOI: 10.3389/fonc.2022.792297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/02/2022] [Indexed: 01/16/2023] Open
Abstract
BackgroundOral cavity squamous cell carcinoma (OSCC) is an aggressive malignant tumor with high recurrence and poor prognosis in the advanced stage. Patient-derived xenografts (PDXs) serve as powerful preclinical platforms for drug testing and precision medicine for cancer therapy. We assess which molecular signatures affect tumor engraftment ability and tumor growth rate in OSCC PDXs.MethodsTreatment-naïve OSCC primary tumors were collected for PDX models establishment. Comprehensive genomic analysis, including whole-exome sequencing and RNA-seq, was performed on case-matched tumors and PDXs. Regulatory genes/pathways were analyzed to clarify which molecular signatures affect tumor engraftment ability and the tumor growth rate in OSCC PDXs.ResultsPerineural invasion was found as an important pathological feature related to engraftment ability. Tumor microenvironment with enriched hypoxia, PI3K-Akt, and epithelial–mesenchymal transition pathways and decreased inflammatory responses had high engraftment ability and tumor growth rates in OSCC PDXs. High matrix metalloproteinase-1 (MMP1) expression was found that have a great graft advantage in xenografts and is associated with pooled disease-free survival in cancer patients.ConclusionThis study provides a panel with detailed genomic characteristics of OSCC PDXs, enabling preclinical studies on personalized therapy options for oral cancer. MMP1 could serve as a biomarker for predicting successful xenografts in OSCC patients.
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Affiliation(s)
- Wei-Chen Yen
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kai‐Ping Chang
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun‐Nan Ouyang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chiao-Rou Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Lin Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Cheng Zhang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-I Wang
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ya-Hui Wang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Alice L. Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
- University of California San Diego, San Diego, CA, United States
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chia-Yu Yang
- Department of Otolaryngology Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- *Correspondence: Chia-Yu Yang,
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14
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Smith RS, Takagishi SR, Amici DR, Metz K, Gayatri S, Alasady MJ, Wu Y, Brockway S, Taiberg SL, Khalatyan N, Taipale M, Santagata S, Whitesell L, Lindquist S, Savas JN, Mendillo ML. HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state. SCIENCE ADVANCES 2022; 8:eabj6526. [PMID: 35294249 PMCID: PMC8926329 DOI: 10.1126/sciadv.abj6526] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/25/2022] [Indexed: 05/14/2023]
Abstract
Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no substantial role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have notably similar chromatin occupancy and regulate a common set of genes that include both HSPs and noncanonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
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Affiliation(s)
- Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
- Tetrad Graduate Program, UCSF, San Francisco, CA 94143, USA
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kyle Metz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sitaram Gayatri
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yaqi Wu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stephanie L. Taiberg
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Natalia Khalatyan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Jeffrey N. Savas
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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15
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Scheidmann MC, Castro-Giner F, Strittmatter K, Krol I, Paasinen-Sohns A, Scherrer R, Donato C, Gkountela S, Szczerba BM, Diamantopoulou Z, Muenst S, Vlajnic T, Kunz L, Vetter M, Rochlitz C, Taylor V, Giachino C, Schroeder T, Platt RJ, Aceto N. An In Vivo CRISPR Screen Identifies Stepwise Genetic Dependencies of Metastatic Progression. Cancer Res 2022; 82:681-694. [PMID: 34916221 PMCID: PMC7612409 DOI: 10.1158/0008-5472.can-21-3908] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Blood-borne metastasis of breast cancer involves a series of tightly regulated sequential steps, including the growth of a primary tumor lesion, intravasation of circulating tumor cells (CTC), and adaptation in various distant metastatic sites. The genes orchestrating each of these steps are poorly understood in physiologically relevant contexts, owing to the rarity of experimental models that faithfully recapitulate the biology, growth kinetics, and tropism of human breast cancer. Here, we conducted an in vivo loss-of-function CRISPR screen in newly derived CTC xenografts, unique in their ability to spontaneously mirror the human disease, and identified specific genetic dependencies for each step of the metastatic process. Validation experiments revealed sensitivities to inhibitors that are already available, such as PLK1 inhibitors, to prevent CTC intravasation. Together, these findings present a new tool to reclassify driver genes involved in the spread of human cancer, providing insights into the biology of metastasis and paving the way to test targeted treatment approaches. SIGNIFICANCE A loss-of-function CRISPR screen in human CTC-derived xenografts identifies genes critical for individual steps of the metastatic cascade, suggesting novel drivers and treatment opportunities for metastatic breast cancers.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/blood
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- CRISPR-Cas Systems
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Neoplasm Metastasis
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA-Seq/methods
- Survival Analysis
- Xenograft Model Antitumor Assays/methods
- Polo-Like Kinase 1
- Mice
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Affiliation(s)
- Manuel C. Scheidmann
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karin Strittmatter
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ilona Krol
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Aino Paasinen-Sohns
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Ramona Scherrer
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Cinzia Donato
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Sofia Gkountela
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Barbara M. Szczerba
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Zoi Diamantopoulou
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Simone Muenst
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Tatjana Vlajnic
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Leo Kunz
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marcus Vetter
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Claudio Giachino
- Department of Biomedicine, Embryology and Stem Cell Biology Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biology, Molecular Oncology Laboratory, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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16
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Mout L, van Royen ME, de Ridder C, Stuurman D, van de Geer WS, Marques R, Buck SAJ, French PJ, van de Werken HJG, Mathijssen RHJ, de Wit R, Lolkema MP, van Weerden WM. Continued Androgen Signalling Inhibition improves Cabazitaxel Efficacy in Prostate Cancer. EBioMedicine 2021; 73:103681. [PMID: 34749299 PMCID: PMC8586743 DOI: 10.1016/j.ebiom.2021.103681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The androgen receptor (AR) pathway is a key driver of neoplastic behaviour in the different stages of metastatic prostate cancer (mPCa). Targeting the AR therefore remains the cornerstone for mPCa treatment. We have previously reported that activation of AR signalling affects taxane chemo-sensitivity in preclinical models of castration resistant PCa (CRPC). Here, we explored the anti-tumour efficacy of the AR targeted inhibitor enzalutamide combined with cabazitaxel. METHODS We used the AR positive CRPC model PC346C-DCC-K to assess the in vitro and in vivo activity of combining enzalutamide with cabazitaxel. Subsequent validation studies were performed using an enzalutamide resistant VCaP model. To investigate the impact of AR signalling on cabazitaxel activity we used quantitative live-cell imaging of tubulin stabilization and apoptosis related nuclear fragmentation. FINDINGS Enzalutamide strongly amplified cabazitaxel anti-tumour activity in the patient-derived xenograft models PC346C-DCC-K (median time to humane endpoint 77 versus 48 days, P<0.0001) and VCaP-Enza-B (median time to humane endpoint 80 versus 53 days, P<0.001). Although enzalutamide treatment by itself was ineffective in reducing tumour growth, it significantly suppressed AR signalling in PC346C-DCC-K tumours as shown by AR target gene expression. The addition of enzalutamide enhanced cabazitaxel induced apoptosis as shown by live-cell imaging (P<0.001). INTERPRETATION Our study demonstrates that cabazitaxel efficacy can be improved by simultaneous blocking of AR signalling by enzalutamide, even if AR targeted treatment no longer affects tumour growth. These findings support clinical studies that combine AR targeted inhibitors with cabazitaxel in CRPC.
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Affiliation(s)
- Lisanne Mout
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Martin E van Royen
- Department of Pathology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Corrina de Ridder
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Debra Stuurman
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Wesley S van de Geer
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Rute Marques
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Stefan A J Buck
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Pim J French
- Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Neurology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Pathology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Treatment Screening Facility Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Department of Neurology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands; Cancer Computational Biology Center Erasmus MC Cancer Institute, University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Ronald de Wit
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology Erasmus MC Cancer Institute, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Wytske M van Weerden
- Department of Urology Erasmus University MC, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands.
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17
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Pandita A, Ekstrand M, Bjursten S, Zhao Z, Fogelstrand P, Le Gal K, Ny L, Bergo MO, Karlsson J, Nilsson JA, Akyürek LM, Levin MC, Borén J, Ewald AJ, Mostov KE, Levin M. Intussusceptive Angiogenesis in Human Metastatic Malignant Melanoma. THE AMERICAN JOURNAL OF PATHOLOGY 2021; 191:2023-2038. [PMID: 34400131 PMCID: PMC8579244 DOI: 10.1016/j.ajpath.2021.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/03/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022]
Abstract
Angiogenesis supplies oxygen and nutrients to growing tumors. Inhibiting angiogenesis may stop tumor growth, but vascular endothelial growth factor inhibitors have limited effect in most tumors. This limited effect may be explained by an additional, less vascular endothelial growth factor-driven form of angiogenesis known as intussusceptive angiogenesis. The importance of intussusceptive angiogenesis in human tumors is not known. Epifluorescence and confocal microscopy was used to visualize intravascular pillars, the hallmark structure of intussusceptive angiogenesis, in tumors. Human malignant melanoma metastases, patient-derived melanoma xenografts in mice (PDX), and genetically engineered v-raf murine sarcoma viral oncogene homolog B1 (BRAF)-induced, phosphatase and TENsin homolog deleted on chromosome 10 (PTEN)-deficient (BPT) mice (BrafCA/+Ptenf/fTyr-Cre+/0-mice) were analyzed for pillars. Gene expression in human melanoma metastases and PDXs was analyzed by RNA sequencing. Matrix metalloproteinase 9 (MMP9) protein expression and T-cell and macrophage infiltration in tumor sections were determined with multiplex immunostaining. Intravascular pillars were detected in human metastases but rarely in PDXs and not in BPT mice. The expression of MMP9 mRNA was higher in human metastases compared with PDXs. High expression of MMP9 protein as well as infiltration of macrophages and T-cells were detected in proximity to intravascular pillars. MMP inhibition blocked formation of pillars, but not tubes or tip cells, in vitro. In conclusion, intussusceptive angiogenesis may contribute to the growth of human melanoma metastases. MMP inhibition blocked pillar formation in vitro and should be further investigated as a potential anti-angiogenic drug target in metastatic melanoma.
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Affiliation(s)
- Ankur Pandita
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Matias Ekstrand
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sara Bjursten
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Zhiyuan Zhao
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Fogelstrand
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Kristell Le Gal
- Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | - Lars Ny
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden; Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | - Martin O Bergo
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Karlsson
- Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | - Jonas A Nilsson
- Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | - Levent M Akyürek
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Malin C Levin
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Borén
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Andrew J Ewald
- Department of Cell Biology, Johns Hopkins University, Baltimore, Maryland; Department of Oncology, Cancer Invasion and Metastasis Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Keith E Mostov
- Departments of Anatomy and Biochemistry/Biophysics, University of California, San Francisco, California
| | - Max Levin
- Wallenberg Laboratory for Cardiovascular Research, Department of Molecular and Clinical Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden.
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18
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El Said NH, Della Valle F, Liu P, Paytuví-Gallart A, Adroub S, Gimenez J, Orlando V. Malat-1-PRC2-EZH1 interaction supports adaptive oxidative stress dependent epigenome remodeling in skeletal myotubes. Cell Death Dis 2021; 12:850. [PMID: 34531374 PMCID: PMC8445987 DOI: 10.1038/s41419-021-04082-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/24/2022]
Abstract
PRC2-mediated epigenetic function involves the interaction with long non-coding RNAs (lncRNAs). Although the identity of some of these RNAs has been elucidated in the context of developmental programs, their counterparts in postmitotic adult tissue homeostasis remain uncharacterized. To this aim, we used terminally differentiated postmitotic skeletal muscle cells in which oxidative stress induces the dynamic activation of PRC2-Ezh1 through Embryonic Ectoderm Develpment (EED) shuttling to the nucleus. We identify lncRNA Malat-1 as a necessary partner for PRC2-Ezh1-dependent response to oxidative stress. We show that in this pathway, PRC2-EZH1 dynamic assembly, and in turn stress induced skeletal muscle targeted genes repression, depends specifically on Malat-1. Our study reports about PRC2-RNA interactions in the physiological context of adaptive oxidative stress response and identifies the first lncRNA involved in PRC2-Ezh1 function.
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Affiliation(s)
- Nadine Hosny El Said
- Biological Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Francesco Della Valle
- Biological Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Peng Liu
- Biological Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
| | | | - Sabir Adroub
- Biological Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Valerio Orlando
- Biological Environmental Science and Engineering Division, KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.
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19
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Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nat Commun 2021; 12:5086. [PMID: 34429404 PMCID: PMC8384880 DOI: 10.1038/s41467-021-25177-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.
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Affiliation(s)
- Hua Sun
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Song Cao
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - R. Jay Mashl
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Chia-Kuei Mo
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Simone Zaccaria
- grid.16750.350000 0001 2097 5006Department of Computer Science, Princeton University, Princeton, NJ USA ,grid.83440.3b0000000121901201Computational Cancer Genomics Research Group and Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michael C. Wendl
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Mathematics, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University in St. Louis, St. Louis, MO USA
| | - Sherri R. Davies
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Matthew H. Bailey
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Tina M. Primeau
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Jeremy Hoog
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Jacqueline L. Mudd
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Dennis A. Dean
- grid.492568.4Seven Bridges Genomics, Inc., Cambridge, Charlestown, MA USA
| | - Rajesh Patidar
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Li Chen
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Matthew A. Wyczalkowski
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Reyka G. Jayasinghe
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Fernanda Martins Rodrigues
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Nadezhda V. Terekhanova
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Yize Li
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA
| | - Kian-Huat Lim
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Andrea Wang-Gillam
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Brian A. Van Tine
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Cynthia X. Ma
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Rebecca Aft
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Katherine C. Fuh
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Julie K. Schwarz
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO USA
| | - Jose P. Zevallos
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Otolaryngology, Washington University St. Louis, St. Louis, MO USA
| | - Sidharth V. Puram
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Otolaryngology, Washington University St. Louis, St. Louis, MO USA
| | - John F. Dipersio
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | | | | | - Matthew J. Ellis
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Michael T. Lewis
- grid.39382.330000 0001 2160 926XLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Michael A. Davies
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Meenhard Herlyn
- grid.251075.40000 0001 1956 6678The Wistar Institute, Philadelphia, PA USA
| | - Bingliang Fang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jack A. Roth
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Alana L. Welm
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Bryan E. Welm
- grid.412722.00000 0004 0515 3663Huntsman Cancer Institute, University of Utah, Salt Lake City, UT USA
| | - Funda Meric-Bernstam
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Feng Chen
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Ryan C. Fields
- grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Shunqiang Li
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - Ramaswamy Govindan
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
| | - James H. Doroshow
- grid.48336.3a0000 0004 1936 8075Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD USA
| | - Jeffrey A. Moscow
- grid.48336.3a0000 0004 1936 8075Investigational Drug Branch, National Cancer Institute, Bethesda, MD USA
| | - Yvonne A. Evrard
- grid.418021.e0000 0004 0535 8394Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Jeffrey H. Chuang
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Benjamin J. Raphael
- grid.16750.350000 0001 2097 5006Department of Computer Science, Princeton University, Princeton, NJ USA
| | - Li Ding
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University in St. Louis, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO USA
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20
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Mannarino L, Craparotta I, Ballabio S, Frapolli R, Meroni M, Bello E, Panini N, Callari M, Sanfilippo R, Casali PG, Barisella M, Fabbroni C, Marchini S, D'Incalci M. Mechanisms of responsiveness to and resistance against trabectedin in murine models of human myxoid liposarcoma. Genomics 2021; 113:3439-3448. [PMID: 34339817 DOI: 10.1016/j.ygeno.2021.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
Myxoid liposarcoma (MLPS) is a rare soft-tissue sarcoma characterised by the expression of FUS-DDIT3 chimera. Trabectedin has shown significant clinical anti-tumour activity against MLPS. To characterise the molecular mechanism of trabectedin sensitivity and of resistance against it, we integrated genomic and transcriptomic data from treated mice bearing ML017 or ML017/ET, two patient-derived MLPS xenograft models, sensitive to and resistant against trabectedin, respectively. Longitudinal RNA-Seq analysis of ML017 showed that trabectedin acts mainly as a transcriptional regulator: 15 days after the third dose trabectedin modulates the transcription of 4883 genes involved in processes that sustain adipocyte differentiation. No such differences were observed in ML017/ET. Genomic analysis showed that prolonged treatment causes losses in 4p15.2, 4p16.3 and 17q21.3 cytobands leading to acquired-resistance against the drug. The results dissect the complex mechanism of action of trabectedin and provide the basis for novel combinatorial approaches for the treatment of MLPS that could overcome drug-resistance.
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Affiliation(s)
- Laura Mannarino
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele - Milan, Italy.; Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Ilaria Craparotta
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Sara Ballabio
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Roberta Frapolli
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Marina Meroni
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Ezia Bello
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Nicolò Panini
- Department of Oncology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, via Mario Negri 2, 20156 Milan, Italy
| | - Maurizio Callari
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Roberta Sanfilippo
- Adult Mesenchymal Tumour Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy
| | - Paolo G Casali
- Adult Mesenchymal Tumour Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy
| | - Marta Barisella
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Fabbroni
- Adult Mesenchymal Tumour Medical Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy
| | - Sergio Marchini
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy
| | - Maurizio D'Incalci
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, 20072 Pieve Emanuele - Milan, Italy.; Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano - Milan, Italy..
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21
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Zhang C, Oguz C, Huse S, Xia L, Wu J, Peng YC, Smith M, Chen J, Long CA, Lack J, Su XZ. Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67. BMC Genomics 2021; 22:303. [PMID: 33902452 PMCID: PMC8072299 DOI: 10.1186/s12864-021-07555-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Background Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. Results We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. Conclusions The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07555-9.
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Affiliation(s)
- Cui Zhang
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA
| | - Cihan Oguz
- NIAID Collaborative Bioinformatics Resource (NCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Sue Huse
- NIAID Collaborative Bioinformatics Resource (NCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Lu Xia
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA.,State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA
| | - Yu-Chih Peng
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA
| | - Margaret Smith
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA
| | - Jack Chen
- The NCI sequencing facility, 8560 Progress Drive, Room 3007, Frederick, MD, 21701, USA
| | - Carole A Long
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA.
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22
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Dozmorov MG, Tyc KM, Sheffield NC, Boyd DC, Olex AL, Reed J, Harrell JC. Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines. Gigascience 2021; 10:6242846. [PMID: 33880552 DOI: 10.1093/gigascience/giab022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/14/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined. RESULTS We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated 2 experimental PDX Hi-C datasets using different library preparation strategies. We evaluated 3 alignment strategies (Direct, Xenome, Combined) and 3 pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality. CONCLUSIONS Removal of mouse reads had little-to-no effect on data quality as compared with the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
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Affiliation(s)
- Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Katarzyna M Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA.,Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - David C Boyd
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA.,Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Amy L Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jason Reed
- Virginia Commonwealth University, Massey Cancer Center, Richmond, VA, 23298, USA.,Department of Physics, Virginia Commonwealth University, Richmond, VA 23220, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, USA
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23
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Abstract
Motivation With an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species’ (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Recent studies compare different approaches and tools, with varying results. Results We show that alignment-free methods for xenograft sorting are superior concerning CPU time usage and equivalent in accuracy. We improve upon the state of the art sorting by presenting a fast lightweight approach based on three-way bucketed quotiented Cuckoo hashing. Our hash table requires memory comparable to an FM index typically used for read alignment and less than other alignment-free approaches. It allows extremely fast lookups and uses less CPU time than other alignment-free methods and alignment-based methods at similar accuracy. Several engineering steps (e.g., shortcuts for unsuccessful lookups, software prefetching) improve the performance even further. Availability Our software xengsort is available under the MIT license at http://gitlab.com/genomeinformatics/xengsort. It is written in numba-compiled Python and comes with sample Snakemake workflows for hash table construction and dataset processing.
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24
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Tucker ER, George S, Angelini P, Bruna A, Chesler L. The Promise of Patient-Derived Preclinical Models to Accelerate the Implementation of Personalised Medicine for Children with Neuroblastoma. J Pers Med 2021; 11:248. [PMID: 33808071 PMCID: PMC8065808 DOI: 10.3390/jpm11040248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 01/02/2023] Open
Abstract
Patient-derived preclinical models are now a core component of cancer research and have the ability to drastically improve the predictive power of preclinical therapeutic studies. However, their development and maintenance can be challenging, time consuming, and expensive. For neuroblastoma, a developmental malignancy of the neural crest, it is possible to establish patient-derived models as xenografts in mice and zebrafish, and as spheroids and organoids in vitro. These varied approaches have contributed to comprehensive packages of preclinical evidence in support of new therapeutics for neuroblastoma. We discuss here the ethical and technical considerations for the creation of patient-derived models of neuroblastoma and how their use can be optimized for the study of tumour evolution and preclinical therapies. We also discuss how neuroblastoma patient-derived models might become avatars for personalised medicine for children with this devastating disease.
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Affiliation(s)
- Elizabeth R. Tucker
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
| | - Sally George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
| | - Paola Angelini
- Children and Young People’s Unit, The Royal Marsden, Downs Road, Sutton, Surrey SM2 5PT, UK;
| | - Alejandra Bruna
- Preclinical Paediatric Cancer Evolution, Centre for Cancer Drug Discovery, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK;
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Cotswold Road, London SM2 5NG, UK; (E.R.T.); (S.G.)
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25
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Dehner C, Moon CI, Zhang X, Zhou Z, Miller C, Xu H, Wan X, Yang K, Mashl J, Gosline SJ, Wang Y, Zhang X, Godec A, Jones PA, Dahiya S, Bhatia H, Primeau T, Li S, Pollard K, Rodriguez FJ, Ding L, Pratilas CA, Shern JF, Hirbe AC. Chromosome 8 gain is associated with high-grade transformation in MPNST. JCI Insight 2021; 6:146351. [PMID: 33591953 PMCID: PMC8026192 DOI: 10.1172/jci.insight.146351] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
One of the most common malignancies affecting adults with Neurofibromatosis type 1 (NF1) is the malignant peripheral nerve sheath tumor (MPNST), an aggressive and often fatal sarcoma that commonly arises from benign plexiform neurofibromas. Despite advances in our understanding of MPNST pathobiology, there are few effective therapeutic options, and no investigational agents have proven successful in clinical trials. To further understand the genomic heterogeneity of MPNST, and to generate a preclinical platform that encompasses this heterogeneity, we developed a collection of NF1-MPNST patient-derived xenografts (PDX). These PDX were compared with the primary tumors from which they were derived using copy number analysis, whole exome sequencing, and RNA sequencing. We identified chromosome 8 gain as a recurrent genomic event in MPNST and validated its occurrence by FISH in the PDX and parental tumors, in a validation cohort, and by single-cell sequencing in the PDX. Finally, we show that chromosome 8 gain is associated with inferior overall survival in soft-tissue sarcomas. These data suggest that chromosome 8 gain is a critical event in MPNST pathogenesis and may account for the aggressive nature and poor outcomes in this sarcoma subtype.
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Affiliation(s)
| | - Chang In Moon
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Zhaohe Zhou
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chris Miller
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hua Xu
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Xiaodan Wan
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,The First Affiliated Hospital, Nanchang University, Nangchang, China
| | - Kuangying Yang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jay Mashl
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sara Jc Gosline
- Pacific Northwest National Laboratory, Seattle, Washington, USA
| | - Yuxi Wang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Xiaochun Zhang
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abigail Godec
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Paul A Jones
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology and.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Himanshi Bhatia
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tina Primeau
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shunqiang Li
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Kai Pollard
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Fausto J Rodriguez
- Department of Pathology, John Hopkins University, Baltimore, Maryland, USA
| | - Li Ding
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
| | - Christine A Pratilas
- Division of Pediatric Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Angela C Hirbe
- Department of Internal Medicine, Division of Oncology, Washington University in St. Louis, St. Louis, Missouri, USA.,Siteman Cancer Center Division of Pediatric Oncology, St. Louis, Missouri, USA
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26
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Profiling of conditionally reprogrammed cell lines for in vitro chemotherapy response prediction of pancreatic cancer. EBioMedicine 2021; 65:103218. [PMID: 33639403 PMCID: PMC7921470 DOI: 10.1016/j.ebiom.2021.103218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The establishment of patient-derived models for pancreatic ductal adenocarcinoma (PDAC) using conventional methods has been fraught with low success rate, mainly because of the small number of tumour cells and dense fibrotic stroma. Here, we sought to establish patient-derived model of PDAC and perform genetic analysis with responses to anticancer drug by using the conditionally reprogrammed cell (CRC) methodology. METHODS We performed in vitro and in vivo tumourigenicity assays and analysed histological characteristics by immunostaining. We investigated genetic profiles including mutation patterns and copy number variations using targeted deep sequencing and copy-number analyses. We assessed the responses of cultured CRCs to the available clinical anticancer drugs based on patient responsiveness. FINDINGS We established a total of 28 CRCs from patients. Of the 28 samples, 27 showed KRAS mutations in codon 12/13 or codon 61. We found that somatic mutations were shared in the primary-CRC pairs and shared mutations included key oncogenic mutations such as KRAS (9 pairs), TP53 (8 pairs), and SMAD4 (3 pairs). Overall, CRCs preserved the genetic characteristics of primary tumours with high concordance, with additional confirmation of low-AF NPM1 mutation in CRC (35 shared mutations out of 36 total, concordance rate=97.2%). CRCs of the responder group were more sensitive to anticancer agents than those of the non-responder group (P < 0.001). INTERPRETATION These results show that a pancreatic cancer cell line model can be efficiently established using the CRC methodology, to better support a personalized therapeutic approach for pancreatic cancer patients. FUNDING 2014R1A1A1006272, HI19C0642-060019, 2019R1A2C2008050, 2020R1A2C209958611, and 2020M3E5E204028211.
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27
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Proteomic Resistance Biomarkers for PI3K Inhibitor in Triple Negative Breast Cancer Patient-Derived Xenograft Models. Cancers (Basel) 2020; 12:cancers12123857. [PMID: 33371187 PMCID: PMC7765949 DOI: 10.3390/cancers12123857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The objective of this study is to identify potential proteomic biomarkers in triple negative breast cancer (TNBC) that associate with response to PI3K inhibitors which are in clinical trials. We tested a panel of TNBC patient-derived xenograft (PDX) models for their tumor growth response to a pan-PI3K inhibitor, BKM120. Proteomic analyses by reverse phase protein array (RPPA) of 182 markers were performed on baseline and post short-term treatment PDX samples, to correlate with tumor growth response. We identified several baseline and treatment induced proteomic biomarkers in association with resistance. These results provide important insights for the development of PI3K inhibitors in TNBC. Abstract PI3K pathway activation is frequently observed in triple negative breast cancer (TNBC). However, single agent PI3K inhibitors have shown limited anti-tumor activity. To investigate biomarkers of response and resistance mechanisms, we tested 17 TNBC patient-derived xenograft (PDX) models representing diverse genomic backgrounds and varying degrees of PI3K pathway signaling activities for their tumor growth response to the pan-PI3K inhibitor, BKM120. Baseline and post-treatment PDX tumors were subjected to reverse phase protein array (RPPA) to identify protein markers associated with tumor growth response. While BKM120 consistently reduced PI3K pathway activity, as demonstrated by reduced levels of phosphorylated AKT, percentage tumor growth inhibition (%TGI) ranged from 35% in the least sensitive to 84% in the most sensitive model. Several biomarkers showed significant association with resistance, including elevated baseline levels of growth factor receptors (EGFR, pHER3 Y1197), PI3Kp85 regulatory subunit, anti-apoptotic protein BclXL, EMT (Vimentin, MMP9, IntegrinaV), NFKB pathway (IkappaB, RANKL), and intracellular signaling molecules including Caveolin, CBP, and KLF4, as well as treatment-induced increases in the levels of phosphorylated forms of Aurora kinases. Interestingly, increased AKT phosphorylation or PTEN loss at baseline were not significantly correlated to %TGI. These results provide important insights into biomarker development for PI3K inhibitors in TNBC.
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28
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Wang Y, Park JYP, Pacis A, Denroche RE, Jang GH, Zhang A, Cuggia A, Domecq C, Monlong J, Raitses-Gurevich M, Grant RC, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu IM, Bartlett JM, Wilson JM, Gao ZH, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher LM, Valenti D, Biagi J, Greenwood CM, Polak P, Foulkes WD, Golan T, O'Kane GM, Fischer SE, Knox JJ, Gallinger S, Zogopoulos G. A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination–deficient Pancreatic Cancer. Clin Cancer Res 2020; 26:5462-5476. [DOI: 10.1158/1078-0432.ccr-20-1439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/24/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022]
Abstract
Abstract
Purpose:
Pancreatic ductal adenocarcinoma (PDAC) arising in patients with a germline BRCA1 or BRCA2 (gBRCA) mutation may be sensitive to platinum and PARP inhibitors (PARPi). However, treatment stratification based on gBRCA mutational status alone is associated with heterogeneous responses.
Experimental Design:
We performed a seven-arm preclinical trial consisting of 471 mice, representing 12 unique PDAC patient-derived xenografts, of which nine were gBRCA mutated. From 179 patients whose PDAC was whole-genome and transcriptome sequenced, we identified 21 cases with homologous recombination deficiency (HRD), and investigated prognostic biomarkers.
Results:
We found that biallelic inactivation of BRCA1/BRCA2 is associated with genomic hallmarks of HRD and required for cisplatin and talazoparib (PARPi) sensitivity. However, HRD genomic hallmarks persisted in xenografts despite the emergence of therapy resistance, indicating the presence of a genomic scar. We identified tumor polyploidy and a low Ki67 index as predictors of poor cisplatin and talazoparib response. In patients with HRD PDAC, tumor polyploidy and a basal-like transcriptomic subtype were independent predictors of shorter survival. To facilitate clinical assignment of transcriptomic subtype, we developed a novel pragmatic two-marker assay (GATA6:KRT17).
Conclusions:
In summary, we propose a predictive and prognostic model of gBRCA-mutated PDAC on the basis of HRD genomic hallmarks, Ki67 index, tumor ploidy, and transcriptomic subtype.
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Affiliation(s)
- Yifan Wang
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jin Yong Patrick Park
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Alain Pacis
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 3Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | | | - Gun Ho Jang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Adeline Cuggia
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Celine Domecq
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jean Monlong
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Maria Raitses-Gurevich
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Robert C. Grant
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ayelet Borgida
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- 8Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Chani Stossel
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Simeng Bu
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Mehdi Masoomian
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ilinca M. Lungu
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M.S. Bartlett
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Julie M. Wilson
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Zu-Hua Gao
- 11Department of Pathology, McGill University, Montreal, Quebec, Canada
| | | | - Jamil Asselah
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
| | | | - Tatiana Cabrera
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - Louis-Martin Boucher
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - David Valenti
- 13Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada
| | - James Biagi
- 14Department of Oncology, Queen's University, Kingston, Ontario, Canada
| | - Celia M.T. Greenwood
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- 12Department of Oncology, McGill University, Montreal, Quebec, Canada
- 15Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
- 16Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Paz Polak
- 17Icahn School of Medicine at Mount Sinai Hospital, New York, New York
| | - William D. Foulkes
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Talia Golan
- 6Pancreatic Cancer Translational Research Laboratory, Oncology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- 9Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Grainne M. O'Kane
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sandra E. Fischer
- 10Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer J. Knox
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- 7Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - George Zogopoulos
- 1Rosalind and Morris Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
- 2Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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29
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Honselmann KC, Finetti P, Birnbaum DJ, Monsalve CS, Wellner UF, Begg SKS, Nakagawa A, Hank T, Li A, Goldsworthy MA, Sharma H, Bertucci F, Birnbaum D, Tai E, Ligorio M, Ting DT, Schilling O, Biniossek ML, Bronsert P, Ferrone CR, Keck T, Mino-Kenudson M, Lillemoe KD, Warshaw AL, Fernández-Del Castillo C, Liss AS. Neoplastic-Stromal Cell Cross-talk Regulates Matrisome Expression in Pancreatic Cancer. Mol Cancer Res 2020; 18:1889-1902. [PMID: 32873625 DOI: 10.1158/1541-7786.mcr-20-0439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/28/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by a highly desmoplastic reaction, warranting intense cancer-stroma communication. In this study, we interrogated the contribution of the BET family of chromatin adaptors to the cross-talk between PDAC cells and the tumor stroma. Short-term treatment of orthotopic xenograft tumors with CPI203, a small-molecule inhibitor of BET proteins, resulted in broad changes in the expression of genes encoding components of the extracellular matrix (matrisome) in both cancer and stromal cells. Remarkably, more than half of matrisome genes were expressed by cancer cells. In vitro cocultures of PDAC cells and cancer-associated fibroblasts (CAF) demonstrated that matrisome expression was regulated by BET-dependent cancer-CAF cross-talk. Disrupting this cross-talk in vivo resulted in diminished growth of orthotopic patient-derived xenograft tumors, reduced proliferation of cancer cells, and changes in collagen structure consistent with that of patients who experienced better survival. Examination of matrisome gene expression in publicly available data sets of 573 PDAC tumors identified a 65-gene signature that was able to distinguish long- and short-term PDAC survivors. Importantly, the expression of genes predictive of short-term survival was diminished in the cancer cells of orthotopic xenograft tumors of mice treated with CPI203. Taken together, these results demonstrate that inhibiting the activity BET proteins results in transcriptional and structural differences in the matrisome are associated with better patient survival. IMPLICATIONS: These studies highlight the biological relevance of the matrisome program in PDAC and suggest targeting of epigenetically driven tumor-stroma cross-talk as a potential therapeutic avenue.
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Affiliation(s)
- Kim C Honselmann
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Pascal Finetti
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR7258, Aix-Marseille University, Marseille, France
| | - David J Birnbaum
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR7258, Aix-Marseille University, Marseille, France.,Département de Chirurgie Générale et Viscérale, AP-HM, Marseille, France
| | - Christian S Monsalve
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ulrich F Wellner
- Department of Surgery, University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sebastian K S Begg
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Akifumi Nakagawa
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Thomas Hank
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Annie Li
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mathew A Goldsworthy
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Himanshu Sharma
- Partners Healthcare Personalized Medicine Center, Cambridge, Massachusetts
| | - François Bertucci
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR7258, Aix-Marseille University, Marseille, France.,Département d'Oncologie Médicale, Institut Paoli-Calmettes, Marseille, France
| | - Daniel Birnbaum
- Laboratoire d'Oncologie Prédictive, Centre de Recherche en Cancérologie de Marseille, INSERM UMR1068, CNRS UMR7258, Aix-Marseille University, Marseille, France
| | - Eric Tai
- MGH Cancer Research Center, Harvard Medical School, Boston, Massachusetts
| | - Matteo Ligorio
- MGH Cancer Research Center, Harvard Medical School, Boston, Massachusetts
| | - David T Ting
- MGH Cancer Research Center, Harvard Medical School, Boston, Massachusetts
| | - Oliver Schilling
- Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Tobias Keck
- Department of Surgery, University Medical Center Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keith D Lillemoe
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrew L Warshaw
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Andrew S Liss
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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30
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Hofmann MH, Gmachl M, Ramharter J, Savarese F, Gerlach D, Marszalek JR, Sanderson MP, Kessler D, Trapani F, Arnhof H, Rumpel K, Botesteanu DA, Ettmayer P, Gerstberger T, Kofink C, Wunberg T, Zoephel A, Fu SC, Teh JL, Böttcher J, Pototschnig N, Schachinger F, Schipany K, Lieb S, Vellano CP, O'Connell JC, Mendes RL, Moll J, Petronczki M, Heffernan TP, Pearson M, McConnell DB, Kraut N. BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition. Cancer Discov 2020; 11:142-157. [PMID: 32816843 DOI: 10.1158/2159-8290.cd-20-0142] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/14/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022]
Abstract
KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proved challenging, and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success because of activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective, and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1, thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors. SIGNIFICANCE: To date, there are no effective targeted pan-KRAS therapies. In-depth characterization of BI-3406 activity and identification of MEK inhibitors as effective combination partners provide an attractive therapeutic concept for the majority of KRAS-mutant cancers, including those fueled by the most prevalent mutant KRAS oncoproteins, G12D, G12V, G12C, and G13D.See related commentary by Zhao et al., p. 17.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
| | | | | | | | | | - Joseph R Marszalek
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | | | | | - Szu-Chin Fu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica L Teh
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simone Lieb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Christopher P Vellano
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jurgen Moll
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Timothy P Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Norbert Kraut
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
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31
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Somerville TDD, Biffi G, Daßler-Plenker J, Hur SK, He XY, Vance KE, Miyabayashi K, Xu Y, Maia-Silva D, Klingbeil O, Demerdash OE, Preall JB, Hollingsworth MA, Egeblad M, Tuveson DA, Vakoc CR. Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation. eLife 2020; 9:e53381. [PMID: 32329713 PMCID: PMC7200154 DOI: 10.7554/elife.53381] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
A highly aggressive subset of pancreatic ductal adenocarcinomas undergo trans-differentiation into the squamous lineage during disease progression. Here, we investigated whether squamous trans-differentiation of human and mouse pancreatic cancer cells can influence the phenotype of non-neoplastic cells in the tumor microenvironment. Conditioned media experiments revealed that squamous pancreatic cancer cells secrete factors that recruit neutrophils and convert pancreatic stellate cells into cancer-associated fibroblasts (CAFs) that express inflammatory cytokines at high levels. We use gain- and loss-of-function approaches to show that squamous-subtype pancreatic tumor models become enriched with neutrophils and inflammatory CAFs in a p63-dependent manner. These effects occur, at least in part, through p63-mediated activation of enhancers at pro-inflammatory cytokine loci, which includes IL1A and CXCL1 as key targets. Taken together, our findings reveal enhanced tissue inflammation as a consequence of squamous trans-differentiation in pancreatic cancer, thus highlighting an instructive role of tumor cell lineage in reprogramming the stromal microenvironment.
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Affiliation(s)
| | - Giulia Biffi
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborUnited States
- Cancer Research United Kingdom Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
| | | | - Stella K Hur
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Xue-Yan He
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Krysten E Vance
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Koji Miyabayashi
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborUnited States
| | - Yali Xu
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Diogo Maia-Silva
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Watson School of Biological SciencesCold Spring HarborUnited States
| | - Olaf Klingbeil
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | | | | | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical CenterOmahaUnited States
| | - Mikala Egeblad
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - David A Tuveson
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Lustgarten Foundation Pancreatic Cancer Research LaboratoryCold Spring HarborUnited States
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32
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Karlsson J, Nilsson LM, Mitra S, Alsén S, Shelke GV, Sah VR, Forsberg EMV, Stierner U, All-Eriksson C, Einarsdottir B, Jespersen H, Ny L, Lindnér P, Larsson E, Olofsson Bagge R, Nilsson JA. Molecular profiling of driver events in metastatic uveal melanoma. Nat Commun 2020; 11:1894. [PMID: 32313009 PMCID: PMC7171146 DOI: 10.1038/s41467-020-15606-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.
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Affiliation(s)
- Joakim Karlsson
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Lisa M Nilsson
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Suman Mitra
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Samuel Alsén
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Ganesh Vilas Shelke
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Vasu R Sah
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Elin M V Forsberg
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Ulrika Stierner
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | | | - Berglind Einarsdottir
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Henrik Jespersen
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Lars Ny
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Per Lindnér
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30, Göteborg, Sweden
| | - Roger Olofsson Bagge
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden
| | - Jonas A Nilsson
- Sahlgrenska Cancer Center, Departments of Surgery, Oncology or Transplantation Surgery, Institute of Clinical Sciences at University of Gothenburg and Sahlgrenska University Hospital, Box 425, 40530, Gothenburg, Sweden.
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33
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Kenter AT, Rentmeester E, van Riet J, Boers R, Boers J, Ghazvini M, Xavier VJ, van Leenders GJLH, Verhagen PCMS, van Til ME, Eussen B, Losekoot M, de Klein A, Peters DJM, van IJcken WFJ, van de Werken HJG, Zietse R, Hoorn EJ, Jansen G, Gribnau JH. Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients. Stem Cells Transl Med 2020; 9:478-490. [PMID: 32163234 PMCID: PMC7103626 DOI: 10.1002/sctm.18-0283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 11/08/2019] [Indexed: 12/25/2022] Open
Abstract
Autosomal‐dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease, leading to kidney failure in most patients. In approximately 85% of cases, the disease is caused by mutations in PKD1. How dysregulation of PKD1 leads to cyst formation on a molecular level is unknown. Induced pluripotent stem cells (iPSCs) are a powerful tool for in vitro modeling of genetic disorders. Here, we established ADPKD patient‐specific iPSCs to study the function of PKD1 in kidney development and cyst formation in vitro. Somatic mutations are proposed to be the initiating event of cyst formation, and therefore, iPSCs were derived from cystic renal epithelial cells rather than fibroblasts. Mutation analysis of the ADPKD iPSCs revealed germline mutations in PKD1 but no additional somatic mutations in PKD1/PKD2. Although several somatic mutations in other genes implicated in ADPKD were identified in cystic renal epithelial cells, only few of these mutations were present in iPSCs, indicating a heterogeneous mutational landscape, and possibly in vitro cell selection before and during the reprogramming process. Whole‐genome DNA methylation analysis indicated that iPSCs derived from renal epithelial cells maintain a kidney‐specific DNA methylation memory. In addition, comparison of PKD1+/− and control iPSCs revealed differences in DNA methylation associated with the disease history. In conclusion, we generated and characterized iPSCs derived from cystic and healthy control renal epithelial cells, which can be used for in vitro modeling of kidney development in general and cystogenesis in particular.
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Affiliation(s)
- Annegien T Kenter
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands.,Department of Cell Biology, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands.,Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands
| | - Job van Riet
- Cancer Computational Biology Center, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Ruben Boers
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands.,Delft Diagnostic Laboratories (DDL), Rijswijk, The Netherlands
| | - Mehrnaz Ghazvini
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands
| | - Vanessa J Xavier
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands
| | | | - Paul C M S Verhagen
- Department of Urology, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Marjan E van Til
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Bert Eussen
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Robert Zietse
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Ewout J Hoorn
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Gert Jansen
- Department of Cell Biology, Erasmus Medical Center Rotterdam (EMC), Rotterdam, The Netherlands
| | - Joost H Gribnau
- Department of Developmental Biology, Erasmus Medical Center Rotterdam (EMC), Oncode Institute, Rotterdam, The Netherlands
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34
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Shats I, Williams JG, Liu J, Makarov MV, Wu X, Lih FB, Deterding LJ, Lim C, Xu X, Randall TA, Lee E, Li W, Fan W, Li JL, Sokolsky M, Kabanov AV, Li L, Migaud ME, Locasale JW, Li X. Bacteria Boost Mammalian Host NAD Metabolism by Engaging the Deamidated Biosynthesis Pathway. Cell Metab 2020; 31:564-579.e7. [PMID: 32130883 PMCID: PMC7194078 DOI: 10.1016/j.cmet.2020.02.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 11/07/2019] [Accepted: 01/31/2020] [Indexed: 12/31/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD), a cofactor for hundreds of metabolic reactions in all cell types, plays an essential role in metabolism, DNA repair, and aging. However, how NAD metabolism is impacted by the environment remains unclear. Here, we report an unexpected trans-kingdom cooperation between bacteria and mammalian cells wherein bacteria contribute to host NAD biosynthesis. Bacteria confer resistance to inhibitors of NAMPT, the rate-limiting enzyme in the amidated NAD salvage pathway, in cancer cells and xenograft tumors. Mechanistically, a microbial nicotinamidase (PncA) that converts nicotinamide to nicotinic acid, a precursor in the alternative deamidated NAD salvage pathway, is necessary and sufficient for this protective effect. Using stable isotope tracing and microbiota-depleted mice, we demonstrate that this bacteria-mediated deamidation contributes substantially to the NAD-boosting effect of oral nicotinamide and nicotinamide riboside supplementation in several tissues. Collectively, our findings reveal an important role of bacteria-enabled deamidated pathway in host NAD metabolism.
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Affiliation(s)
- Igor Shats
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| | - Jason G Williams
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mikhail V Makarov
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36606, USA
| | - Xiaoyue Wu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Department of Nutrition and Food Hygiene, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Fred B Lih
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Leesa J Deterding
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Chaemin Lim
- Center for Nanotechnology in Drug Delivery, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Thomas A Randall
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ethan Lee
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Wenling Li
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Marina Sokolsky
- Center for Nanotechnology in Drug Delivery, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Alexander V Kabanov
- Center for Nanotechnology in Drug Delivery, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Leping Li
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36606, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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35
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Novel Breast Cancer Brain Metastasis Patient-Derived Orthotopic Xenograft Model for Preclinical Studies. Cancers (Basel) 2020; 12:cancers12020444. [PMID: 32074948 PMCID: PMC7072242 DOI: 10.3390/cancers12020444] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 12/20/2022] Open
Abstract
The vast majority of mortality in breast cancer results from distant metastasis. Brain metastases occur in as many as 30% of patients with advanced breast cancer, and the 1-year survival rate of these patients is around 20%. Pre-clinical animal models that reliably reflect the biology of breast cancer brain metastasis are needed to develop and test new treatments for this deadly condition. The patient-derived xenograft (PDX) model maintains many features of a donor tumor, such as intra-tumor heterogeneity, and permits the testing of individualized treatments. However, the establishment of orthotopic PDXs of brain metastasis is procedurally difficult. We have developed a method for generating such PDXs with high tumor engraftment and growth rates. Here, we describe this method and identify variables that affect its outcomes. We also compare the brain-orthotopic PDXs with ectopic PDXs grown in mammary pads of mice, and show that the responsiveness of PDXs to chemotherapeutic reagents can be dramatically affected by the site that they are in.
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Clonal competition within complex evolutionary hierarchies shapes AML over time. Nat Commun 2020; 11:579. [PMID: 32024830 PMCID: PMC7002407 DOI: 10.1038/s41467-019-14106-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Clonal heterogeneity and evolution has major implications for disease progression and relapse in acute myeloid leukemia (AML). To model clonal dynamics in vivo, we serially transplanted 23 AML cases to immunodeficient mice and followed clonal composition for up to 15 months by whole-exome sequencing of 84 xenografts across two generations. We demonstrate vast changes in clonality that both progress and reverse over time, and define five patterns of clonal dynamics: Monoclonal, Stable, Loss, Expansion and Burst. We also show that subclonal expansion in vivo correlates with a more adverse prognosis. Furthermore, clonal expansion enabled detection of very rare clones with AML driver mutations that were undetectable by sequencing at diagnosis, demonstrating that the vast majority of AML cases harbor multiple clones already at diagnosis. Finally, the rise and fall of related clones enabled deconstruction of the complex evolutionary hierarchies of the clones that compete to shape AML over time. Clonal evolution and heterogeneity has strong implications for treatment response in acute myeloid leukemia. Here, the authors use patient derived in vivo modelling to highlight the complex clonal and evolutionary dynamics underpinning acute myeloid leukemia progression.
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Jo SY, Kim E, Kim S. Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis. Genome Biol 2019; 20:231. [PMID: 31707992 PMCID: PMC6844030 DOI: 10.1186/s13059-019-1849-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Patient-derived xenograft and cell line models are popular models for clinical cancer research. However, the inevitable inclusion of a mouse genome in a patient-derived model is a remaining concern in the analysis. Although multiple tools and filtering strategies have been developed to account for this, research has yet to demonstrate the exact impact of the mouse genome and the optimal use of these tools and filtering strategies in an analysis pipeline. RESULTS We construct a benchmark dataset of 5 liver tissues from 3 mouse strains using human whole-exome sequencing kit. Next-generation sequencing reads from mouse tissues are mappable to 49% of the human genome and 409 cancer genes. In total, 1,207,556 mouse-specific alleles are aligned to the human genome reference, including 467,232 (38.7%) alleles with high sensitivity to contamination, which are pervasive causes of false cancer mutations in public databases and are signatures for predicting global contamination. Next, we assess the performance of 8 filtering methods in terms of mouse read filtration and reduction of mouse-specific alleles. All filtering tools generally perform well, although differences in algorithm strictness and efficiency of mouse allele removal are observed. Therefore, we develop a best practice pipeline that contains the estimation of contamination level, mouse read filtration, and variant filtration. CONCLUSIONS The inclusion of mouse cells in patient-derived models hinders genomic analysis and should be addressed carefully. Our suggested guidelines improve the robustness and maximize the utility of genomic analysis of these models.
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Affiliation(s)
- Se-Young Jo
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Eunyoung Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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Morandi E, Cereda M, Incarnato D, Parlato C, Basile G, Anselmi F, Lauria A, Simon LM, Laurence Polignano I, Arruga F, Deaglio S, Tirtei E, Fagioli F, Oliviero S. HaTSPiL: A modular pipeline for high-throughput sequencing data analysis. PLoS One 2019; 14:e0222512. [PMID: 31613890 PMCID: PMC6793853 DOI: 10.1371/journal.pone.0222512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/30/2019] [Indexed: 11/25/2022] Open
Abstract
Background Next generation sequencing methods are widely adopted for a large amount of scientific purposes, from pure research to health-related studies. The decreasing costs per analysis led to big amounts of generated data and to the subsequent improvement of software for the respective analyses. As a consequence, many approaches have been developed to chain different software in order to obtain reliable and reproducible workflows. However, the large range of applications for NGS approaches entails the challenge to manage many different workflows without losing reliability. Methods We here present a high-throughput sequencing pipeline (HaTSPiL), a Python-powered CLI tool designed to handle different approaches for data analysis with a high level of reliability. The software relies on the barcoding of filenames using a human readable naming convention that contains any information regarding the sample needed by the software to automatically choose different workflows and parameters. HaTSPiL is highly modular and customisable, allowing the users to extend its features for any specific need. Conclusions HaTSPiL is licensed as Free Software under the MIT license and it is available at https://github.com/dodomorandi/hatspil.
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Affiliation(s)
- Edoardo Morandi
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Danny Incarnato
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | | | - Giulia Basile
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Francesca Anselmi
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Andrea Lauria
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Lisa Marie Simon
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | | | | | - Silvia Deaglio
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elisa Tirtei
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children’s Hospital, Turin, Italy
| | - Franca Fagioli
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children’s Hospital, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- * E-mail: ,
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Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, Beane G, Grubb S, Ananda G, Liu R, Stafford G, Chuang JH, Airhart SD, Karuturi RKM, George J, Bult CJ. Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. BMC Med Genomics 2019; 12:92. [PMID: 31262303 PMCID: PMC6604205 DOI: 10.1186/s12920-019-0551-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients. The Jackson Laboratory (JAX) PDX resource comprises 455 models originating from 34 different primary sites (as of 05/08/2019). The models undergo rigorous quality control and are genomically characterized to identify somatic mutations, copy number alterations, and transcriptional profiles. Bioinformatics workflows for analyzing genomic data obtained from human tumors engrafted in a mouse host (i.e., Patient-Derived Xenografts; PDXs) must address challenges such as discriminating between mouse and human sequence reads and accurately identifying somatic mutations and copy number alterations when paired non-tumor DNA from the patient is not available for comparison. RESULTS We report here data analysis workflows and guidelines that address these challenges and achieve reliable identification of somatic mutations, copy number alterations, and transcriptomic profiles of tumors from PDX models that lack genomic data from paired non-tumor tissue for comparison. Our workflows incorporate commonly used software and public databases but are tailored to address the specific challenges of PDX genomics data analysis through parameter tuning and customized data filters and result in improved accuracy for the detection of somatic alterations in PDX models. We also report a gene expression-based classifier that can identify EBV-transformed tumors. We validated our analytical approaches using data simulations and demonstrated the overall concordance of the genomic properties of xenograft tumors with data from primary human tumors in The Cancer Genome Atlas (TCGA). CONCLUSIONS The analysis workflows that we have developed to accurately predict somatic profiles of tumors from PDX models that lack normal tissue for comparison enable the identification of the key oncogenic genomic and expression signatures to support model selection and/or biomarker development in therapeutic studies. A reference implementation of our analysis recommendations is available at https://github.com/TheJacksonLaboratory/PDX-Analysis-Workflows .
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Affiliation(s)
- Xing Yi Woo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Joel H Graber
- MDI Biological Laboratory, Bar Harbor, ME, 04609, USA
| | - Vinod Yadav
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Present Address: Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vishal Kumar Sarsani
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
- Present Address: University of Massachusetts, Amherst, MA, 01003, USA
| | - Al Simons
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Glen Beane
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Stephen Grubb
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Guruprasad Ananda
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Rangjiao Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Present Address: Novogene Corporation, Rockville, MD, 20850, USA
| | - Grace Stafford
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Susan D Airhart
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | | | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA.
| | - Carol J Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA.
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40
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Khandelwal G, Miller C. Improved PDX and CDX Data Processing-Response. Mol Cancer Res 2019; 16:1814. [PMID: 30385666 DOI: 10.1158/1541-7786.mcr-18-0535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Garima Khandelwal
- RNABiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Crispin Miller
- RNABiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.
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41
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Castroviejo-Bermejo M, Cruz C, Llop-Guevara A, Gutiérrez-Enríquez S, Ducy M, Ibrahim YH, Gris-Oliver A, Pellegrino B, Bruna A, Guzmán M, Rodríguez O, Grueso J, Bonache S, Moles-Fernández A, Villacampa G, Viaplana C, Gómez P, Vidal M, Peg V, Serres-Créixams X, Dellaire G, Simard J, Nuciforo P, Rubio IT, Dienstmann R, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Déas O, Jonkers J, Masson JY, Cairo S, Judde JG, O'Connor MJ, Díez O, Balmaña J, Serra V. A RAD51 assay feasible in routine tumor samples calls PARP inhibitor response beyond BRCA mutation. EMBO Mol Med 2018; 10:e9172. [PMID: 30377213 PMCID: PMC6284440 DOI: 10.15252/emmm.201809172] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with defective homologous recombination DNA repair (HRR), including BRCA1/2-related cancers. A test to identify additional HRR-deficient tumors will help to extend their use in new indications. We evaluated the activity of the PARPi olaparib in patient-derived tumor xenografts (PDXs) from breast cancer (BC) patients and investigated mechanisms of sensitivity through exome sequencing, BRCA1 promoter methylation analysis, and immunostaining of HRR proteins, including RAD51 nuclear foci. In an independent BC PDX panel, the predictive capacity of the RAD51 score and the homologous recombination deficiency (HRD) score were compared. To examine the clinical feasibility of the RAD51 assay, we scored archival breast tumor samples, including PALB2-related hereditary cancers. The RAD51 score was highly discriminative of PARPi sensitivity versus PARPi resistance in BC PDXs and outperformed the genomic test. In clinical samples, all PALB2-related tumors were classified as HRR-deficient by the RAD51 score. The functional biomarker RAD51 enables the identification of PARPi-sensitive BC and broadens the population who may benefit from this therapy beyond BRCA1/2-related cancers.
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Affiliation(s)
| | - Cristina Cruz
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Mandy Ducy
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Yasir Hussein Ibrahim
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Albert Gris-Oliver
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Benedetta Pellegrino
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, University Hospital of Parma, Parma, Italy
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Marta Guzmán
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Olga Rodríguez
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judit Grueso
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Guillermo Villacampa
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Viaplana
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Patricia Gómez
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Maria Vidal
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Vicente Peg
- Pathology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Serres-Créixams
- Department of Radiology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jacques Simard
- CHU de Quebec - Université Laval Research Center, Genomics Center CHUL, Québec City, QC, Canada
| | - Paolo Nuciforo
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Isabel T Rubio
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Breast Surgical Unit, Breast Cancer Center, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Oncology Data Science (OdysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Breast Cancer Programme, Cancer Research UK (CRUK) Cambridge Cancer Centre, Cambridge, UK
| | - José Baselga
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina Saura
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Breast Cancer and Melanoma Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Javier Cortés
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
- Department of Oncology, Ramón y Cajal University Hospital, Madrid, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Jos Jonkers
- Division of Molecular Pathology and Cancer Genomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
| | | | | | - Mark J O'Connor
- Oncology Innovative Medicines and Early Clinical Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Clinical and Molecular Genetics Area, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Familial Cancer Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
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Ahdesmäki MJ. Improved PDX and CDX Data Processing-Letter. Mol Cancer Res 2018; 16:1813. [PMID: 30385665 DOI: 10.1158/1541-7786.mcr-18-0534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022]
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43
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Qiu J, Dando O, Baxter PS, Hasel P, Heron S, Simpson TI, Hardingham GE. Mixed-species RNA-seq for elucidation of non-cell-autonomous control of gene transcription. Nat Protoc 2018; 13:2176-2199. [DOI: 10.1038/s41596-018-0029-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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44
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Chen S, Cai C, Sowalsky AG, Ye H, Ma F, Yuan X, Simon NI, Gray NS, Balk SP. BMX-Mediated Regulation of Multiple Tyrosine Kinases Contributes to Castration Resistance in Prostate Cancer. Cancer Res 2018; 78:5203-5215. [PMID: 30012673 PMCID: PMC6139052 DOI: 10.1158/0008-5472.can-17-3615] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/21/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022]
Abstract
Prostate cancer responds to therapies that suppress androgen receptor (AR) activity (androgen deprivation therapy, ADT) but invariably progresses to castration-resistant prostate cancer (CRPC). The Tec family nonreceptor tyrosine kinase BMX is activated downstream of PI3K and has been implicated in regulation of multiple pathways and in the development of cancers including prostate cancer. However, its precise mechanisms of action, and particularly its endogenous substrates, remain to be established. Here, we demonstrate that BMX expression in prostate cancer is suppressed directly by AR via binding to the BMX gene and that BMX expression is subsequently rapidly increased in response to ADT. BMX contributed to CRPC development in cell line and xenograft models by positively regulating the activities of multiple receptor tyrosine kinases through phosphorylation of a phosphotyrosine-tyrosine (pYY) motif in their activation loop, generating pYpY that is required for full kinase activity. To assess BMX activity in vivo, we generated a BMX substrate-specific antibody (anti-pYpY) and found that its reactivity correlated with BMX expression in clinical samples, supporting pYY as an in vivo substrate. Inhibition of BMX with ibrutinib (developed as an inhibitor of the related Tec kinase BTK) or another BMX inhibitor BMX-IN-1 markedly enhanced the response to castration in a prostate cancer xenograft model. These data indicate that increased BMX in response to ADT contributes to enhanced tyrosine kinase signaling and the subsequent emergence of CRPC, and that combination therapies targeting AR and BMX may be effective in a subset of patients.Significance: The tyrosine kinase BMX is negatively regulated by androgen and contributes to castration-resistant prostate cancer by enhancing the phosphorylation and activation of multiple receptor tyrosine kinases following ADT. Cancer Res; 78(18); 5203-15. ©2018 AACR.
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MESH Headings
- Adenine/analogs & derivatives
- Amino Acid Motifs
- Androgen Antagonists/therapeutic use
- Androgens/metabolism
- Animals
- Antibodies/metabolism
- Cell Line, Tumor
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Male
- Mice
- Mice, Inbred ICR
- Mice, SCID
- Neoplasm Transplantation
- Phosphorylation
- Piperidines
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Protein Binding
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/metabolism
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Receptors, Androgen/metabolism
- Sequence Analysis, RNA
- Signal Transduction
- Tissue Array Analysis
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Affiliation(s)
- Sen Chen
- Hematology-Oncology Division, Department of Medicine, and Cancer Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, NIH, Bethesda, Maryland
| | - Huihui Ye
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Fen Ma
- Hematology-Oncology Division, Department of Medicine, and Cancer Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Xin Yuan
- Hematology-Oncology Division, Department of Medicine, and Cancer Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Nicholas I Simon
- Hematology-Oncology Division, Department of Medicine, and Cancer Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, and Cancer Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
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45
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Dev H, Chiang TWW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M, Herzog M, Lam J, Shea A, Demir M, Wu Q, Yang F, Fu B, Lai Z, Balmus G, Belotserkovskaya R, Serra V, O'Connor MJ, Bruna A, Beli P, Pellegrini L, Caldas C, Deriano L, Jacobs JJL, Galanty Y, Jackson SP. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Nat Cell Biol 2018; 20:954-965. [PMID: 30022119 PMCID: PMC6145444 DOI: 10.1038/s41556-018-0140-1] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 02/02/2023]
Abstract
BRCA1 deficiencies cause breast, ovarian, prostate and other cancers, and render tumours hypersensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. To understand the resistance mechanisms, we conducted whole-genome CRISPR-Cas9 synthetic-viability/resistance screens in BRCA1-deficient breast cancer cells treated with PARP inhibitors. We identified two previously uncharacterized proteins, C20orf196 and FAM35A, whose inactivation confers strong PARP-inhibitor resistance. Mechanistically, we show that C20orf196 and FAM35A form a complex, 'Shieldin' (SHLD1/2), with FAM35A interacting with single-stranded DNA through its C-terminal oligonucleotide/oligosaccharide-binding fold region. We establish that Shieldin acts as the downstream effector of 53BP1/RIF1/MAD2L2 to promote DNA double-strand break (DSB) end-joining by restricting DSB resection and to counteract homologous recombination by antagonizing BRCA2/RAD51 loading in BRCA1-deficient cells. Notably, Shieldin inactivation further sensitizes BRCA1-deficient cells to cisplatin, suggesting how defining the SHLD1/2 status of BRCA1-deficient tumours might aid patient stratification and yield new treatment opportunities. Highlighting this potential, we document reduced SHLD1/2 expression in human breast cancers displaying intrinsic or acquired PARP-inhibitor resistance.
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Affiliation(s)
- Harveer Dev
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Academic Urology Group, Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Ting-Wei Will Chiang
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chloe Lescale
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands
| | - Alistair G Martin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Domenic Pilger
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wenming Wei
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | | | - Mareike Herzog
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan Lam
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Abigail Shea
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Qian Wu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Gabriel Balmus
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rimma Belotserkovskaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Alejandra Bruna
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands.
| | - Yaron Galanty
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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46
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Wellberg EA, Kabos P, Gillen AE, Jacobsen BM, Brechbuhl HM, Johnson SJ, Rudolph MC, Edgerton SM, Thor AD, Anderson SM, Elias A, Zhou XK, Iyengar NM, Morrow M, Falcone DJ, El-Hely O, Dannenberg AJ, Sartorius CA, MacLean PS. FGFR1 underlies obesity-associated progression of estrogen receptor-positive breast cancer after estrogen deprivation. JCI Insight 2018; 3:120594. [PMID: 30046001 PMCID: PMC6124402 DOI: 10.1172/jci.insight.120594] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
Obesity increases breast cancer mortality by promoting resistance to therapy. Here, we identified regulatory pathways in estrogen receptor-positive (ER-positive) tumors that were shared between patients with obesity and those with resistance to neoadjuvant aromatase inhibition. Among these was fibroblast growth factor receptor 1 (FGFR1), a known mediator of endocrine therapy resistance. In a preclinical model with patient-derived ER-positive tumors, diet-induced obesity promoted a similar gene expression signature and sustained the growth of FGFR1-overexpressing tumors after estrogen deprivation. Tumor FGFR1 phosphorylation was elevated with obesity and predicted a shorter disease-free and disease-specific survival for patients treated with tamoxifen. In both human and mouse mammary adipose tissue, FGF1 ligand expression was associated with metabolic dysfunction, weight gain, and adipocyte hypertrophy, implicating the impaired response to a positive energy balance in growth factor production within the tumor niche. In conjunction with these studies, we describe a potentially novel graft-competent model that can be used with patient-derived tissue to elucidate factors specific to extrinsic (host) and intrinsic (tumor) tissue that are critical for obesity-associated tumor promotion. Taken together, we demonstrate that obesity and excess energy establish a tumor environment with features of endocrine therapy resistance and identify a role for ligand-dependent FGFR1 signaling in obesity-associated breast cancer progression.
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Affiliation(s)
| | - Peter Kabos
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Austin E. Gillen
- University of Colorado School of Medicine, RNA Bioscience Initiative, Aurora, Colorado, USA
| | - Britta M. Jacobsen
- Department of Pathology and
- Division of Endocrinology, Metabolism, & Diabetes, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Heather M. Brechbuhl
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | | | - Michael C. Rudolph
- Division of Endocrinology, Metabolism, & Diabetes, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | | | | | | | - Anthony Elias
- Division of Medical Oncology, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Xi Kathy Zhou
- Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, New York, USA
| | - Neil M. Iyengar
- Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Monica Morrow
- Department of Surgery, MSKCC, New York, New York, USA
| | - Domenick J. Falcone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical Center, New York, New York, USA
| | - Omar El-Hely
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | | | | | - Paul S. MacLean
- Division of Endocrinology, Metabolism, & Diabetes, Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
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47
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Dai W, Liu J, Li Q, Liu W, Li YX, Li YY. A comparison of next-generation sequencing analysis methods for cancer xenograft samples. J Genet Genomics 2018; 45:345-350. [PMID: 30055875 DOI: 10.1016/j.jgg.2018.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/15/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022]
Abstract
The application of next-generation sequencing (NGS) technology in cancer is influenced by the quality and purity of tissue samples. This issue is especially critical for patient-derived xenograft (PDX) models, which have proven to be by far the best preclinical tool for investigating human tumor biology, because the sensitivity and specificity of NGS analysis in xenograft samples would be compromised by the contamination of mouse DNA and RNA. This definitely affects downstream analyses by causing inaccurate mutation calling and gene expression estimates. The reliability of NGS data analysis for cancer xenograft samples is therefore highly dependent on whether the sequencing reads derived from the xenograft could be distinguished from those originated from the host. That is, each sequence read needs to be accurately assigned to its original species. Here, we review currently available methodologies in this field, including Xenome, Disambiguate, bamcmp and pdxBlacklist, and provide guidelines for users.
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Affiliation(s)
- Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, Shanghai 201203, China; Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Jixiang Liu
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, Shanghai 201203, China; Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Quanxue Li
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Liu
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, Shanghai 201203, China; Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, Shanghai 201203, China; School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; Shanghai Industrial Technology Institute, Shanghai 201203, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China; Shanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology Institute, Shanghai 201203, China; Shanghai Industrial Technology Institute, Shanghai 201203, China.
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48
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Callari M, Batra AS, Batra RN, Sammut SJ, Greenwood W, Clifford H, Hercus C, Chin SF, Bruna A, Rueda OM, Caldas C. Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts. BMC Genomics 2018; 19:19. [PMID: 29304755 PMCID: PMC5755132 DOI: 10.1186/s12864-017-4414-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. RESULTS In this study we generated Whole Exome Sequencing (WES), Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA and from a cohort of human breast cancers and their derived PDTXs. We show that using an In silico Combined human-mouse Reference Genome (ICRG) for alignment discriminates between human and mouse reads with up to 99.9% accuracy and decreases the number of false positive somatic mutations caused by misalignment by >99.9%. We also derived a model to estimate the human DNA content in independent PDTX samples. For RNA-seq and RRBS data analysis, the use of the ICRG allows dissecting computationally the transcriptome and methylome of human tumour cells and mouse stroma. In a direct comparison with previously reported approaches, our method showed similar or higher accuracy while requiring significantly less computing time. CONCLUSIONS The computational pipeline we describe here is a valuable tool for the molecular analysis of PDTXs as well as any other mixture of DNA or RNA species.
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Affiliation(s)
- Maurizio Callari
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Ankita Sati Batra
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Rajbir Nath Batra
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Stephen-John Sammut
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Wendy Greenwood
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Harry Clifford
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Colin Hercus
- Novocraft Technologies Sdn Bhd, C-23A-05, 3 Two Square, Jalan 19/1, Section 19, 46300 Petaling Jaya, Selangor Darul Ehsan Malaysia
| | - Suet-Feung Chin
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Alejandra Bruna
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Oscar M. Rueda
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Carlos Caldas
- CRUK Cambridge Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
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49
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Contreras-Zárate MJ, Ormond DR, Gillen AE, Hanna C, Day NL, Serkova NJ, Jacobsen BM, Edgerton SM, Thor AD, Borges VF, Lillehei KO, Graner MW, Kabos P, Cittelly DM. Development of Novel Patient-Derived Xenografts from Breast Cancer Brain Metastases. Front Oncol 2017; 7:252. [PMID: 29164052 PMCID: PMC5673842 DOI: 10.3389/fonc.2017.00252] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022] Open
Abstract
Brain metastases are an increasing burden among breast cancer patients, particularly for those with HER2+ and triple negative (TN) subtypes. Mechanistic insight into the pathophysiology of brain metastases and preclinical validation of therapies has relied almost exclusively on intracardiac injection of brain-homing cells derived from highly aggressive TN MDA-MB-231 and HER2+ BT474 breast cancer cell lines. Yet, these well characterized models are far from representing the tumor heterogeneity observed clinically and, due to their fast progression in vivo, their suitability to validate therapies for established brain metastasis remains limited. The goal of this study was to develop and characterize novel human brain metastasis breast cancer patient-derived xenografts (BM-PDXs) to study the biology of brain metastasis and to serve as tools for testing novel therapeutic approaches. We obtained freshly resected brain metastases from consenting donors with breast cancer. Tissue was immediately implanted in the mammary fat pad of female immunocompromised mice and expanded as BM-PDXs. Brain metastases from 3/4 (75%) TN, 1/1 (100%) estrogen receptor positive (ER+), and 5/9 (55.5%) HER2+ clinical subtypes were established as transplantable BM-PDXs. To facilitate tracking of metastatic dissemination using BM-PDXs, we labeled PDX-dissociated cells with EGFP-luciferase followed by reimplantation in mice, and generated a BM-derived cell line (F2-7). Immunohistologic analyses demonstrated that parental and labeled BM-PDXs retained expression of critical clinical markers such as ER, progesterone receptor, epidermal growth factor receptor, HER2, and the basal cell marker cytokeratin 5. Similarly, RNA sequencing analysis showed clustering of parental, labeled BM-PDXs and their corresponding cell line derivative. Intracardiac injection of dissociated cells from BM-E22-1, resulted in magnetic resonance imaging-detectable macrometastases in 4/8 (50%) and micrometastases (8/8) (100%) mice, suggesting that BM-PDXs remain capable of colonizing the brain at high frequencies. Brain metastases developed 8-12 weeks after ic injection, located to the brain parenchyma, grew around blood vessels, and elicited astroglia activation characteristic of breast cancer brain metastasis. These novel BM-PDXs represent heterogeneous and clinically relevant models to study mechanisms of brain metastatic colonization, with the added benefit of a slower progression rate that makes them suitable for preclinical testing of drugs in therapeutic settings.
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Affiliation(s)
| | - D. Ryan Ormond
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Austin E. Gillen
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Colton Hanna
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nicole L. Day
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Natalie J. Serkova
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Britta M. Jacobsen
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Susan M. Edgerton
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ann D. Thor
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Virginia F. Borges
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kevin O. Lillehei
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael W. Graner
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Peter Kabos
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Diana M. Cittelly
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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