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Wang Y, Cho JW, Kastrunes G, Buck A, Razimbaud C, Culhane AC, Sun J, Braun DA, Choueiri TK, Wu CJ, Jones K, Nguyen QD, Zhu Z, Wei K, Zhu Q, Signoretti S, Freeman GJ, Hemberg M, Marasco WA. Immune-restoring CAR-T cells display antitumor activity and reverse immunosuppressive TME in a humanized ccRCC mouse model. iScience 2024; 27:108879. [PMID: 38327771 PMCID: PMC10847687 DOI: 10.1016/j.isci.2024.108879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/01/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
One of the major barriers that have restricted successful use of chimeric antigen receptor (CAR) T cells in the treatment of solid tumors is an unfavorable tumor microenvironment (TME). We engineered CAR-T cells targeting carbonic anhydrase IX (CAIX) to secrete anti-PD-L1 monoclonal antibody (mAb), termed immune-restoring (IR) CAR G36-PDL1. We tested CAR-T cells in a humanized clear cell renal cell carcinoma (ccRCC) orthotopic mouse model with reconstituted human leukocyte antigen (HLA) partially matched human leukocytes derived from fetal CD34+ hematopoietic stem cells (HSCs) and bearing human ccRCC skrc-59 cells under the kidney capsule. G36-PDL1 CAR-T cells, haploidentical to the tumor cells, had a potent antitumor effect compared to those without immune-restoring effect. Analysis of the TME revealed that G36-PDL1 CAR-T cells restored active antitumor immunity by promoting tumor-killing cytotoxicity, reducing immunosuppressive cell components such as M2 macrophages and exhausted CD8+ T cells, and enhancing T follicular helper (Tfh)-B cell crosstalk.
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Affiliation(s)
- Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Jae-Won Cho
- Harvard Medical School, Boston, MA 02215, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Gabriella Kastrunes
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alicia Buck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cecile Razimbaud
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Aedin C. Culhane
- School of Medicine, University of Limerick, V94 T9PX Limerick, Ireland
| | - Jiusong Sun
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David A. Braun
- Harvard Medical School, Boston, MA 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06525, USA
| | - Toni K. Choueiri
- Harvard Medical School, Boston, MA 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catherine J. Wu
- Harvard Medical School, Boston, MA 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristen Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhu Zhu
- Harvard Medical School, Boston, MA 02215, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kevin Wei
- Harvard Medical School, Boston, MA 02215, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Quan Zhu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
| | - Sabina Signoretti
- Harvard Medical School, Boston, MA 02215, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Gordon J. Freeman
- Harvard Medical School, Boston, MA 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin Hemberg
- Harvard Medical School, Boston, MA 02215, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Wayne A. Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02215, USA
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2
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Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L. Curated single cell multimodal landmark datasets for R/Bioconductor. PLoS Comput Biol 2023; 19:e1011324. [PMID: 37624866 PMCID: PMC10497156 DOI: 10.1371/journal.pcbi.1011324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 09/12/2023] [Accepted: 07/03/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. RESULTS We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data. CONCLUSIONS We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.
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Affiliation(s)
- Kelly B. Eckenrode
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Marcel Ramos
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Ricard Argelaguet
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | | | - Ludwig Geistlinger
- Center for Computational Biomedicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Laurent Gatto
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Vincent Carey
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Martin Morgan
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, NY, NY, United States of America
- Institute for Implementation Science in Public Health, City University of New York, NY, NY, United States of America
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3
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de Matos Simoes R, Shirasaki R, Downey-Kopyscinski SL, Matthews GM, Barwick BG, Gupta VA, Dupéré-Richer D, Yamano S, Hu Y, Sheffer M, Dhimolea E, Dashevsky O, Gandolfi S, Ishiguro K, Meyers RM, Bryan JG, Dharia NV, Hengeveld PJ, Brüggenthies JB, Tang H, Aguirre AJ, Sievers QL, Ebert BL, Glassner BJ, Ott CJ, Bradner JE, Kwiatkowski NP, Auclair D, Levy J, Keats JJ, Groen RWJ, Gray NS, Culhane AC, McFarland JM, Dempster JM, Licht JD, Boise LH, Hahn WC, Vazquez F, Tsherniak A, Mitsiades CS. Genome-scale functional genomics identify genes preferentially essential for multiple myeloma cells compared to other neoplasias. Nat Cancer 2023; 4:754-773. [PMID: 37237081 PMCID: PMC10918623 DOI: 10.1038/s43018-023-00550-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/29/2023] [Indexed: 05/28/2023]
Abstract
Clinical progress in multiple myeloma (MM), an incurable plasma cell (PC) neoplasia, has been driven by therapies that have limited applications beyond MM/PC neoplasias and do not target specific oncogenic mutations in MM. Instead, these agents target pathways critical for PC biology yet largely dispensable for malignant or normal cells of most other lineages. Here we systematically characterized the lineage-preferential molecular dependencies of MM through genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) studies in 19 MM versus hundreds of non-MM lines and identified 116 genes whose disruption more significantly affects MM cell fitness compared with other malignancies. These genes, some known, others not previously linked to MM, encode transcription factors, chromatin modifiers, endoplasmic reticulum components, metabolic regulators or signaling molecules. Most of these genes are not among the top amplified, overexpressed or mutated in MM. Functional genomics approaches thus define new therapeutic targets in MM not readily identifiable by standard genomic, transcriptional or epigenetic profiling analyses.
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Affiliation(s)
- Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Vikas A Gupta
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | | | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Kazuya Ishiguro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robin M Meyers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Richard W J Groen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Nathanael S Gray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aedin C Culhane
- Department of Data Sciences, Dana-Farber Cancer Institute & Harvard School of Public Health, Boston, MA, USA
- Limerick Digital Cancer Research Center, Health Research Institute, School of Medicine, University of Limerick, Limerick, Ireland
| | - James M McFarland
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Francisca Vazquez
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
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4
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Wang Y, Buck A, Kastrunes G, Abbas R, Lynch M, Zhong Z, Hoang SM, Miklosi A, Huang K, Cho JW, Grimaud M, Razimbaud C, Chang M, Fayed A, Apollon A, Murugan N, Li ZH, Thai T, Zerefa L, Piel B, Ivanova E, Cameron A, Nguyen QD, Zhu Z, Wei K, Laimon YN, Sheshdeh AB, Signoretti S, Braun DA, Wu CJ, Choueiri TK, Wee J, Paweletz CP, Hemberg M, Culhane AC, Barbie DA, Freeman GJ, Marasco WA. Abstract 886: Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Chimeric Antigen Receptor (CAR) T cell therapy is a new type of “living drug” that has proven to be a powerful immunotherapy for hematologic malignancies. To date, there are six CAR-T products approved by the FDA for hematologic malignancies, four targeting CD19, and two targeting B-cell maturation antigen (BCMA). However, this success has not yet been transferred to solid tumors. A major hurdle is the on-target off-tumor toxicities due to the shared expression of target antigen on normal tissues. Carbonic anhydrase IX (CAIX) is highly expressed in clear cell renal cell carcinoma (ccRCC); however, it is also expressed on bile duct at a lower physiological level leading to off-tumor toxicity of CAIX targeted therapies. The first anti-CAIX CAR-T studies, using the 1st generation G250 CAR-T cells plus IL-2 to treat patients with metastatic ccRCC, caused severe liver enzyme abnormalities in the treated patients after CAR-T cell infusions. To understand CAIX expression on tumor and normal tissues, we quantified CAIX expression on ccRCC patient samples and healthy bile duct tissues using direct stochastic optical reconstruction microscopy (dSTORM) which provides single-molecule resolution. Tet-On inducible CAIX expressing cell lines were established to mimic various CAIX densities on normal tissue and tumor samples. Using biolayer interferometry (BLI) and avidity analyzer, we identified a low-affinity, high-avidity anti-CAIX CAR G9. G9 CAR-T cells only kill CAIX high ccRCC tumor cells but not CAIX low normal cholangiocytes, and exhibited a CAIX density dependent response to Tet-On inducible CAIX expressing cell lines. Compared to high-affinity G250 CAR-T cells, G9 showed a better safety profile and a wider therapeutic window. G9 demonstrated a superior ex vivo efficacy on ccRCC patient derived organotypic tumor spheroids (PDOTS) 3D cultures which recapitulate ccRCC patient tumor microenvironment (TME), as well as low toxicity on cholangiocyte derived organotypic spheroids (CDOS). In summary, affinity/avidity fine-tuned CAIX targeted CAR-T cell therapy holds promise to achieve cures of ccRCC by efficaciously killing tumor cells and mitigating on-target off-tumor toxicity on normal tissues.
Citation Format: Yufei Wang, Alicia Buck, Gabriella Kastrunes, Rabia Abbas, Michael Lynch, Zhou Zhong, Song-My Hoang, Andras Miklosi, Kun Huang, Jae-Won Cho, Marion Grimaud, Cecile Razimbaud, Matthew Chang, Atef Fayed, Audrey Apollon, Nithyassree Murugan, Ze-Hua Li, Tran Thai, Luann Zerefa, Brandon Piel, Elena Ivanova, Amy Cameron, Quang-De Nguyen, Zhu Zhu, Kevin Wei, Yasmin Nabil Laimon, Aseman Bagheri Sheshdeh, Sabina Signoretti, David A. Braun, Catherine J. Wu, Toni K. Choueiri, Jon Wee, Cloud P. Paweletz, Martin Hemberg, Aedin C. Culhane, David A. Barbie, Gordon J. Freeman, Wayne A. Marasco. Fine-tuned CAIX targeted CAR-T cells exhibit superior efficacy and mitigate on-target off-tumor side effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 886.
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Affiliation(s)
- Yufei Wang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Kun Huang
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | - Atef Fayed
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Ze-Hua Li
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Tran Thai
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Zhu Zhu
- 5Brigham and Women's Hospital, Boston, MA
| | - Kevin Wei
- 5Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | | | | | - Jon Wee
- 5Brigham and Women's Hospital, Boston, MA
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5
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Wang Y, Buck A, Grimaud M, Culhane AC, Kodangattil S, Razimbaud C, Bonal DM, Nguyen QD, Zhu Z, Wei K, O'Donnell ML, Huang Y, Signoretti S, Choueiri TK, Freeman GJ, Zhu Q, Marasco WA. Anti-CAIX BBζ CAR4/8 T cells exhibit superior efficacy in a ccRCC mouse model. Mol Ther Oncolytics 2022; 24:385-399. [PMID: 35118195 PMCID: PMC8792103 DOI: 10.1016/j.omto.2021.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Improving CAR-T cell therapy for solid tumors requires a better understanding of CAR design and cellular composition. Here, we compared second-generation (BBζ and 28ζ) with third-generation (28BBζ) carbonic anhydrase IX (CAIX)-targeted CAR constructs and investigated the antitumor effect of CAR-T cells with different CD4/CD8 proportions in vitro and in vivo. The results demonstrated that BBζ exhibited superior efficacy compared with 28ζ and 28BBζ CAR-T cells in a clear-cell renal cell carcinoma (ccRCC) skrc-59 cell bearing NSG-SGM3 mouse model. The mice treated with a single dose of BBζ CD4/CD8 mixture (CAR4/8) showed complete tumor remission and remained tumor-free 72 days after CAR-T cells infusion. In the other CAR-T and control groups, tumor-infiltrating T cells were recovered and profiled. We found that BBζ CAR8 cells upregulated expression of major histocompatibility complex (MHC) class II and cytotoxicity-associated genes, while downregulating inhibitory immune checkpoint receptor genes and diminishing differentiation of regulatory T cells (Treg cells), leading to excellent therapeutic efficacy in vivo. Increased memory phenotype, elevated tumor infiltration, and decreased exhaustion genes were observed in the CD4/8 untransduced T (UNT) cells compared with CD8 alone, indicating that CD4/8 would be the favored cellular composition for CAR-T cell therapy with long-term persistence. In summary, these findings support that BBζ CAR4/8 cells are a highly potent, clinically translatable cell therapy for ccRCC.
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Affiliation(s)
- Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Alicia Buck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marion Grimaud
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Aedin C. Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
- Limerick Digital Cancer Research Center, Health Research Institute, School of Medicine, University of Limerick, Limerick V94 T9PX, Ireland
| | - Sreekumar Kodangattil
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Cecile Razimbaud
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dennis M. Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhu Zhu
- Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin Wei
- Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Madison L. O'Donnell
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sabina Signoretti
- Harvard Medical School, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Toni K. Choueiri
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gordon J. Freeman
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Quan Zhu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Wayne A. Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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6
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Roel E, Pistillo A, Recalde M, Sena AG, Fernández-Bertolín S, Aragón M, Puente D, Ahmed WUR, Alghoul H, Alser O, Alshammari TM, Areia C, Blacketer C, Carter W, Casajust P, Culhane AC, Dawoud D, DeFalco F, DuVall SL, Falconer T, Golozar A, Gong M, Hester L, Hripcsak G, Tan EH, Jeon H, Jonnagaddala J, Lai LYH, Lynch KE, Matheny ME, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Posada JD, Prats-Uribe A, Reich CG, Rivera DR, Schilling LM, Soerjomataram I, Shah K, Shah NH, Shen Y, Spotniz M, Subbian V, Suchard MA, Trama A, Zhang L, Zhang Y, Ryan PB, Prieto-Alhambra D, Kostka K, Duarte-Salles T. Characteristics and Outcomes of Over 300,000 Patients with COVID-19 and History of Cancer in the United States and Spain. Cancer Epidemiol Biomarkers Prev 2021; 30:1884-1894. [PMID: 34272262 PMCID: PMC8974356 DOI: 10.1158/1055-9965.epi-21-0266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2021] [Accepted: 07/07/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND We described the demographics, cancer subtypes, comorbidities, and outcomes of patients with a history of cancer and coronavirus disease 2019 (COVID-19). Second, we compared patients hospitalized with COVID-19 to patients diagnosed with COVID-19 and patients hospitalized with influenza. METHODS We conducted a cohort study using eight routinely collected health care databases from Spain and the United States, standardized to the Observational Medical Outcome Partnership common data model. Three cohorts of patients with a history of cancer were included: (i) diagnosed with COVID-19, (ii) hospitalized with COVID-19, and (iii) hospitalized with influenza in 2017 to 2018. Patients were followed from index date to 30 days or death. We reported demographics, cancer subtypes, comorbidities, and 30-day outcomes. RESULTS We included 366,050 and 119,597 patients diagnosed and hospitalized with COVID-19, respectively. Prostate and breast cancers were the most frequent cancers (range: 5%-18% and 1%-14% in the diagnosed cohort, respectively). Hematologic malignancies were also frequent, with non-Hodgkin's lymphoma being among the five most common cancer subtypes in the diagnosed cohort. Overall, patients were aged above 65 years and had multiple comorbidities. Occurrence of death ranged from 2% to 14% and from 6% to 26% in the diagnosed and hospitalized COVID-19 cohorts, respectively. Patients hospitalized with influenza (n = 67,743) had a similar distribution of cancer subtypes, sex, age, and comorbidities but lower occurrence of adverse events. CONCLUSIONS Patients with a history of cancer and COVID-19 had multiple comorbidities and a high occurrence of COVID-19-related events. Hematologic malignancies were frequent. IMPACT This study provides epidemiologic characteristics that can inform clinical care and etiologic studies.
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Affiliation(s)
- Elena Roel
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
- Universitat Autònoma de Barcelona, Spain
| | - Andrea Pistillo
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Martina Recalde
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
- Universitat Autònoma de Barcelona, Spain
| | - Anthony G Sena
- Janssen Research and Development, Titusville, New Jersey
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sergio Fernández-Bertolín
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Maria Aragón
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Diana Puente
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
- Universitat Autònoma de Barcelona, Spain
| | - Waheed-Ul-Rahman Ahmed
- NDORMS, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, United Kingdom
- College of Medicine and Health, University of Exeter, St Luke's Campus, Heavitree Road, Exeter, United Kingdom
| | - Heba Alghoul
- Faculty of Medicine, Islamic University of Gaza, Gaza, Palestine
| | - Osaid Alser
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Thamir M Alshammari
- Medication Safety Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Carlos Areia
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | | | - William Carter
- Data Science to Patient Value Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Paula Casajust
- Real-World Evidence, Trial Form Support, Barcelona, Spain
| | - Aedin C Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Dalia Dawoud
- Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Frank DeFalco
- Janssen Research and Development, Titusville, New Jersey
| | - Scott L DuVall
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Thomas Falconer
- Department of Biomedical Informatics, Columbia University, New York, New York
- New York-Presbyterian Hospital, New York, New York
| | - Asieh Golozar
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland
- Pharmacoepidemiology, Regeneron Pharmaceuticals, Westchester County, New York
| | - Mengchun Gong
- Digital Health China Technologies Co., Ltd., Beijing, China
| | - Laura Hester
- Janssen Research and Development, LLC, Raritan, New Jersey
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, New York
- New York-Presbyterian Hospital, New York, New York
| | - Eng Hooi Tan
- Centre for Statistics in Medicine, NDORMS, University of Oxford, Oxford, United Kingdom
| | - Hokyun Jeon
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Gyeonggi-do, Republic of Korea
| | | | - Lana Y H Lai
- School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Kristine E Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Michael E Matheny
- Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel R Morales
- Division of Population Health and Genomics, University of Dundee, Dundee, United Kingdom
- University of Southern Denmark, Odense, Denmark
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, New York
- New York-Presbyterian Hospital, New York, New York
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Ostropolets
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - José D Posada
- Department of Medicine, School of Medicine, Stanford University, Redwood City, California
| | - Albert Prats-Uribe
- Centre for Statistics in Medicine, NDORMS, University of Oxford, Oxford, United Kingdom
| | | | - Donna R Rivera
- Division of Cancer Control and Population Sciences, National Cancer Institute, Rockville, Maryland
| | - Lisa M Schilling
- Data Science to Patient Value Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Isabelle Soerjomataram
- Section of Cancer Surveillance, International Agency for Research on Cancer, Lyon, France
| | - Karishma Shah
- NDORMS, University of Oxford, Botnar Research Centre, Windmill Road, Oxford, United Kingdom
| | - Nigam H Shah
- Department of Medicine, School of Medicine, Stanford University, Redwood City, California
| | - Yang Shen
- Digital Health China Technologies Co., Ltd., Beijing, China
| | - Matthew Spotniz
- Department of Biomedical Informatics, Columbia University, New York, New York
| | - Vignesh Subbian
- College of Engineering, University of Arizona, Tucson, Arizona
| | - Marc A Suchard
- Fielding School of Public Health, University of California, Los Angeles, California
| | - Annalisa Trama
- Fondazione IRCSS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lin Zhang
- School of Population Medicine and Public Health, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- School of Population Health and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Ying Zhang
- Digital Health China Technologies Co., Ltd., Beijing, China
| | - Patrick B Ryan
- Janssen Research and Development, Titusville, New Jersey
- Department of Biomedical Informatics, Columbia University, New York, New York
| | | | | | - Talita Duarte-Salles
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain.
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7
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Cao KAL, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol 2021; 22:246. [PMID: 34433496 PMCID: PMC8385897 DOI: 10.1186/s13059-021-02468-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
| | - Al J Abadi
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Emily F Davis-Marcisak
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lauren Hsu
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Arshi Arora
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexis Coullomb
- Centre de Recherches en Cancérologie de Toulouse (INSERM), Université Paul Sabatier III, Toulouse, France
| | - Atul Deshpande
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yuzhou Feng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | | | - Melanie Loth
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Wancen Mu
- Department of Biostatistics, UNC, Chapel Hill, NC, USA
| | - Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (INSERM), Université Paul Sabatier III, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Kris Sankaran
- Department of Statistics, University of Wisconsin, Madison, WI, USA
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Padova, PD, Italy
| | - Amrit Singh
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- PROOF Centre of Excellence, Vancouver, BC, Canada
| | - Joshua S Sodicoff
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Genevieve L Stein-O'Brien
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | | | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yue You
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | | | - Vincent J Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ruben Dries
- Department of Hematology and Oncology, Boston Medical Center, Boston, MA, USA
- Department of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
- Center for Regenerative Medicine (CReM), Boston University, Boston, MA, USA
| | - Casey S Greene
- Center for Health AI and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Michael I Love
- Department of Biostatistics, UNC, Chapel Hill, NC, USA
- Department of Genetics, UNC, Chapel Hill, NC, USA
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aedin C Culhane
- Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Elana Fertig
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
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8
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Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O’Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol 2021; 22:220. [PMID: 34353350 PMCID: PMC8340473 DOI: 10.1186/s13059-021-02433-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Al J. Abadi
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Emily F. Davis-Marcisak
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Lauren Hsu
- Data Science, Dana-Farber Cancer Institute, Boston, MA USA
- Department of Genetics, UNC, Chapel Hill, NC USA
| | - Arshi Arora
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Alexis Coullomb
- Centre de Recherches en Cancérologie de Toulouse (INSERM), Université Paul Sabatier III, Toulouse, France
| | - Atul Deshpande
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Yuzhou Feng
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | | | - Melanie Loth
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Wancen Mu
- Department of Biostatistics, UNC, Chapel Hill, NC USA
| | - Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (INSERM), Université Paul Sabatier III, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Kris Sankaran
- Department of Statistics, University of Wisconsin, Madison, WI USA
| | - Dario Righelli
- Department of Statistical Sciences, University of Padova, Padova, PD Italy
| | - Amrit Singh
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC Canada
- PROOF Centre of Excellence, Vancouver, BC Canada
| | - Joshua S. Sodicoff
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI USA
| | - Genevieve L. Stein-O’Brien
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD USA
| | | | - Joshua D. Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI USA
| | - Yue You
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | | | - Vincent J. Carey
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ruben Dries
- Department of Hematology and Oncology, Boston Medical Center, Boston, MA USA
- Department of Computational Biomedicine, Boston University School of Medicine, Boston, MA USA
- Center for Regenerative Medicine (CReM), Boston University, Boston, MA USA
| | - Casey S. Greene
- Center for Health AI and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA USA
| | - Michael I. Love
- Department of Biostatistics, UNC, Chapel Hill, NC USA
- Department of Genetics, UNC, Chapel Hill, NC USA
| | - Matthew E. Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Aedin C. Culhane
- Data Science, Dana-Farber Cancer Institute, Boston, MA USA
- Biostatistics, Harvard TH Chan School of Public Health, Boston, MA USA
| | - Elana Fertig
- Cancer Convergence Institute and Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD USA
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9
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Sheffer M, Lowry E, Beelen N, Borah M, Amara SNA, Mader CC, Roth JA, Tsherniak A, Freeman SS, Dashevsky O, Gandolfi S, Bender S, Bryan JG, Zhu C, Wang L, Tariq I, Kamath GM, Simoes RDM, Dhimolea E, Yu C, Hu Y, Dufva O, Giannakis M, Syrgkanis V, Fraenkel E, Golub T, Romee R, Mustjoki S, Culhane AC, Wieten L, Mitsiades CS. Genome-scale screens identify factors regulating tumor cell responses to natural killer cells. Nat Genet 2021; 53:1196-1206. [PMID: 34253920 DOI: 10.1038/s41588-021-00889-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022]
Abstract
To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated 'DNA-barcoded' solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell-sensitive tumor cells tend to exhibit 'mesenchymal-like' transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 (NCR3LG1); and low levels of HLA-E/antigen presentation genes. Importantly, transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.
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MESH Headings
- Allogeneic Cells/physiology
- Animals
- B7 Antigens/genetics
- Cell Line, Tumor
- Chromatin Assembly and Disassembly/physiology
- Cytotoxicity Tests, Immunologic/methods
- Cytotoxicity, Immunologic/genetics
- Cytotoxicity, Immunologic/physiology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Killer Cells, Natural/physiology
- Mice, Inbred NOD
- Xenograft Model Antitumor Assays
- HLA-E Antigens
- Mice
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Affiliation(s)
- Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
| | - Emily Lowry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicky Beelen
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Minasri Borah
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Chris C Mader
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jennifer A Roth
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aviad Tsherniak
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Samantha Bender
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Jordan G Bryan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Cong Zhu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Li Wang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ifrah Tariq
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Ludwig Center, Harvard Medical School, Boston, MA, USA
| | - Channing Yu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Sichuan University, Chengdu, China
| | - Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Ernest Fraenkel
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Todd Golub
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Aedin C Culhane
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center+, Maastricht, the Netherlands
- School for Oncology and Developmental Biology, Maastricht University Medical Center+ GROW, Maastricht, the Netherlands
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Ludwig Center, Harvard Medical School, Boston, MA, USA.
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10
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Dhimolea E, de Matos Simoes R, Kansara D, Al'Khafaji A, Bouyssou J, Weng X, Sharma S, Raja J, Awate P, Shirasaki R, Tang H, Glassner BJ, Liu Z, Gao D, Bryan J, Bender S, Roth J, Scheffer M, Jeselsohn R, Gray NS, Georgakoudi I, Vazquez F, Tsherniak A, Chen Y, Welm A, Duy C, Melnick A, Bartholdy B, Brown M, Culhane AC, Mitsiades CS. An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. Cancer Cell 2021; 39:240-256.e11. [PMID: 33417832 PMCID: PMC8670073 DOI: 10.1016/j.ccell.2020.12.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/19/2020] [Accepted: 12/02/2020] [Indexed: 01/23/2023]
Abstract
Treatment-persistent residual tumors impede curative cancer therapy. To understand this cancer cell state we generated models of treatment persistence that simulate the residual tumors. We observe that treatment-persistent tumor cells in organoids, xenografts, and cancer patients adopt a distinct and reversible transcriptional program resembling that of embryonic diapause, a dormant stage of suspended development triggered by stress and associated with suppressed Myc activity and overall biosynthesis. In cancer cells, depleting Myc or inhibiting Brd4, a Myc transcriptional co-activator, attenuates drug cytotoxicity through a dormant diapause-like adaptation with reduced apoptotic priming. Conversely, inducible Myc upregulation enhances acute chemotherapeutic activity. Maintaining residual cells in dormancy after chemotherapy by inhibiting Myc activity or interfering with the diapause-like adaptation by inhibiting cyclin-dependent kinase 9 represent potential therapeutic strategies against chemotherapy-persistent tumor cells. Our study demonstrates that cancer co-opts a mechanism similar to diapause with adaptive inactivation of Myc to persist during treatment.
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Affiliation(s)
- Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
| | - Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Dhvanir Kansara
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | | | - Juliette Bouyssou
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiang Weng
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA
| | - Shruti Sharma
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA
| | - Joseline Raja
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA
| | - Pallavi Awate
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Zhiyi Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Dong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jordan Bryan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jennifer Roth
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Scheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Nathanael S Gray
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | | | | | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alana Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Cihangir Duy
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Cancer Signaling and Epigenetics Program, Institute for Cancer Research, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aedin C Culhane
- Department of Data Sciences, Dana-Farber Cancer Institute & Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
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11
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Sheffer M, Lowry E, Beelen N, Borah M, Amara SNA, Mader CC, Roth J, Tsherniak A, Dashevsky O, Gandolfi S, Bender S, Bryan J, Zhu C, Wang L, Simoes RDM, Yu C, Hu Y, Dufva O, Giannakis M, Golub T, Romee R, Mustjoki S, Culhane AC, Wieten L, Mitsiades CS. Abstract PO041: Landscape of molecular events regulating tumor cell responses to natural killer cells. Cancer Immunol Res 2021. [DOI: 10.1158/2326-6074.tumimm20-po041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Natural killer (NK) cells exhibit potent activity in pre-clinical models of diverse hematologic malignancies and solid tumors and infusion of high numbers of NK cells, either autologous or allogeneic, after their ex vivo expansion and activation, has been feasible and safe in clinical studies. To systematically define molecular features in human tumor cells which determine their degree of sensitivity to human allogeneic NK cells, we quantified the NK cell responsiveness of hundreds of molecularly-annotated “DNA-barcoded” solid tumor cell lines in multiplexed format (PRISM; Profiling Relative Inhibition Simultaneously in Mixtures approach), correlating cytotoxicity scores for each cell line with the CCLE transcriptional data (RNA-seq), to reveal genes that are associated with resistance or sensitivity to NK cells. In addition, we applied genome-scale CRISPR-based gene editing screens in several solid tumor cell lines to interrogate, at a functional level, which genes regulate tumor cell response to NK cells. Based on these orthogonal studies, NK sensitive tumor cells tend to exhibit high levels of the NK cell-activating ligand B7-H6 (NCR3LG1); low levels of the inhibitory ligand HLA-E; microsatellite instability (MSI) status; high transcriptional signature for chromatin remodeling complexes and low antigen presentation machinery genes. Treatment with an HDAC inhibitor reduced the sensitivity of SW620 colon cancer cells, increased antigen presentation machinery, including HLA-E, and reduced B7-H6. Importantly, we observe that transcriptional signatures of NK cell-sensitive tumor cells correlate with immune checkpoint inhibitor resistance in clinical samples. Strikingly, comprehensive analysis of the CCLE transcriptional signatures revealed that cell lines with mesenchymal-like program tend to be more sensitive to NK cells treatment, compared with cell lines of epithelial-like program. Indeed, mesenchymal tumors tend to have lower expression of antigen presentation machinery in both CCLE and TCGA, suggesting a link between these two machieneries. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies.
Citation Format: Michal Sheffer, Emily Lowry, Nicky Beelen, Minasri Borah, Suha Naffar-Abu Amara, Chris C. Mader, Jennifer Roth, Aviad Tsherniak, Olga Dashevsky, Sara Gandolfi, Samantha Bender, Jordan Bryan, Cong Zhu, Li Wang, Ricardo De-Matos Simoes, Channing Yu, Yiguo Hu, Olli Dufva, Marios Giannakis, Todd Golub, Rizwan Romee, Satu Mustjoki, Aedin C. Culhane, Lotte Wieten, Constantine S. Mitsiades. Landscape of molecular events regulating tumor cell responses to natural killer cells [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO041.
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Affiliation(s)
- Michal Sheffer
- 1Dana-Farber Cancer Institute; Broad Institute, Boston; Cambridge, MA, USA,
| | - Emily Lowry
- 2Dana-Farber Cancer Institute, Boston, MA, USA,
| | - Nicky Beelen
- 3Maastricht University, Maastricht, The Netherlands,
| | | | | | | | | | | | - Olga Dashevsky
- 1Dana-Farber Cancer Institute; Broad Institute, Boston; Cambridge, MA, USA,
| | - Sara Gandolfi
- 1Dana-Farber Cancer Institute; Broad Institute, Boston; Cambridge, MA, USA,
| | | | | | - Cong Zhu
- 5Broad Institute, Cambridge, MA, USA,
| | - Li Wang
- 5Broad Institute, Cambridge, MA, USA,
| | | | | | - Yiguo Hu
- 6Sichuan University, Chengdu, China,
| | - Olli Dufva
- 7Helsinki University Hospital Comprehensive Cancer Center; University of Helsinki, Helsinki, Finland
| | - Marios Giannakis
- 1Dana-Farber Cancer Institute; Broad Institute, Boston; Cambridge, MA, USA,
| | - Todd Golub
- 1Dana-Farber Cancer Institute; Broad Institute, Boston; Cambridge, MA, USA,
| | | | - Satu Mustjoki
- 7Helsinki University Hospital Comprehensive Cancer Center; University of Helsinki, Helsinki, Finland
| | | | - Lotte Wieten
- 3Maastricht University, Maastricht, The Netherlands,
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12
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Shirasaki R, Matthews GM, Gandolfi S, de Matos Simoes R, Buckley DL, Raja Vora J, Sievers QL, Brüggenthies JB, Dashevsky O, Poarch H, Tang H, Bariteau MA, Sheffer M, Hu Y, Downey-Kopyscinski SL, Hengeveld PJ, Glassner BJ, Dhimolea E, Ott CJ, Zhang T, Kwiatkowski NP, Laubach JP, Schlossman RL, Richardson PG, Culhane AC, Groen RWJ, Fischer ES, Vazquez F, Tsherniak A, Hahn WC, Levy J, Auclair D, Licht JD, Keats JJ, Boise LH, Ebert BL, Bradner JE, Gray NS, Mitsiades CS. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins. Cell Rep 2021; 34:108532. [PMID: 33406420 DOI: 10.1016/j.celrep.2020.108532] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 06/14/2019] [Accepted: 11/25/2020] [Indexed: 12/15/2022] Open
Abstract
Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR-Cas9-based gene editing studies. We observed that myeloma cell resistance to degraders of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; and this involves loss of function of the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for resistance mechanisms to CRBN- versus VHL-based degraders explains mechanistically the lack of cross-resistance with sequential administration of these two degrader classes. Development of degraders leveraging more diverse E3 ligases/CRLs may facilitate sequential/alternating versus combined uses of these agents toward potentially delaying or preventing resistance.
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Affiliation(s)
- Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Geoffrey M Matthews
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Gandolfi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Ricardo de Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseline Raja Vora
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan L Sievers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Johanna B Brüggenthies
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Haley Poarch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Huihui Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Megan A Bariteau
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Yiguo Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sondra L Downey-Kopyscinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul J Hengeveld
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Brian J Glassner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ludwig Center at Harvard, Boston, MA, USA
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tinghu Zhang
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas P Kwiatkowski
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob P Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Robert L Schlossman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Richard W J Groen
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Eric S Fischer
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joan Levy
- Multiple Myeloma Research Foundation, Norwalk, CT, USA
| | | | - Jonathan D Licht
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | | | - Lawrence H Boise
- Department of Hematology and Medical Oncology and the Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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13
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Burn E, You SC, Sena AG, Kostka K, Abedtash H, Abrahão MTF, Alberga A, Alghoul H, Alser O, Alshammari TM, Aragon M, Areia C, Banda JM, Cho J, Culhane AC, Davydov A, DeFalco FJ, Duarte-Salles T, DuVall S, Falconer T, Fernandez-Bertolin S, Gao W, Golozar A, Hardin J, Hripcsak G, Huser V, Jeon H, Jing Y, Jung CY, Kaas-Hansen BS, Kaduk D, Kent S, Kim Y, Kolovos S, Lane JCE, Lee H, Lynch KE, Makadia R, Matheny ME, Mehta PP, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Park RW, Park J, Posada JD, Prats-Uribe A, Rao G, Reich C, Rho Y, Rijnbeek P, Schilling LM, Schuemie M, Shah NH, Shoaibi A, Song S, Spotnitz M, Suchard MA, Swerdel JN, Vizcaya D, Volpe S, Wen H, Williams AE, Yimer BB, Zhang L, Zhuk O, Prieto-Alhambra D, Ryan P. Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study. Nat Commun 2020; 11:5009. [PMID: 33024121 PMCID: PMC7538555 DOI: 10.1038/s41467-020-18849-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Comorbid conditions appear to be common among individuals hospitalised with coronavirus disease 2019 (COVID-19) but estimates of prevalence vary and little is known about the prior medication use of patients. Here, we describe the characteristics of adults hospitalised with COVID-19 and compare them with influenza patients. We include 34,128 (US: 8362, South Korea: 7341, Spain: 18,425) COVID-19 patients, summarising between 4811 and 11,643 unique aggregate characteristics. COVID-19 patients have been majority male in the US and Spain, but predominantly female in South Korea. Age profiles vary across data sources. Compared to 84,585 individuals hospitalised with influenza in 2014-19, COVID-19 patients have more typically been male, younger, and with fewer comorbidities and lower medication use. While protecting groups vulnerable to influenza is likely a useful starting point in the response to COVID-19, strategies will likely need to be broadened to reflect the particular characteristics of individuals being hospitalised with COVID-19.
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Affiliation(s)
- Edward Burn
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
- Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK
| | - Seng Chan You
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Anthony G Sena
- Janssen Research and Development, Titusville, NJ, USA
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | | | - Amanda Alberga
- Observational Health Data Sciences and Informatics Network, Alberta, Canada
| | - Heba Alghoul
- Faculty of Medicine, Islamic University of Gaza, Gaza, Palestine
| | - Osaid Alser
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thamir M Alshammari
- Medication Safety Research Chair, King Saud University, Riyadh, Saudi Arabia
| | - Maria Aragon
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Carlos Areia
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Juan M Banda
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Jaehyeong Cho
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Aedin C Culhane
- Data Science, Dana-Farber Cancer Institute. Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Alexander Davydov
- Odysseus Data Services, Inc., Cambridge, MA, USA
- Department for Microbiology, Virology and Immunology, Belarusian State Medical University, Minsk, Belarus
| | | | - Talita Duarte-Salles
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Scott DuVall
- Department of Veterans Affairs, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Thomas Falconer
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Sergio Fernandez-Bertolin
- Fundació Institut Universitari per a la recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Weihua Gao
- Health Economics and Outcomes Research, AbbVie, North Chicago, IL, USA
| | - Asieh Golozar
- Pharmacoepidemiology, Regeneron, NY, USA
- Department of Epidemiology, Johns Hopkins School of Public, Baltimore, MD, USA
| | - Jill Hardin
- Janssen Research and Development, Titusville, NJ, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- New York-Presbyterian Hospital, New York, NY, USA
| | - Vojtech Huser
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hokyun Jeon
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea
| | - Yonghua Jing
- Health Economics and Outcomes Research, AbbVie, North Chicago, IL, USA
| | - Chi Young Jung
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Daegu Catholic University Medical Center, Daegu, Korea
| | - Benjamin Skov Kaas-Hansen
- Clinical Pharmacology Unit, Zealand University Hospital, Køge, Denmark
- NNF Centre for Protein Research, University of Copenhagen, København, Denmark
| | - Denys Kaduk
- Odysseus Data Services, Inc., Cambridge, MA, USA
- Department of Pediatrics № 2, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Seamus Kent
- Science Policy and Research, National Institute for Health and Care Excellence, London, UK
| | - Yeesuk Kim
- Department of Orthopaedic Surgery, College of Medicine, Hanyang University, Seoul, Korea
| | - Spyros Kolovos
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK
| | - Jennifer C E Lane
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK
| | - Hyejin Lee
- Bigdata Department, Health Insurance Review & Assessment Service, Wonju, Korea
| | - Kristine E Lynch
- Department of Veterans Affairs, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rupa Makadia
- Janssen Research and Development, Titusville, NJ, USA
| | - Michael E Matheny
- GRECC, Tennessee Valley Healthcare System VA, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paras P Mehta
- College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Daniel R Morales
- Division of Population Health and Genomics, University of Dundee, Dundee, UK
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- New York-Presbyterian Hospital, New York, NY, USA
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Ostropolets
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rae Woong Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea
| | - Jimyung Park
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea
| | - Jose D Posada
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Albert Prats-Uribe
- Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK
| | - Gowtham Rao
- Janssen Research and Development, Titusville, NJ, USA
| | | | - Yeunsook Rho
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK
| | - Peter Rijnbeek
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lisa M Schilling
- Data Science to Patient Value Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Martijn Schuemie
- Janssen Research and Development, Titusville, NJ, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Nigam H Shah
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Azza Shoaibi
- Janssen Research and Development, Titusville, NJ, USA
| | - Seokyoung Song
- Department of Anesthesiology and Pain Medicine, Catholic University of Daegu, School of Medicine, Gyeongsan, Korea
| | - Matthew Spotnitz
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Marc A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | | | | | - Salvatore Volpe
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Haini Wen
- Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Andrew E Williams
- Tufts Institute for Clinical Research and Health Policy Studies, Boston, MA, USA
| | - Belay B Yimer
- Centre for Epidemiology Versus Arthritis, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Lin Zhang
- School of Public Health, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Oleg Zhuk
- Odysseus Data Services, Inc., Cambridge, MA, USA
| | - Daniel Prieto-Alhambra
- Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, Oxford, UK.
| | - Patrick Ryan
- Janssen Research and Development, Titusville, NJ, USA
- Columbia University, New York, NY, USA
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14
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Lane JCE, Weaver J, Kostka K, Duarte-Salles T, Abrahao MTF, Alghoul H, Alser O, Alshammari TM, Biedermann P, Banda JM, Burn E, Casajust P, Conover MM, Culhane AC, Davydov A, DuVall SL, Dymshyts D, Fernandez-Bertolin S, Fišter K, Hardin J, Hester L, Hripcsak G, Kaas-Hansen BS, Kent S, Khosla S, Kolovos S, Lambert CG, van der Lei J, Lynch KE, Makadia R, Margulis AV, Matheny ME, Mehta P, Morales DR, Morgan-Stewart H, Mosseveld M, Newby D, Nyberg F, Ostropolets A, Park RW, Prats-Uribe A, Rao GA, Reich C, Reps J, Rijnbeek P, Sathappan SMK, Schuemie M, Seager S, Sena AG, Shoaibi A, Spotnitz M, Suchard MA, Torre CO, Vizcaya D, Wen H, de Wilde M, Xie J, You SC, Zhang L, Zhuk O, Ryan P, Prieto-Alhambra D. Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study. Lancet Rheumatol 2020; 2:e698-e711. [PMID: 32864627 PMCID: PMC7442425 DOI: 10.1016/s2665-9913(20)30276-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Hydroxychloroquine, a drug commonly used in the treatment of rheumatoid arthritis, has received much negative publicity for adverse events associated with its authorisation for emergency use to treat patients with COVID-19 pneumonia. We studied the safety of hydroxychloroquine, alone and in combination with azithromycin, to determine the risk associated with its use in routine care in patients with rheumatoid arthritis. Methods In this multinational, retrospective study, new user cohort studies in patients with rheumatoid arthritis aged 18 years or older and initiating hydroxychloroquine were compared with those initiating sulfasalazine and followed up over 30 days, with 16 severe adverse events studied. Self-controlled case series were done to further establish safety in wider populations, and included all users of hydroxychloroquine regardless of rheumatoid arthritis status or indication. Separately, severe adverse events associated with hydroxychloroquine plus azithromycin (compared with hydroxychloroquine plus amoxicillin) were studied. Data comprised 14 sources of claims data or electronic medical records from Germany, Japan, the Netherlands, Spain, the UK, and the USA. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate calibrated hazard ratios (HRs) according to drug use. Estimates were pooled where the I 2 value was less than 0·4. Findings The study included 956 374 users of hydroxychloroquine, 310 350 users of sulfasalazine, 323 122 users of hydroxychloroquine plus azithromycin, and 351 956 users of hydroxychloroquine plus amoxicillin. No excess risk of severe adverse events was identified when 30-day hydroxychloroquine and sulfasalazine use were compared. Self-controlled case series confirmed these findings. However, long-term use of hydroxychloroquine appeared to be associated with increased cardiovascular mortality (calibrated HR 1·65 [95% CI 1·12-2·44]). Addition of azithromycin appeared to be associated with an increased risk of 30-day cardiovascular mortality (calibrated HR 2·19 [95% CI 1·22-3·95]), chest pain or angina (1·15 [1·05-1·26]), and heart failure (1·22 [1·02-1·45]). Interpretation Hydroxychloroquine treatment appears to have no increased risk in the short term among patients with rheumatoid arthritis, but in the long term it appears to be associated with excess cardiovascular mortality. The addition of azithromycin increases the risk of heart failure and cardiovascular mortality even in the short term. We call for careful consideration of the benefit-risk trade-off when counselling those on hydroxychloroquine treatment. Funding National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, NIHR Senior Research Fellowship programme, US National Institutes of Health, US Department of Veterans Affairs, Janssen Research and Development, IQVIA, Korea Health Industry Development Institute through the Ministry of Health and Welfare Republic of Korea, Versus Arthritis, UK Medical Research Council Doctoral Training Partnership, Foundation Alfonso Martin Escudero, Innovation Fund Denmark, Novo Nordisk Foundation, Singapore Ministry of Health's National Medical Research Council Open Fund Large Collaborative Grant, VINCI, Innovative Medicines Initiative 2 Joint Undertaking, EU's Horizon 2020 research and innovation programme, and European Federation of Pharmaceutical Industries and Associations.
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Affiliation(s)
- Jennifer C E Lane
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - James Weaver
- Janssen Research and Development, Titusville, NJ, USA
| | | | - Talita Duarte-Salles
- Fundació Institut Universitari per a la Recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | | | - Heba Alghoul
- Faculty of Medicine, Islamic University of Gaza, Palestine
| | - Osaid Alser
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thamir M Alshammari
- Medication Safety Research Chair, King Saud University, Riyadh, Saudi Arabia
| | | | - Juan M Banda
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Edward Burn
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,Fundació Institut Universitari per a la Recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Paula Casajust
- Real-World Evidence, Trial Form Support, Barcelona, Spain
| | | | - Aedin C Culhane
- Department of Data Sciences, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Alexander Davydov
- Medical Ontology Solutions, Odysseus Data Services, Cambridge MA, USA
| | - Scott L DuVall
- Western Institute for Biomedical Research, Department of Veterans Affairs, Salt Lake City, UT, USA.,Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Dmitry Dymshyts
- Medical Ontology Solutions, Odysseus Data Services, Cambridge MA, USA
| | - Sergio Fernandez-Bertolin
- Fundació Institut Universitari per a la Recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
| | - Kristina Fišter
- School of Medicine, Andrija Štampar School of Public Health, University of Zagreb, Zagreb, Croatia
| | - Jill Hardin
- Janssen Research and Development, Titusville, NJ, USA
| | - Laura Hester
- Janssen Research and Development, Titusville, NJ, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.,New York-Presbyterian Hospital, New York, NY, USA
| | - Benjamin Skov Kaas-Hansen
- Clinical Pharmacology Unit, Zealand University Hospital, Roskilde, Denmark.,NNF Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Seamus Kent
- National Institute for Health and Care Excellence, London, UK
| | - Sajan Khosla
- Real World Science and Digital, AstraZeneca, Cambridge, UK
| | - Spyros Kolovos
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Christophe G Lambert
- Department of Internal Medicine, Center for Global Health and Division of Translational Informatics, Albuquerque, NM, USA
| | - Johan van der Lei
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kristine E Lynch
- Western Institute for Biomedical Research, Department of Veterans Affairs, Salt Lake City, UT, USA.,Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rupa Makadia
- Janssen Research and Development, Titusville, NJ, USA
| | | | - Michael E Matheny
- Geriatrics Research Education and Clinical Care Center, Tennessee Valley Healthcare System VA, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paras Mehta
- College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Daniel R Morales
- Division of Population Health and Genomics, University of Dundee, UK
| | | | - Mees Mosseveld
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Danielle Newby
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Ostropolets
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Rae Woong Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon-si Gyeonggi-do, South Korea
| | - Albert Prats-Uribe
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Gowtham A Rao
- Janssen Research and Development, Titusville, NJ, USA
| | | | - Jenna Reps
- Janssen Research and Development, Titusville, NJ, USA
| | - Peter Rijnbeek
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | | | | | - Anthony G Sena
- Janssen Research and Development, Titusville, NJ, USA.,Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Azza Shoaibi
- Janssen Research and Development, Titusville, NJ, USA
| | - Matthew Spotnitz
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Marc A Suchard
- Department of Biomathematics and Department of Human Genetics, David Geffen School of Medicine at UCLA, and Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | | | | | - Haini Wen
- Department of Pharmacy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Marcel de Wilde
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Junqing Xie
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Seng Chan You
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon-si Gyeonggi-do, South Korea
| | - Lin Zhang
- School of Population Medicine and Public Health, Peking Union Medical College/Chinese Academy of Medical Sciences, Beijing, China.,Melbourne School of Population and Global Health, University of Melbourne, VIC, Australia
| | - Oleg Zhuk
- Medical Ontology Solutions, Odysseus Data Services, Cambridge MA, USA
| | - Patrick Ryan
- Janssen Research and Development, Titusville, NJ, USA.,Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Daniel Prieto-Alhambra
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,Fundació Institut Universitari per a la Recerca a l'Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain
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15
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Burn E, You SC, Sena A, Kostka K, Abedtash H, Abrahao MTF, Alberga A, Alghoul H, Alser O, Alshammari TM, Aragon M, Areia C, Banda JM, Cho J, Culhane AC, Davydov A, DeFalco FJ, Duarte-Salles T, DuVall SL, Falconer T, Fernandez-Bertolin S, Gao W, Golozar A, Hardin J, Hripcsak G, Huser V, Jeon H, Jing Y, Jung CY, Kaas-Hansen BS, Kaduk D, Kent S, Kim Y, Kolovos S, Lane J, Lee H, Lynch KE, Makadia R, Matheny ME, Mehta P, Morales DR, Natarajan K, Nyberg F, Ostropolets A, Park RW, Park J, Posada JD, Prats-Uribe A, Rao GA, Reich C, Rho Y, Rijnbeek P, Schilling LM, Schuemie M, Shah NH, Shoaibi A, Song S, Spotnitz M, Suchard MA, Swerdel J, Vizcaya D, Volpe S, Wen H, Williams AE, Yimer BB, Zhang L, Zhuk O, Prieto-Alhambra D, Ryan P. Deep phenotyping of 34,128 patients hospitalised with COVID-19 and a comparison with 81,596 influenza patients in America, Europe and Asia: an international network study. medRxiv 2020. [PMID: 32511443 DOI: 10.1101/2020.04.22.20074336] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background In this study we phenotyped individuals hospitalised with coronavirus disease 2019 (COVID-19) in depth, summarising entire medical histories, including medications, as captured in routinely collected data drawn from databases across three continents. We then compared individuals hospitalised with COVID-19 to those previously hospitalised with influenza. Methods We report demographics, previously recorded conditions and medication use of patients hospitalised with COVID-19 in the US (Columbia University Irving Medical Center [CUIMC], Premier Healthcare Database [PHD], UCHealth System Health Data Compass Database [UC HDC], and the Department of Veterans Affairs [VA OMOP]), in South Korea (Health Insurance Review & Assessment [HIRA]), and Spain (The Information System for Research in Primary Care [SIDIAP] and HM Hospitales [HM]). These patients were then compared with patients hospitalised with influenza in 2014-19. Results 34,128 (US: 8,362, South Korea: 7,341, Spain: 18,425) individuals hospitalised with COVID-19 were included. Between 4,811 (HM) and 11,643 (CUIMC) unique aggregate characteristics were extracted per patient, with all summarised in an accompanying interactive website (http://evidence.ohdsi.org/Covid19CharacterizationHospitalization/). Patients were majority male in the US (CUIMC: 52%, PHD: 52%, UC HDC: 54%, VA OMOP: 94%,) and Spain (SIDIAP: 54%, HM: 60%), but were predominantly female in South Korea (HIRA: 60%). Age profiles varied across data sources. Prevalence of asthma ranged from 4% to 15%, diabetes from 13% to 43%, and hypertensive disorder from 24% to 70% across data sources. Between 14% and 33% were taking drugs acting on the renin-angiotensin system in the 30 days prior to hospitalisation. Compared to 81,596 individuals hospitalised with influenza in 2014-19, patients admitted with COVID-19 were more typically male, younger, and healthier, with fewer comorbidities and lower medication use. Conclusions We provide a detailed characterisation of patients hospitalised with COVID-19. Protecting groups known to be vulnerable to influenza is a useful starting point to minimize the number of hospital admissions needed for COVID-19. However, such strategies will also likely need to be broadened so as to reflect the particular characteristics of individuals hospitalised with COVID-19.
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16
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Abstract
Integrative, single-cell analyses may provide unprecedented insights into cellular and spatial diversity of the tumor microenvironment. The sparsity, noise, and high dimensionality of these data present unique challenges. Whilst approaches for integrating single-cell data are emerging and are far from being standardized, most data integration, cell clustering, cell trajectory, and analysis pipelines employ a dimension reduction step, frequently principal component analysis (PCA), a matrix factorization method that is relatively fast, and can easily scale to large datasets when used with sparse-matrix representations. In this review, we provide a guide to PCA and related methods. We describe the relationship between PCA and singular value decomposition, the difference between PCA of a correlation and covariance matrix, the impact of scaling, log-transforming, and standardization, and how to recognize a horseshoe or arch effect in a PCA. We describe canonical correlation analysis (CCA), a popular matrix factorization approach for the integration of single-cell data from different platforms or studies. We discuss alternatives to CCA and why additional preprocessing or weighting datasets within the joint decomposition should be considered.
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Affiliation(s)
- Lauren L Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Division of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Aedin C Culhane
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Division of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
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17
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2019; 51:411-412. [PMID: 31433971 DOI: 10.1016/j.immuni.2019.08.004] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | | | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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18
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2019. [PMID: 31433971 DOI: 10.1016/j.immuni.2019.08.004.erratumfor:immunity.2018;48(4),812-830.e14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | | | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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19
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Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet 2018; 34:790-805. [PMID: 30143323 PMCID: PMC6309559 DOI: 10.1016/j.tig.2018.07.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix factorization (MF) techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in applications ranging from pathway discovery to timecourse analysis. We review exemplary applications of MF for systems-level analyses. We discuss appropriate applications of these methods, their limitations, and focus on the analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with MF enables discovery from high-throughput data beyond the limits of current biological knowledge - answering questions from high-dimensional data that we have not yet thought to ask.
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Affiliation(s)
- Genevieve L Stein-O'Brien
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Raman Arora
- Department of Computer Science, Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Alexander V Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, PA, USA; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, PA, USA
| | - Loyal A Goff
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifeng Li
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Aloune Ngom
- School of Computer Science, University of Windsor, Windsor, ON, Canada
| | - Michael F Ochs
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ, USA
| | - Yanxun Xu
- Department of Applied Mathematics and Statistics, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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20
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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity 2018; 48:812-830.e14. [PMID: 29628290 PMCID: PMC5982584 DOI: 10.1016/j.immuni.2018.03.023] [Citation(s) in RCA: 3110] [Impact Index Per Article: 518.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/23/2018] [Accepted: 03/21/2018] [Indexed: 02/08/2023]
Abstract
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes-wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant-characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field.
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Affiliation(s)
- Vésteinn Thorsson
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
| | - David L Gibbs
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Denise Wolf
- University of California, San Francisco, Box 0808, 2340 Sutter Street, S433, San Francisco, CA 94115, USA
| | - Dante S Bortone
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Eduard Porta-Pardo
- Barcelona Supercomputing Centre, c/Jordi Girona, 29, 08034 Barcelona, Spain; SBP Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Galen F Gao
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Christopher L Plaisier
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - James A Eddy
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd St, San Francisco, CA 94143, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Evan O Paull
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - I K Ashok Sivakumar
- Department of Computer Science, Institute for Computational Medicine; Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew J Gentles
- Departments of Medicine and Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Farshad Farshidfar
- Department of Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Antonio Colaprico
- Universite libre de Bruxelles (ULB), Computer Science Department, Faculty of Sciences, Boulevard du Triomphe - CP212, 1050 Bruxelles, Belgium
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Yuexin Liu
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Janet Rader
- Medical College of Wisconsin, 9200 Wisconsin Avenue, Milwaukee, WI 53226 USA
| | - Varsha Dhankani
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Sheila M Reynolds
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Andrea Califano
- Irving Cancer Research Center, Room 913,1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Dimitris Anastassiou
- Department of Systems Biology and Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Younes Mokrab
- Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Arvind Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Andrew Lamb
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Justin Guinney
- Sage Bionetworks, 2901 Third Ave, Suite 330, Seattle, WA 98121, USA
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook Medicine, 100 Nicolls Rd, Stony Brook, NY 11794, USA
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Bethesda, MD 20892, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomics Medicine and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, TX 77030, USA
| | - Jonathan S Serody
- Department of Medicine and Microbiology and Lineberger Comprehensive Cancer Center, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA
| | - Elizabeth G Demicco
- Mount Sinai Hospital, Department of Pathology and Laboratory Medicine, 600 University Ave., Toronto, ON M5G 1X5, Canada
| | - Mary L Disis
- UW Medicine Cancer Vaccine Institute, 850 Republican Street, Brotman Building, 2nd Floor, Room 221, Box 358050, University of Washington, Seattle, WA 98109-4714, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, Curriculum in Bioinformatics and Computational Biology, University of North Carolina, 125 Mason Farm Road, Chapel Hill, NC 27599-7295, USA.
| | - Ilya Shmulevich
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA.
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21
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Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res 2017; 77:e39-e42. [PMID: 29092936 DOI: 10.1158/0008-5472.can-17-0344] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/30/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022]
Abstract
Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR.
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Affiliation(s)
- Marcel Ramos
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York.,Roswell Park Cancer Institute, University of Buffalo, Buffalo, New York
| | - Lucas Schiffer
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Angela Re
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Corso Trento, Torino, Italy
| | - Rimsha Azhar
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Azfar Basunia
- Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Carmen Rodriguez
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Tiffany Chan
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Phil Chapman
- Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Sean R Davis
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - David Gomez-Cabrero
- Mucosal and Salivary Biology Division, King's College London Dental Institute, London, United Kingdom
| | - Aedin C Culhane
- Harvard TH Chan School of Public Health, Boston, Massachusetts.,Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Hanish Kodali
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Marie S Louis
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York.,Institute for Implementation Science in Population Health, City University of New York, New York, New York
| | - Arvind S Mer
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Martin Morgan
- Roswell Park Cancer Institute, University of Buffalo, Buffalo, New York
| | - Vince Carey
- Harvard TH Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Levi Waldron
- Graduate School of Public Health & Health Policy, City University of New York, New York, New York. .,Institute for Implementation Science in Population Health, City University of New York, New York, New York
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22
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Neupane M, Clark AP, Landini S, Birkbak NJ, Eklund AC, Lim E, Culhane AC, Barry WT, Schumacher SE, Beroukhim R, Szallasi Z, Vidal M, Hill DE, Silver DP. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. Cancer Discov 2015; 6:45-58. [PMID: 26546296 DOI: 10.1158/2159-8290.cd-15-0341] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 11/04/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified methyl cytosine-guanine dinucleotide (CpG) binding protein 2 (MECP2) as a novel oncogene. MECP2 resides in a region of the X-chromosome that is significantly amplified across 18% of cancers, and many cancer cell lines have amplified, overexpressed MECP2 and are dependent on MECP2 expression for growth. MECP2 copy-number gain and RAS family member alterations are mutually exclusive in several cancer types. The MECP2 splicing isoforms activate the major growth factor pathways targeted by activated RAS, the MAPK and PI3K pathways. MECP2 rescued the growth of a KRAS(G12C)-addicted cell line after KRAS downregulation, and activated KRAS rescues the growth of an MECP2-addicted cell line after MECP2 downregulation. MECP2 binding to the epigenetic modification 5-hydroxymethylcytosine is required for efficient transformation. These observations suggest that MECP2 is a commonly amplified oncogene with an unusual epigenetic mode of action. SIGNIFICANCE MECP2 is a commonly amplified oncogene in human malignancies with a unique epigenetic mechanism of action. Cancer Discov; 6(1); 45-58. ©2015 AACR.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Manish Neupane
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Serena Landini
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicolai J Birkbak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Aron C Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Elgene Lim
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - William T Barry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Steven E Schumacher
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard and MIT, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, and Harvard Medical School, Boston, Massachusetts
| | - Marc Vidal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - David E Hill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Silver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Kochupurakkal BS, Wang ZC, Hua T, Culhane AC, Rodig SJ, Rajkovic-Molek K, Lazaro JB, Richardson AL, Biswas DK, Iglehart JD. RelA-Induced Interferon Response Negatively Regulates Proliferation. PLoS One 2015; 10:e0140243. [PMID: 26460486 PMCID: PMC4604146 DOI: 10.1371/journal.pone.0140243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022] Open
Abstract
Both oncogenic and tumor-suppressor activities are attributed to the Nuclear Factor kappa B (NF-kB) pathway. Moreover, NF-kB may positively or negatively regulate proliferation. The molecular determinants of these opposing roles of NF-kB are unclear. Using primary human mammary epithelial cells (HMEC) as a model, we show that increased RelA levels and consequent increase in basal transcriptional activity of RelA induces IRF1, a target gene. Induced IRF1 upregulates STAT1 and IRF7, and in consort, these factors induce the expression of interferon response genes. Activation of the interferon pathway down-regulates CDK4 and up-regulates p27 resulting in Rb hypo-phosphorylation and cell cycle arrest. Stimulation of HMEC with IFN-γ elicits similar phenotypic and molecular changes suggesting that basal activity of RelA and IFN-γ converge on IRF1 to regulate proliferation. The anti-proliferative RelA-IRF1-CDK4 signaling axis is retained in ER+/HER2- breast tumors analyzed by The Cancer Genome Atlas (TCGA). Using immuno-histochemical analysis of breast tumors, we confirm the negative correlation between RelA levels and proliferation rate in ER+/HER2- breast tumors. These findings attribute an anti-proliferative tumor-suppressor role to basal RelA activity. Inactivation of Rb, down-regulation of RelA or IRF1, or upregulation of CDK4 or IRF2 rescues the RelA-IRF1-CDK4 induced proliferation arrest in HMEC and are points of disruption in aggressive tumors. Activity of the RelA-IRF1-CDK4 axis may explain favorable response to CDK4/6 inhibition observed in patients with ER+ Rb competent tumors.
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Affiliation(s)
- Bose S. Kochupurakkal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (JDI); (BSK)
| | - Zhigang C. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Tony Hua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Aedin C. Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Jean-Bernard Lazaro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrea L. Richardson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Debajit K. Biswas
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - J. Dirk Iglehart
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail: (JDI); (BSK)
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Riester M, Wei W, Culhane AC, Trippa L, Michor F, Huttenhower C, Parmigiani G, Birrer M. Abstract 2355: Risk prediction for late-stage ovarian cancer by meta-analysis of 1,525 patient samples. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Ovarian cancer causes over 15,000 deaths per year in the United States. The survival of patients is quite heterogeneous, and accurate prognostic tools would help with the clinical management of these patients. However, existing ovarian cancer gene signatures did not make it to the clinic so far. Expression data of thousands of patients from a large number of different cohorts is now available in the public domain. Harvesting all this information for building signatures is a challenging “big data” problem, but has the potential to yield more robust and accurate signatures.
Methods: We developed and validated two gene expression signatures of potential clinical relevance in advanced stage serous ovarian cancer, the first for predicting survival and the second for predicting the outcome of initial debulking surgery. We integrated 13 publicly available datasets totaling 1,525 subjects. We trained prediction models using a meta-analysis variation on the Compound Covariate method, tested models via a “leave-one-dataset-out” procedure, and validated models in additional independent datasets. Selected genes from the debulking signature were validated by immunohistochemistry and qRT-PCR in two further independent cohorts of 179 and 78 patients, respectively.
Results: The survival signature stratified patients into high- and low-risk groups (HR=2.19; 95% CI, 1.84 to 2.61) significantly better than the best previously published overall survival signature (P = 0.039). POSTN, CXCL14, FAP, NUAK1, PTCH1, and TGFBR2) were validated by qRT-PCR (P < 0.05) and POSTN, CXCL14 and phosphorylated Smad2/3 by immunohistochemistry (P < 0.001) as independent predictors of debulking status. The sum of IHC intensities for these three proteins provided a tool that classified 92.8% of samples correctly in high- and low-risk groups for suboptimal debulking (AUC 0.89; 95% CI 0.84 to 0.93). We present the strongest evidence to date for the existence of a biologic basis of suboptimal outcome of debulking surgery.
Conclusions: Our survival signature provides the most accurate and validated prognostic model for early and advanced stage high-grade serous ovarian cancer. The debulking signature accurately (92.8%) predicts the outcome of cytoreductive surgery and will have clinical utility if the accuracy of the immunohistochemistry tool observed in our initial 179-patient validation cohort is confirmed in prospective validation. This tool will potentially allow for the identification of those patients who will not benefit from primary debulking surgery, sparing them the toxicity of extensive surgery and the delay until the initiation of chemotherapy. These patients can be triaged to neoadjuvant chemotherapy with interval debulking.
Citation Format: Markus Riester, Wei Wei, Aedin C. Culhane, Lorenzo Trippa, Franziska Michor, Curtis Huttenhower, Giovanni Parmigiani, Michael Birrer. Risk prediction for late-stage ovarian cancer by meta-analysis of 1,525 patient samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2355. doi:10.1158/1538-7445.AM2014-2355
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Affiliation(s)
| | - Wei Wei
- 2Massachusetts General Hospital, Boston, MA
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Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst 2014; 106:dju048. [PMID: 24700803 DOI: 10.1093/jnci/dju048] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ovarian cancer causes more than 15000 deaths per year in the United States. The survival of patients is quite heterogeneous, and accurate prognostic tools would help with the clinical management of these patients. METHODS We developed and validated two gene expression signatures, the first for predicting survival in advanced-stage, serous ovarian cancer and the second for predicting debulking status. We integrated 13 publicly available datasets totaling 1525 subjects. We trained prediction models using a meta-analysis variation on the compound covariable method, tested models by a "leave-one-dataset-out" procedure, and validated models in additional independent datasets. Selected genes from the debulking signature were validated by immunohistochemistry and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in two further independent cohorts of 179 and 78 patients, respectively. All statistical tests were two-sided. RESULTS The survival signature stratified patients into high- and low-risk groups (hazard ratio = 2.19; 95% confidence interval [CI] = 1.84 to 2.61) statistically significantly better than the TCGA signature (P = .04). POSTN, CXCL14, FAP, NUAK1, PTCH1, and TGFBR2 were validated by qRT-PCR (P < .05) and POSTN, CXCL14, and phosphorylated Smad2/3 were validated by immunohistochemistry (P < .001) as independent predictors of debulking status. The sum of immunohistochemistry intensities for these three proteins provided a tool that classified 92.8% of samples correctly in high- and low-risk groups for suboptimal debulking (area under the curve = 0.89; 95% CI = 0.84 to 0.93). CONCLUSIONS Our survival signature provides the most accurate and validated prognostic model for early- and advanced-stage high-grade, serous ovarian cancer. The debulking signature accurately predicts the outcome of cytoreductive surgery, potentially allowing for stratification of patients for primary vs secondary cytoreduction.
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Affiliation(s)
- Markus Riester
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Wei Wei
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Levi Waldron
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Aedin C Culhane
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Lorenzo Trippa
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Esther Oliva
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Sung-Hoon Kim
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Franziska Michor
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Curtis Huttenhower
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Giovanni Parmigiani
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Michael J Birrer
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK).
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Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst 2014. [PMID: 24700803 DOI: 10.1093/jnci/dju048.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Ovarian cancer causes more than 15000 deaths per year in the United States. The survival of patients is quite heterogeneous, and accurate prognostic tools would help with the clinical management of these patients. METHODS We developed and validated two gene expression signatures, the first for predicting survival in advanced-stage, serous ovarian cancer and the second for predicting debulking status. We integrated 13 publicly available datasets totaling 1525 subjects. We trained prediction models using a meta-analysis variation on the compound covariable method, tested models by a "leave-one-dataset-out" procedure, and validated models in additional independent datasets. Selected genes from the debulking signature were validated by immunohistochemistry and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in two further independent cohorts of 179 and 78 patients, respectively. All statistical tests were two-sided. RESULTS The survival signature stratified patients into high- and low-risk groups (hazard ratio = 2.19; 95% confidence interval [CI] = 1.84 to 2.61) statistically significantly better than the TCGA signature (P = .04). POSTN, CXCL14, FAP, NUAK1, PTCH1, and TGFBR2 were validated by qRT-PCR (P < .05) and POSTN, CXCL14, and phosphorylated Smad2/3 were validated by immunohistochemistry (P < .001) as independent predictors of debulking status. The sum of immunohistochemistry intensities for these three proteins provided a tool that classified 92.8% of samples correctly in high- and low-risk groups for suboptimal debulking (area under the curve = 0.89; 95% CI = 0.84 to 0.93). CONCLUSIONS Our survival signature provides the most accurate and validated prognostic model for early- and advanced-stage high-grade, serous ovarian cancer. The debulking signature accurately predicts the outcome of cytoreductive surgery, potentially allowing for stratification of patients for primary vs secondary cytoreduction.
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Affiliation(s)
- Markus Riester
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Wei Wei
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Levi Waldron
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Aedin C Culhane
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Lorenzo Trippa
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Esther Oliva
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Sung-Hoon Kim
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Franziska Michor
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Curtis Huttenhower
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Giovanni Parmigiani
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK)
| | - Michael J Birrer
- Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK).
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Santagata S, Thakkar A, Ergonul A, Wang B, Woo T, Hu R, Harrell JC, McNamara G, Schwede M, Culhane AC, Kindelberger D, Rodig S, Richardson A, Schnitt SJ, Tamimi RM, Ince TA. Taxonomy of breast cancer based on normal cell phenotype predicts outcome. J Clin Invest 2014; 124:859-70. [PMID: 24463450 DOI: 10.1172/jci70941] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/17/2013] [Indexed: 01/13/2023] Open
Abstract
Accurate classification is essential for understanding the pathophysiology of a disease and can inform therapeutic choices. For hematopoietic malignancies, a classification scheme based on the phenotypic similarity between tumor cells and normal cells has been successfully used to define tumor subtypes; however, use of normal cell types as a reference by which to classify solid tumors has not been widely emulated, in part due to more limited understanding of epithelial cell differentiation compared with hematopoiesis. To provide a better definition of the subtypes of epithelial cells comprising the breast epithelium, we performed a systematic analysis of a large set of breast epithelial markers in more than 15,000 normal breast cells, which identified 11 differentiation states for normal luminal cells. We then applied information from this analysis to classify human breast tumors based on normal cell types into 4 major subtypes, HR0-HR3, which were differentiated by vitamin D, androgen, and estrogen hormone receptor (HR) expression. Examination of 3,157 human breast tumors revealed that these HR subtypes were distinct from the current classification scheme, which is based on estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Patient outcomes were best when tumors expressed all 3 hormone receptors (subtype HR3) and worst when they expressed none of the receptors (subtype HR0). Together, these data provide an ontological classification scheme associated with patient survival differences and provides actionable insights for treating breast tumors.
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Thakkar A, Santagata S, Ergonul A, Wang B, Woo T, Hu R, Harrell JC, McNamara G, Schwede M, Culhane AC, Kindelberger D, Rodig S, Richardson A, Schnitt SJ, Tamimi RM, Ince TA. Abstract B067: Taxonomy of breast cancer based on normal cell phenotype and ontology. Mol Cancer Res 2013. [DOI: 10.1158/1557-3125.advbc-b067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The classification of lymphoma and leukemia is successfully done by using normal cell types as a reference point which is one of the many reasons that better therapies are available for their treatment. In case of breast cancer, clinically it is classified as Estrogen Receptor positive, Human Epidermal Growth Factor Receptor 2 (Her2) positive and triple negative breast cancer while in the research settings, it has been classified by mRNA expression profiling but these classification systems are still evolving. Our laboratory attempted to classify breast cancer by examining the expression of different keratin isoforms and Hormone Receptors (HR) studied through immunostaining in 36 normal breast samples and later in 1731 breast tumors from the Nurses' Health Study (NHS) cohort with a patient follow up extending beyond 25 years. Among the various receptors tested, three of these receptors: Androgen Receptor, Estrogen Receptor and Vitamin D Receptor were capable of identifying four major subgroups being designated as HR0-3, depending on the number of hormone receptors present. More importantly, radically different survival outcomes were observed between these HR sub-groups through Kaplan Meier curve analysis; which highlights their usefulness as vital biological markers as wells as targets for breast cancer treatment. Furthermore, the characterization of these HR was carried out in 20 different breast cancer cell lines and the combination of different receptor modulators alone or in combination was attempted with better anti-proliferative effects being observed in the combinatorial group than either treatment alone. Thus, our new classification not only re-classifies breast cancer but also gives insight on how patients could be treated through targeting hormone receptors.
Citation Format: Ankita Thakkar, Sandro Santagata, Ayse Ergonul, Bin Wang, Terri Woo, Rong Hu, J. Chuck Harrell, George McNamara, Matthew Schwede, Aedin C. Culhane, David Kindelberger, Scott Rodig, Andrea Richardson, Stuart J. Schnitt, Rulla M. Tamimi, Tan A. Ince. Taxonomy of breast cancer based on normal cell phenotype and ontology. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B067.
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Affiliation(s)
| | - Sandro Santagata
- 2Brigham and Women's Hospital, and Harvard Medical School, Boston, MA,
| | | | - Bin Wang
- 1University of Miami, Miami, FL,
| | - Terri Woo
- 2Brigham and Women's Hospital, and Harvard Medical School, Boston, MA,
| | - Rong Hu
- 3Harvard School of Public Health, Boston, MA,
| | | | | | - Matthew Schwede
- 5Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA,
| | - Aedin C. Culhane
- 5Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA,
| | | | - Scott Rodig
- 2Brigham and Women's Hospital, and Harvard Medical School, Boston, MA,
| | - Andrea Richardson
- 2Brigham and Women's Hospital, and Harvard Medical School, Boston, MA,
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Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. A three-gene model to robustly identify breast cancer molecular subtypes. J Natl Cancer Inst 2012; 104:311-25. [PMID: 22262870 DOI: 10.1093/jnci/djr545] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Single sample predictors (SSPs) and Subtype classification models (SCMs) are gene expression-based classifiers used to identify the four primary molecular subtypes of breast cancer (basal-like, HER2-enriched, luminal A, and luminal B). SSPs use hierarchical clustering, followed by nearest centroid classification, based on large sets of tumor-intrinsic genes. SCMs use a mixture of Gaussian distributions based on sets of genes with expression specifically correlated with three key breast cancer genes (estrogen receptor [ER], HER2, and aurora kinase A [AURKA]). The aim of this study was to compare the robustness, classification concordance, and prognostic value of these classifiers with those of a simplified three-gene SCM in a large compendium of microarray datasets. METHODS Thirty-six publicly available breast cancer datasets (n = 5715) were subjected to molecular subtyping using five published classifiers (three SSPs and two SCMs) and SCMGENE, the new three-gene (ER, HER2, and AURKA) SCM. We used the prediction strength statistic to estimate robustness of the classification models, defined as the capacity of a classifier to assign the same tumors to the same subtypes independently of the dataset used to fit it. We used Cohen κ and Cramer V coefficients to assess concordance between the subtype classifiers and association with clinical variables, respectively. We used Kaplan-Meier survival curves and cross-validated partial likelihood to compare prognostic value of the resulting classifications. All statistical tests were two-sided. RESULTS SCMs were statistically significantly more robust than SSPs, with SCMGENE being the most robust because of its simplicity. SCMGENE was statistically significantly concordant with published SCMs (κ = 0.65-0.70) and SSPs (κ = 0.34-0.59), statistically significantly associated with ER (V = 0.64), HER2 (V = 0.52) status, and histological grade (V = 0.55), and yielded similar strong prognostic value. CONCLUSION Our results suggest that adequate classification of the major and clinically relevant molecular subtypes of breast cancer can be robustly achieved with quantitative measurements of three key genes.
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Affiliation(s)
- Benjamin Haibe-Kains
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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Brennan DJ, O'Connor DP, Laursen H, McGee SF, McCarthy S, Zagozdzon R, Rexhepaj E, Culhane AC, Martin FM, Duffy MJ, Landberg G, Ryden L, Hewitt SM, Kuhar MJ, Bernards R, Millikan RC, Crown JP, Jirström K, Gallagher WM. The cocaine- and amphetamine-regulated transcript mediates ligand-independent activation of ERα, and is an independent prognostic factor in node-negative breast cancer. Oncogene 2011; 31:3483-94. [PMID: 22139072 DOI: 10.1038/onc.2011.519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Personalized medicine requires the identification of unambiguous prognostic and predictive biomarkers to inform therapeutic decisions. Within this context, the management of lymph node-negative breast cancer is the subject of much debate with particular emphasis on the requirement for adjuvant chemotherapy. The identification of prognostic and predictive biomarkers in this group of patients is crucial. Here, we demonstrate by tissue microarray and automated image analysis that the cocaine- and amphetamine-regulated transcript (CART) is expressed in primary and metastatic breast cancer and is an independent poor prognostic factor in estrogen receptor (ER)-positive, lymph node-negative tumors in two separate breast cancer cohorts (n=690; P=0.002, 0.013). We also show that CART increases the transcriptional activity of ERα in a ligand-independent manner via the mitogen-activated protein kinase pathway and that CART stimulates an autocrine/paracrine loop within tumor cells to amplify the CART signal. Additionally, we demonstrate that CART expression in ER-positive breast cancer cell lines protects against tamoxifen-mediated cell death and that high CART expression predicts disease outcome in tamoxifen-treated patients in vivo in three independent breast cancer cohorts. We believe that CART profiling will help facilitate stratification of lymph node-negative breast cancer patients into high- and low-risk categories and allow for the personalization of therapy.
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Affiliation(s)
- D J Brennan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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Smith MJ, Culhane AC, Donovan M, Coffey JC, Barry BD, Kelly MA, Higgins DG, Wang JH, Kirwan WO, Cotter TG, Redmond HP. Analysis of differential gene expression in colorectal cancer and stroma using fluorescence-activated cell sorting purification. Br J Cancer 2009; 100:1452-64. [PMID: 19401702 PMCID: PMC2694425 DOI: 10.1038/sj.bjc.6604931] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Tumour stroma gene expression in biopsy specimens may obscure the expression of tumour parenchyma, hampering the predictive power of microarrays. We aimed to assess the utility of fluorescence-activated cell sorting (FACS) for generating cell populations for gene expression analysis and to compare the gene expression of FACS-purified tumour parenchyma to that of whole tumour biopsies. Single cell suspensions were generated from colorectal tumour biopsies and tumour parenchyma was separated using FACS. Fluorescence-activated cell sorting allowed reliable estimation and purification of cell populations, generating parenchymal purity above 90%. RNA from FACS-purified and corresponding whole tumour biopsies was hybridised to Affymetrix oligonucleotide microarrays. Whole tumour and parenchymal samples demonstrated differential gene expression, with 289 genes significantly overexpressed in the whole tumour, many of which were consistent with stromal gene expression (e.g., COL6A3, COL1A2, POSTN, TIMP2). Genes characteristic of colorectal carcinoma were overexpressed in the FACS-purified cells (e.g., HOX2D and RHOB). We found FACS to be a robust method for generating samples for gene expression analysis, allowing simultaneous assessment of parenchymal and stromal compartments. Gross stromal contamination may affect the interpretation of cancer gene expression microarray experiments, with implications for hypotheses generation and the stability of expression signatures used for predicting clinical outcomes.
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Affiliation(s)
- M J Smith
- Department of Academic Surgery, University College Cork, Cork, Ireland
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Gallagher WM, Bergin OE, Rafferty M, Kelly ZD, Nolan IM, Fox EJP, Culhane AC, McArdle L, Fraga MF, Hughes L, Currid CA, O'Mahony F, Byrne A, Murphy AA, Moss C, McDonnell S, Stallings RL, Plumb JA, Esteller M, Brown R, Dervan PA, Easty DJ. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies. Carcinogenesis 2005; 26:1856-67. [PMID: 15958521 DOI: 10.1093/carcin/bgi152] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The incidence of melanoma is increasing rapidly, with advanced lesions generally failing to respond to conventional chemotherapy. Here, we utilized DNA microarray-based gene expression profiling techniques to identify molecular determinants of melanoma progression within a unique panel of isogenic human melanoma cell lines. When a poorly tumorigenic cell line, derived from an early melanoma, was compared with two increasingly aggressive derivative cell lines, the expression of 66 genes was significantly changed. A similar pattern of differential gene expression was found with an independently derived metastatic cell line. We further examined these melanoma progression-associated genes via use of a tailored TaqMan Low Density Array (LDA), representing the majority of genes within our cohort of interest. Considerable concordance was seen between the transcriptomic profiles determined by DNA microarray and TaqMan LDA approaches. A range of novel markers were identified that correlated here with melanoma progression. Most notable was TSPY, a Y chromosome-specific gene that displayed extensive down-regulation in expression between the parental and derivative cell lines. Examination of a putative CpG island within the TSPY gene demonstrated that this region was hypermethylated in the derivative cell lines, as well as metastatic melanomas from male patients. Moreover, treatment of the derivative cell lines with the DNA methyltransferase inhibitor, 2'-deoxy-5-azacytidine (DAC), restored expression of the TSPY gene to levels comparable with that found in the parental cells. Additional DNA microarray studies uncovered a subset of 13 genes from the above-mentioned 66 gene cohort that displayed re-activation of expression following DAC treatment, including TSPY, CYBA and MT2A. DAC suppressed tumor cell growth in vitro. Moreover, systemic treatment of mice with DAC attenuated growth of melanoma xenografts, with consequent re-expression of TSPY mRNA. Overall, our data support the hypothesis that multiple genes are targeted, either directly or indirectly, by DNA hypermethylation during melanoma progression.
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MESH Headings
- Animals
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Azacitidine/therapeutic use
- Biomarkers, Tumor
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- DNA Methylation
- DNA Modification Methylases/antagonists & inhibitors
- DNA Modification Methylases/genetics
- DNA Modification Methylases/metabolism
- Decitabine
- Disease Progression
- Enzyme Inhibitors/pharmacology
- Enzyme Inhibitors/therapeutic use
- Epigenesis, Genetic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Melanoma, Experimental/genetics
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/prevention & control
- Mice
- Mice, Nude
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/metabolism
- RNA, Neoplasm/metabolism
- Skin Neoplasms/genetics
- Skin Neoplasms/prevention & control
- Skin Neoplasms/secondary
- Transplantation, Heterologous
- Tumor Cells, Cultured
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McArdle L, McDermott M, Purcell R, Grehan D, O'Meara A, Breatnach F, Catchpoole D, Culhane AC, Jeffery I, Gallagher WM, Stallings RL. Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 2004; 25:1599-609. [PMID: 15090470 DOI: 10.1093/carcin/bgh173] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A number of distinct subtypes of neuroblastoma exist with different genetic abnormalities that are predicative of outcome. Whole chromosome gains are usually associated with low stage disease and favourable outcome, whereas loss of 1p, 3p and 11q, unbalanced gain of 17q and MYCN amplification (MNA) are indicative of high stage disease and unfavourable prognosis. Although MNA and loss of 11q appear to represent two distinct genetic subtypes of advanced stage neuroblastoma, a detailed understanding of how these subtypes differ in terms of global gene expression is still lacking. We have used metaphase comparative genomic hybridization (CGH) analysis in combination with oligonucleotide technology to identify patterns of gene expression that correlate with specific genomic imbalances found in primary neuroblastic tumours and cell lines. The tumours analysed in this manner included a ganglioneuroma, along with various ganglioneuroblastoma and neuroblastoma of different stages and histopathological classifications. Oligonucleotide microarray-based gene expression profile analysis was performed with Affymetrix HU133A arrays representing approximately 14 500 unique genes. The oligonucleotide microarray results were subsequently validated by quantitative real-time PCR, immunohistochemical staining, and by comparison of specific gene expression patterns with published results. Hierarchical clustering of gene expression data distinguished tumours on the basis of stage, differentiation and genetic abnormalities. A number of genes were identified whose patterns of expression were highly correlated with 11q loss; supporting the concept that loss of 11q represents a distinct genetic subtype of neuroblastoma. The implications of these results in the process of neuroblastoma development and progression are discussed.
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Affiliation(s)
- L McArdle
- National Centre for Medical Genetics, Our Lady's Hospital for Sick Children, Crumlin, Dublin 12, Ireland
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Wheeler RD, Culhane AC, Hall MD, Pickering-Brown S, Rothwell NJ, Luheshi GN. Detection of the interleukin 18 family in rat brain by RT-PCR. Brain Res Mol Brain Res 2000; 77:290-3. [PMID: 10837926 DOI: 10.1016/s0169-328x(00)00069-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interleukin 18, an inflammatory cytokine, mediates its effects by interaction with its receptor complex, consisting of the IL-18 receptor (IL-18R) and receptor accessory protein (AcPL). A functional inhibitor of IL-18, the IL-18 binding protein (IL-18BP), has been identified recently. This study reports the detection of IL-18, IL-18R, AcPL and IL-18BP mRNA expression in the brain of normal adult rats using RT-PCR.
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Affiliation(s)
- R D Wheeler
- School of Biological Sciences, University of Manchester, 1.124 Stopford Building, Oxford Road, M13 9PT, Manchester, UK
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Abstract
The interleukin-1 (IL-1) family comprises IL-1 alpha and IL-1 beta and an endogenous IL-1 receptor antagonist (IL-1ra). IL-1 has diverse actions in the brain and has been implicated in both acute and chronic neurodegeneration. However, neither IL-1 alpha nor IL-1 beta are neurotoxic per se in vivo, so other IL-1 related ligands may be important in neurodegeneration. The cytokine interleukin-18 (also called interferon gamma inducing factor, IGIF) was first isolated from the liver of mice during toxic shock. It was later proposed as a member of the IL-1 family, based on protein sequence homology with IL-1 beta and IL-1ra, and has tentatively been called IL-1 gamma. We cloned IL-18 from adult rat brain and demonstrated, by RT-PCR, that it is expressed constitutively in cerebellum, hippocampus, hypothalamus, cortex and striatum. Rat brain IL-18 shows close homology to mouse and human IL-18, and to the recently published sequence from the rat adrenal gland. Mouse pro-IL-18 and pro-IL-1 beta are processed by caspase-1. We demonstrate that caspase-1 also cleaves rat IL-18 in vitro and that the caspase inhibitor, zVAD-DCB inhibits this cleavage.
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Affiliation(s)
- A C Culhane
- School of Biological Sciences, University of Manchester, UK
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Hale AJ, Smith CA, Sutherland LC, Stoneman VE, Longthorne V, Culhane AC, Williams GT. Apoptosis: molecular regulation of cell death. Eur J Biochem 1996; 237:884. [PMID: 8647138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Abstract
The field of apoptosis is unusual in several respects. Firstly, its general importance has been widely recognised only in the past few years and its surprising significance is still being evaluated in a number of areas of biology. Secondly, although apoptosis is now accepted as a critical element in the repertoire of potential cellular responses, the picture of the intra-cellular processes involved is probably still incomplete, not just in its details, but also in the basic outline of the process as a whole. It is therefore a very interesting and active area at present and is likely to progress rapidly in the next two or three years. This review emphasises recent work on the molecular mechanisms of apoptosis and, in particular, on the intracellular interactions which control this process. This latter area is of crucial importance since dysfunction of the normal control machinery is likely to have serious pathological consequences, probably including oncogenesis, autoimmunity and degenerative disease. The genetic analysis of programmed cell death during the development of the nematode Caenorhabditis elegans has proved very useful in identifying important events in the cell death programme. Recently defined genetic connections between C. elegans cell death and mammalian apoptosis have emphasised the value of this system as a model for cell death in mammalian cells, which, inevitably, is more complex. The signals inducing apoptosis are very varied and the same signals can induce differentiation and proliferation in other situations. However, some pathways appear to be of particular significance in the control of cell death; recent analysis of the apoptosis induced through the cell-surface Fas receptor has been especially important for immunology. Two gene families are dealt with in particular detail because of their likely importance in apoptosis control. These are, first, the genes encoding the interleukin-1 beta-converting enzyme family of cysteine proteases and, second, those related to the proto-oncogene bcl-2. Both of these families are homologous to cell death genes in C. elegans. In mammalian cells the number of members of both families which have been identified is growing rapidly and considerable effort is being directed towards establishing the roles played by each member and the ways in which they interact to regulate apoptosis. Other genes with established roles in the regulation of proliferation and differentiation are also important in controlling apoptosis. Several of these are known proto-oncogenes, e.g. c-myc, or tumour suppressors, e.g. p53, an observation which is consistent with the importance of defective apoptosis in the development of cancer. Viral manipulation of the apoptosis of host cells frequently involves interactions with these cellular proteins. Finally, the biochemistry of the closely controlled cellular self-destruction which ensues when the apoptosis programme has been engaged is also very important. The biochemical changes involved in inducing phagocytosis of the apoptotic cell, for example, allow the process to be neatly integrated within the tissues, under physiological conditions. Molecular defects in this area too may have important pathological consequences.
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Affiliation(s)
- A J Hale
- Biological Sciences Department, Keele University, Staffordshire, UK
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