1
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Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 2023; 379:eabj7412. [PMID: 36656933 PMCID: PMC10515739 DOI: 10.1126/science.abj7412] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 05/29/2021] [Accepted: 12/12/2022] [Indexed: 01/21/2023]
Abstract
Multicellular life requires altruistic cooperation between cells. The adaptive immune system is a notable exception, wherein germinal center B cells compete vigorously for limiting positive selection signals. Studying primary human lymphomas and developing new mouse models, we found that mutations affecting BTG1 disrupt a critical immune gatekeeper mechanism that strictly limits B cell fitness during antibody affinity maturation. This mechanism converted germinal center B cells into supercompetitors that rapidly outstrip their normal counterparts. This effect was conferred by a small shift in MYC protein induction kinetics but resulted in aggressive invasive lymphomas, which in humans are linked to dire clinical outcomes. Our findings reveal a delicate evolutionary trade-off between natural selection of B cells to provide immunity and potentially dangerous features that recall the more competitive nature of unicellular organisms.
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Affiliation(s)
- Coraline Mlynarczyk
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matt Teater
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juhee Pae
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biomedicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ling Wang
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Darko Barisic
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Antonin Papin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonatan Ersching
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Arnab Bandyopadhyay
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ersilia Barin
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hui Xian Poh
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chiara M. Evans
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Hao Shen
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hannah M. Isles
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Benedikt Pelzer
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ioanna Tsialta
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S. Doane
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Muhammad Hassan Rehman
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Medicine–Qatar, Doha, Qatar
| | - Jonah Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wyatt Morgan
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Diu T. T. Nguyen
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - George Khelashvili
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Ari Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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2
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Cohen IJ, Pareja F, Socci ND, Shen R, Doane AS, Schwartz J, Khanin R, Morris EA, Sutton EJ, Blasberg RG. Increased tumor glycolysis is associated with decreased immune infiltration across human solid tumors. Front Immunol 2022; 13:880959. [PMID: 36505421 PMCID: PMC9731115 DOI: 10.3389/fimmu.2022.880959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Response to immunotherapy across multiple cancer types is approximately 25%, with some tumor types showing increased response rates compared to others (i.e. response rates in melanoma and non-small cell lung cancer (NSCLC) are typically 30-60%). Patients whose tumors are resistant to immunotherapy often lack high levels of pre-existing inflammation in the tumor microenvironment. Increased tumor glycolysis, acting through glucose deprivation and lactic acid accumulation, has been shown to have pleiotropic immune suppressive effects using in-vitro and in-vivo models of disease. To determine whether the immune suppressive effect of tumor glycolysis is observed across human solid tumors, we analyzed glycolytic and immune gene expression patterns in multiple solid malignancies. We found that increased expression of a glycolytic signature was associated with decreased immune infiltration and a more aggressive disease across multiple tumor types. Radiologic and pathologic analysis of untreated estrogen receptor (ER)-negative breast cancers corroborated these observations, and demonstrated that protein expression of glycolytic enzymes correlates positively with glucose uptake and negatively with infiltration of CD3+ and CD8+ lymphocytes. This study reveals an inverse relationship between tumor glycolysis and immune infiltration in a large cohort of multiple solid tumor types.
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Affiliation(s)
- Ivan J. Cohen
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States,*Correspondence: Ivan J. Cohen,
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ashley S. Doane
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jazmin Schwartz
- Computational Biology and Medicine Tri-Institutional PhD Program, Weill Cornell Medicine, New York, NY, United States
| | - Raya Khanin
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Elizabeth A. Morris
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Elizabeth J. Sutton
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ronald G. Blasberg
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States,Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, United States,Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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3
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Drozdz MM, Doane AS, Alkallas R, Desman G, Bareja R, Reilly M, Bang J, Yusupova M, You J, Eraslan Z, Wang JZ, Verma A, Aguirre K, Kane E, Watson IR, Elemento O, Piskounova E, Merghoub T, Zippin JH. A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation. Cell Rep 2022; 40:111412. [PMID: 36170819 PMCID: PMC9549417 DOI: 10.1016/j.celrep.2022.111412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/02/2020] [Revised: 07/19/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023] Open
Abstract
Cyclic AMP (cAMP) signaling is localized to multiple spatially distinct microdomains, but the role of cAMP microdomains in cancer cell biology is poorly understood. Here, we present a tunable genetic system that allows us to activate cAMP signaling in specific microdomains. We uncover a nuclear cAMP microdomain that activates a tumor-suppressive pathway in a broad range of cancers by inhibiting YAP, a key effector protein of the Hippo pathway, inside the nucleus. We show that nuclear cAMP induces a LATS-dependent pathway leading to phosphorylation of nuclear YAP solely at serine 397 and export of YAP from the nucleus with no change in YAP protein stability. Thus, nuclear cAMP inhibition of nuclear YAP is distinct from other known mechanisms of Hippo regulation. Pharmacologic targeting of specific cAMP microdomains remains an untapped therapeutic approach for cancer; thus, drugs directed at the nuclear cAMP microdomain may provide avenues for the treatment of cancer.
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Affiliation(s)
- Marek M. Drozdz
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Ashley S. Doane
- Englander Institute for Precision Medicine, Joan and Sanford I. Weill Medical College of Cornell University, New York NY 10065, USA
| | - Rached Alkallas
- Rosalind and Morris Goodman Cancer Institute, Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada,Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada,McGill Genome Centre, McGill University, Montreal, QC H3A 0G1, Canada
| | - Garrett Desman
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rohan Bareja
- Englander Institute for Precision Medicine, Joan and Sanford I. Weill Medical College of Cornell University, New York NY 10065, USA,Institute for Computational Biomedicine, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Michael Reilly
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Jakyung Bang
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Maftuna Yusupova
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Jaewon You
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Zuhal Eraslan
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Jenny Z. Wang
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Akanksha Verma
- Englander Institute for Precision Medicine, Joan and Sanford I. Weill Medical College of Cornell University, New York NY 10065, USA
| | - Kelsey Aguirre
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Elsbeth Kane
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Ian R. Watson
- Rosalind and Morris Goodman Cancer Institute, Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Joan and Sanford I. Weill Medical College of Cornell University, New York NY 10065, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10029, USA
| | - Elena Piskounova
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10029, USA,Senior author
| | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10029, USA,Department of Pharmacology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA,Senior author
| | - Jonathan H. Zippin
- Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA,Englander Institute for Precision Medicine, Joan and Sanford I. Weill Medical College of Cornell University, New York NY 10065, USA,Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10029, USA,Department of Pharmacology, Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10065, USA,Senior author,Lead contact,Correspondence:
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4
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Mlynarczyk C, Teater M, Pae J, Wang L, Ersching J, Papin A, Barisic D, Barin E, Hoehn KB, Chen Z, Nguyen DTT, Evans C, Doane AS, Kharas MG, Scott DW, Victora G, Melnick A. Abstract A24: BTG1 mutations confer a fitness advantage and promote aggressive B cell lymphoma development by lowering the threshold for MYC induction. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a24] [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] Open
Abstract
Abstract
BTG1 somatic mutations are exclusively found in mature B cell malignancies, ~12% diffuse large B cell lymphoma (DLBCL) and are particularly enriched in the MCD/cluster 5 subtype of ABC-DLBCL, characterized by extranodal dissemination and poor clinical outcome. However, the mechanism of action and clinical relevance of BTG1 mutations remain unknown. We find that BTG1 mutations score among the top mutations with DLBCL driver potential, using a rigorous genomic and epigenomic covariates analysis. Most notably, BTG1 mutant patients presented with inferior clinical outcome (p=0.0011) in ABC-DLBCL cases from 5 cohorts and BTG1 mutation was independently associated with lower overall survival in a multivariable Cox regression analysis (p=0.0190) DLBCL originates from mature B cells having experienced the germinal center (GC) reaction. We therefore generated a conditional knockin mouse model to express the most frequent Btg1 Q36H in B cells. Btg1 Q36H GC B cells showed a dramatic fitness advantage in in vivo competitive assays. This effect was specific to the GC compartment and was dependent on T cells. RNAseq showed that Btg1Q36H GC B cells were markedly enriched for genes normally transiently induced upon positive selection by T cells, including MYC targets. The same signatures were enriched in BTG1 mutant DLBCL patients and isogenic BTG1Q36H vs BTG1WT human DLBCL cell lines. We observed a higher proportion of MYC-expressing cells in Btg1Q36H GCs without an increase in maximal MYC levels per cell, also confirmed in human DLBCL lines and primary human tonsillar B cells, suggesting a lowered threshold for MYC induction in mutant cells. Mechanistically, ~800 transcripts associated with BTG1WT, but not BTG1Q36H. These belong to the same gene sets that characterize positively selected GC B cell, including MYC itself. BTG1Q36H therefore showed reduced association with the MYC mRNA. We found that this associated with facilitated MYC protein synthesis. Polysome profiling also showed higher translation capacity in BTG1Q36H DLBCL cells. Crossing our Btg1 Q36H mice to the VavP-Bcl2 model showed that VavP-Bcl2+Btg1Q36H mice displayed shorter survival, earlier onset of lymphoma and dysplastic B cell infiltration into non lymphoid organs. Immunoglobulin genes sequencing showed that VavP-Bcl2+Btg1Q36H lymphoma B cells were highly clonal, extensively mutated and selected. Importantly, the lack of BTG1 deletions suggested that BTG1 missense mutations do not cause a full loss-of-function of the protein. Indeed, we observed that shRNA-mediated knockdown of BTG1 resulted in apoptosis. Collectively, BTG1 mutations contribute to the formation of aggressive lymphomas through an entirely novel mechanism, by lowering the threshold to MYC induction in response to T cell selection signals, conferring dramatic fitness. This effect appears to correspond to a partial loss of function disrupting a novel GC context-specific check point, whereby BTG1 normally attenuates spurious MYC translation to tightly restrict fitness potential.
Citation Format: Coraline Mlynarczyk, Matt Teater, Juhee Pae, Ling Wang, Jonatan Ersching, Antonin Papin, Darko Barisic, Ersilia Barin, Kenneth B. Hoehn, Zhengming Chen, Diu T. T. Nguyen, Chiara Evans, Ashley S. Doane, Michael G. Kharas, David W. Scott, Gabriel Victora, Ari Melnick. BTG1 mutations confer a fitness advantage and promote aggressive B cell lymphoma development by lowering the threshold for MYC induction [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A24.
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Affiliation(s)
| | | | - Juhee Pae
- 3The Rockefeller University, New York, NY,
| | - Ling Wang
- 2Weill Cornell Medicine, New York, NY,
| | | | | | | | | | | | | | | | - Chiara Evans
- 5Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - David W. Scott
- 6BC Cancer’s Centre for Lymphoid Cancer, Vancouver, BC, Canada
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5
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DiNapoli SE, Martinez-McFaline R, Shen H, Doane AS, Perez AR, Verma A, Simon A, Nelson I, Balgobin CA, Bourque CT, Yao J, Raman R, Béguelin W, Zippin JH, Elemento O, Melnick AM, Houvras Y. Histone 3 Methyltransferases Alter Melanoma Initiation and Progression Through Discrete Mechanisms. Front Cell Dev Biol 2022; 10:814216. [PMID: 35223844 PMCID: PMC8866878 DOI: 10.3389/fcell.2022.814216] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Perturbations to the epigenome are known drivers of tumorigenesis. In melanoma, alterations in histone methyltransferases that catalyze methylation at histone 3 lysine 9 and histone 3 lysine 27-two sites of critical post-translational modification-have been reported. To study the function of these methyltransferases in melanoma, we engineered melanocytes to express histone 3 lysine-to-methionine mutations at lysine 9 and lysine 27, which are known to inhibit the activity of histone methyltransferases, in a zebrafish melanoma model. Using this system, we found that loss of histone 3 lysine 9 methylation dramatically suppressed melanoma formation and that inhibition of histone 3 lysine 9 methyltransferases in human melanoma cells increased innate immune response signatures. In contrast, loss of histone 3 lysine 27 methylation significantly accelerated melanoma formation. We identified FOXD1 as a top target of PRC2 that is silenced in melanocytes and found that aberrant overexpression of FOXD1 accelerated melanoma onset. Collectively, these data demonstrate how histone 3 lysine-to-methionine mutations can be used to uncover critical roles for methyltransferases.
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Affiliation(s)
- Sara E. DiNapoli
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Raúl Martinez-McFaline
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Hao Shen
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Ashley S. Doane
- Caryl and Israel Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Alexendar R. Perez
- Department of Anesthesia and Perioperative Care, UCSF, San Francisco, CA, United States
| | - Akanksha Verma
- Caryl and Israel Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Amanda Simon
- Department of Dermatology, Weill Cornell Medicine, New York, NY, United States
| | - Isabel Nelson
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Courtney A. Balgobin
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Caitlin T. Bourque
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Jun Yao
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Renuka Raman
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Wendy Béguelin
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Jonathan H. Zippin
- Department of Dermatology, Weill Cornell Medicine, New York, NY, United States
| | - Olivier Elemento
- Caryl and Israel Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ari M. Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Yariv Houvras
- Department of Surgery, Weill Cornell Medicine, New York, NY, United States
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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6
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Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol 2021; 22:240-253. [PMID: 33432228 PMCID: PMC7855695 DOI: 10.1038/s41590-020-00827-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 02/24/2020] [Accepted: 10/25/2020] [Indexed: 01/28/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/deficiency
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Gene Deletion
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Immunity, Humoral
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction
- Cohesins
- Mice
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Affiliation(s)
- Martín A Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt F Challman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Aaron D Viny
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matt R Teater
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dylan R McNally
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Doane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hao Shen
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiang Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Institute for Computational Medicine, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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7
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Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
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Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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8
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Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell 2019; 35:817-819. [PMID: 31085180 DOI: 10.1016/j.ccell.2019.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell 2019; 35:603-617.e8. [PMID: 30930119 PMCID: PMC6467783 DOI: 10.1016/j.ccell.2019.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 09/05/2018] [Revised: 12/06/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
Deletion of the gene encoding the chromatin remodeler CHD1 is among the most common alterations in prostate cancer (PCa); however, the tumor-suppressive functions of CHD1 and reasons for its tissue-specific loss remain undefined. We demonstrated that CHD1 occupied prostate-specific enhancers enriched for the androgen receptor (AR) and lineage-specific cofactors. Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the murine prostate. Notably, this cistrome shift was associated with a unique AR transcriptional signature enriched for pro-oncogenic pathways unique to this tumor subclass. Collectively, these data credential CHD1 as a tumor suppressor in the prostate that constrains AR binding/function to limit tumor progression.
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Affiliation(s)
- Michael A Augello
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deli Liu
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lesa D Deonarine
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dennis Huang
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam Blattner
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark A Rubin
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Himisha Beltran
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Andrea Sboner
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher E Barbieri
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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10
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Agirre X, Meydan C, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A. Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response. Nat Commun 2019; 10:821. [PMID: 30778059 PMCID: PMC6379396 DOI: 10.1038/s41467-019-08679-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
lncRNAs make up a majority of the human transcriptome and have key regulatory functions. Here we perform unbiased de novo annotation of transcripts expressed during the human humoral immune response to find 30% of the human genome transcribed during this process, yet 58% of these transcripts manifest striking differential expression, indicating an lncRNA phylogenetic relationship among cell types that is more robust than that of coding genes. We provide an atlas of lncRNAs in naive and GC B-cells that indicates their partition into ten functionally categories based on chromatin features, DNase hypersensitivity and transcription factor localization, defining lncRNAs classes such as enhancer-RNAs (eRNA), bivalent-lncRNAs, and CTCF-associated, among others. Specifically, eRNAs are transcribed in 8.6% of regular enhancers and 36.5% of super enhancers, and are associated with coding genes that participate in critical immune regulatory pathways, while plasma cells have uniquely high levels of circular-RNAs accounted for by and reflecting the combinatorial clonal state of the Immunoglobulin loci. Long non-coding RNAs (lncRNA) constitute a large fraction of human transcriptome, and are reported, individually, for context-specific regulatory functions. Here the authors expand our understanding by providing a systemic, unbiased annotation of lncRNA to establish an atlas of lncRNA landscape during the induction of human humoral immune responses.
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Affiliation(s)
- Xabier Agirre
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA. .,Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain.
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Yanwen Jiang
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Leire Garate
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain.,Department of Hematology, Clínica Universidad de Navarra, IDISNA, Pamplona, 31008, Spain
| | - Ashley S Doane
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Zhuoning Li
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Akanksha Verma
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Bruno Paiva
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain
| | - José I Martín-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, 08036, Spain
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA. .,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Felipe Prosper
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain. .,Department of Hematology, Clínica Universidad de Navarra, IDISNA, Pamplona, 31008, Spain.
| | - Ari Melnick
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA.
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11
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Hatzi K, Geng H, Doane AS, Meydan C, LaRiviere R, Cardenas M, Duy C, Shen H, Vidal MNC, Baslan T, Mohammad HP, Kruger RG, Shaknovich R, Haberman AM, Inghirami G, Lowe SW, Melnick AM. Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis. Nat Immunol 2018; 20:86-96. [PMID: 30538335 PMCID: PMC6294324 DOI: 10.1038/s41590-018-0273-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/31/2018] [Indexed: 01/03/2023]
Abstract
Germinal center (GC) B cells feature repression of many gene enhancers to establish their characteristic transcriptome. Here we show that conditional deletion of Lsd1 in GCs significantly impaired GC formation, associated with failure to repress immune synapse genes linked to GC exit, which are also direct targets of the transcriptional repressor BCL6. We found that BCL6 directly binds LSD1 and recruits it primarily to intergenic and intronic enhancers. Conditional deletion of Lsd1 suppressed GC hyperplasia caused by constitutive expression of BCL6 and significantly delayed BCL6-driven lymphomagenesis. Administration of catalytic inhibitors of LSD1 had little effect on GC formation or GC-derived lymphoma cells. Using a CRISPR-Cas9 domain screen, we found instead that the LSD1 Tower domain was critical for dependence on LSD1 in GC-derived B cells. These results indicate an essential role for LSD1 in the humoral immune response, where it modulates enhancer function by forming repression complexes with BCL6.
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Affiliation(s)
- Katerina Hatzi
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Reed LaRiviere
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Mariano Cardenas
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,High Throughput and Spectroscopy Resource Center, Rockefeller University, New York, NY, USA
| | - Cihangir Duy
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Hao Shen
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Maria Nieves Calvo Vidal
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helai P Mohammad
- Cancer Epigenetics Department, GlaxoSmithKline, Collegeville, PA, USA
| | - Ryan G Kruger
- Cancer Epigenetics Department, GlaxoSmithKline, Collegeville, PA, USA
| | - Rita Shaknovich
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Cancer Genetics Incorporated, Rutherford, NJ, USA
| | - Ann M Haberman
- Department of Laboratory Medicine, Department of Immunobiology Yale University School of Medicine, New Haven, CT, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
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12
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Dominguez PM, Ghamlouch H, Rosikiewicz W, Kumar P, Béguelin W, Fontán L, Rivas MA, Pawlikowska P, Armand M, Mouly E, Torres-Martin M, Doane AS, Calvo Fernandez MT, Durant M, Della-Valle V, Teater M, Cimmino L, Droin N, Tadros S, Motanagh S, Shih AH, Rubin MA, Tam W, Aifantis I, Levine RL, Elemento O, Inghirami G, Green MR, Figueroa ME, Bernard OA, Aoufouchi S, Li S, Shaknovich R, Melnick AM. TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis. Cancer Discov 2018; 8:1632-1653. [PMID: 30274972 DOI: 10.1158/2159-8290.cd-18-0657] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/26/2018] [Accepted: 09/26/2018] [Indexed: 01/04/2023]
Abstract
TET2 somatic mutations occur in ∼10% of diffuse large B-cell lymphomas (DLBCL) but are of unknown significance. Herein, we show that TET2 is required for the humoral immune response and is a DLBCL tumor suppressor. TET2 loss of function disrupts transit of B cells through germinal centers (GC), causing GC hyperplasia, impaired class switch recombination, blockade of plasma cell differentiation, and a preneoplastic phenotype. TET2 loss was linked to focal loss of enhancer hydroxymethylation and transcriptional repression of genes that mediate GC exit, such as PRDM1. Notably, these enhancers and genes are also repressed in CREBBP-mutant DLBCLs. Accordingly, TET2 mutation in patients yields a CREBBP-mutant gene-expression signature, CREBBP and TET2 mutations are generally mutually exclusive, and hydroxymethylation loss caused by TET2 deficiency impairs enhancer H3K27 acetylation. Hence, TET2 plays a critical role in the GC reaction, and its loss of function results in lymphomagenesis through failure to activate genes linked to GC exit signals. SIGNIFICANCE: We show that TET2 is required for exit of the GC, B-cell differentiation, and is a tumor suppressor for mature B cells. Loss of TET2 phenocopies CREBBP somatic mutation. These results advocate for sequencing TET2 in patients with lymphoma and for the testing of epigenetic therapies to treat these tumors.See related commentary by Shingleton and Dave, p. 1515.This article is highlighted in the In This Issue feature, p. 1494.
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Affiliation(s)
- Pilar M Dominguez
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Hussein Ghamlouch
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Parveen Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Wendy Béguelin
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Lorena Fontán
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Martín A Rivas
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Patrycja Pawlikowska
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marine Armand
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France.,CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Enguerran Mouly
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Miguel Torres-Martin
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Ashley S Doane
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - María T Calvo Fernandez
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Matt Durant
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Veronique Della-Valle
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Matt Teater
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Luisa Cimmino
- Department of Pathology, Laura and Isaac Perlmutter Cancer Center, and The Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York
| | - Nathalie Droin
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Saber Tadros
- Department of Lymphoma/Myeloma and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Samaneh Motanagh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Alan H Shih
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Wayne Tam
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology, Laura and Isaac Perlmutter Cancer Center, and The Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York
| | - Ross L Levine
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York
| | - Michael R Green
- Department of Lymphoma/Myeloma and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Olivier A Bernard
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Said Aoufouchi
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut. .,The Jackson Laboratory Cancer Center, Bar Harbor, Maine.,Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Rita Shaknovich
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York. .,Cancer Genetics, Inc., Rutherford, New Jersey
| | - Ari M Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.
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13
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Doane AS, Elemento O. Regulatory elements in molecular networks. Wiley Interdiscip Rev Syst Biol Med 2017; 9. [PMID: 28093886 DOI: 10.1002/wsbm.1374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/06/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
Abstract
Regulatory elements determine the connectivity of molecular networks and mediate a variety of regulatory processes ranging from DNA looping to transcriptional, posttranscriptional, and posttranslational regulation. This review highlights our current understanding of the different types of regulatory elements found in molecular networks with a focus on DNA regulatory elements. We highlight technical advances and current challenges for the mapping of regulatory elements at the genome-wide scale, and describe new computational methods to uncover these elements via reconstructing regulatory networks from large genomic datasets. WIREs Syst Biol Med 2017, 9:e1374. doi: 10.1002/wsbm.1374 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ashley S Doane
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
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14
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Jiang Y, Ortega-Molina A, Geng H, Ying HY, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X, Teater M, Meydan C, Li Z, Poloway D, Wang S, Ennishi D, Scott DW, Stengel KR, Kranz JE, Holson E, Sharma S, Young JW, Chu CS, Roeder RG, Shaknovich R, Hiebert SW, Gascoyne RD, Tam W, Elemento O, Wendel HG, Melnick AM. CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas. Cancer Discov 2016; 7:38-53. [PMID: 27733359 DOI: 10.1158/2159-8290.cd-16-0975] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/11/2016] [Accepted: 10/11/2016] [Indexed: 12/18/2022]
Abstract
Somatic mutations in CREBBP occur frequently in B-cell lymphoma. Here, we show that loss of CREBBP facilitates the development of germinal center (GC)-derived lymphomas in mice. In both human and murine lymphomas, CREBBP loss-of-function resulted in focal depletion of enhancer H3K27 acetylation and aberrant transcriptional silencing of genes that regulate B-cell signaling and immune responses, including class II MHC. Mechanistically, CREBBP-regulated enhancers are counter-regulated by the BCL6 transcriptional repressor in a complex with SMRT and HDAC3, which we found to bind extensively to MHC class II loci. HDAC3 loss-of-function rescued repression of these enhancers and corresponding genes, including MHC class II, and more profoundly suppressed CREBBP-mutant lymphomas in vitro and in vivo Hence, CREBBP loss-of-function contributes to lymphomagenesis by enabling unopposed suppression of enhancers by BCL6/SMRT/HDAC3 complexes, suggesting HDAC3-targeted therapy as a precision approach for CREBBP-mutant lymphomas. SIGNIFICANCE Our findings establish the tumor suppressor function of CREBBP in GC lymphomas in which CREBBP mutations disable acetylation and result in unopposed deacetylation by BCL6/SMRT/HDAC3 complexes at enhancers of B-cell signaling and immune response genes. Hence, inhibition of HDAC3 can restore the enhancer histone acetylation and may serve as a targeted therapy for CREBBP-mutant lymphomas. Cancer Discov; 7(1); 38-53. ©2016 AACR.See related commentary by Höpken, p. 14This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Yanwen Jiang
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Ana Ortega-Molina
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California
| | - Hsia-Yuan Ying
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York
| | - Katerina Hatzi
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sara Parsa
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dylan McNally
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York
| | - Ling Wang
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York
| | - Ashley S Doane
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Xabier Agirre
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York.,Area de Oncología, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Pamplona, Spain
| | - Matt Teater
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Zhuoning Li
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York
| | - David Poloway
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York
| | - Shenqiu Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daisuke Ennishi
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | - Sneh Sharma
- Laboratory of Cellular Immunobiology, Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James W Young
- Laboratory of Cellular Immunobiology, Division of Hematologic Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine; The Rockefeller University, New York, New York
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York
| | | | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Ari M Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, New York.
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15
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Shike M, Doane AS, Russo L, Cabal R, Reis-Filho JS, Gerald W, Cody H, Khanin R, Bromberg J, Norton L. The effects of soy supplementation on gene expression in breast cancer: a randomized placebo-controlled study. J Natl Cancer Inst 2014; 106:dju189. [PMID: 25190728 PMCID: PMC4817128 DOI: 10.1093/jnci/dju189] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [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: 02/06/2014] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy supplementation on breast cancer-related genes and pathways. METHODS Women (n = 140) with early-stage breast cancer were randomly assigned to soy protein supplementation (n = 70) or placebo (n = 70) for 7 to 30 days, from diagnosis until surgery. Adherence was determined by plasma isoflavones: genistein and daidzein. Gene expression changes were evaluated by NanoString in pre- and posttreatment tumor tissue. Genome-wide expression analysis was performed on posttreatment tissue. Proliferation (Ki67) and apoptosis (Cas3) were assessed by immunohistochemistry. RESULTS Plasma isoflavones rose in the soy group (two-sided Wilcoxon rank-sum test, P < .001) and did not change in the placebo group. In paired analysis of pre- and posttreatment samples, 21 genes (out of 202) showed altered expression (two-sided Student's t-test, P < .05). Several genes including FANCC and UGT2A1 revealed different magnitude and direction of expression changes between the two groups (two-sided Student's t-test, P < .05). A high-genistein signature consisting of 126 differentially expressed genes was identified from microarray analysis of tumors. This signature was characterized by overexpression (>2-fold) of cell cycle transcripts, including those that promote cell proliferation, such as FGFR2, E2F5, BUB1, CCNB2, MYBL2, CDK1, and CDC20 (P < .01). Soy intake did not result in statistically significant changes in Ki67 or Cas3. CONCLUSIONS Gene expression associated with soy intake and high plasma genistein defines a signature characterized by overexpression of FGFR2 and genes that drive cell cycle and proliferation pathways. These findings raise the concerns that in a subset of women soy could adversely affect gene expression in breast cancer.
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MESH Headings
- Adult
- Aged
- Apoptosis/drug effects
- Biomarkers/blood
- Breast Neoplasms/blood
- Breast Neoplasms/drug therapy
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/blood
- Carcinoma, Ductal, Breast/drug therapy
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Caspase 3/metabolism
- Cell Proliferation/drug effects
- Dietary Supplements/adverse effects
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Genistein/blood
- Humans
- Immunohistochemistry
- Isoflavones/blood
- Ki-67 Antigen/metabolism
- Middle Aged
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Soybean Proteins/administration & dosage
- Soybean Proteins/adverse effects
- Tissue Array Analysis
- Up-Regulation
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Affiliation(s)
- Moshe Shike
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN).
| | - Ashley S Doane
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Lianne Russo
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Rafael Cabal
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Jorge S Reis-Filho
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - William Gerald
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Hiram Cody
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Raya Khanin
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Jacqueline Bromberg
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
| | - Larry Norton
- Department of Medicine (MS, AD, LR, JB, LN) and Department of Pathology (RC, JRF, WG) and Department of Surgery (HC) and Department of Computational Biology (RK), Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College (MS, JRF, WG, HC, JB, LN)
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16
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Gucalp A, Tolaney S, Isakoff SJ, Ingle JN, Liu MC, Carey LA, Blackwell K, Rugo H, Nabell L, Forero A, Stearns V, Doane AS, Danso M, Moynahan ME, Momen LF, Gonzalez JM, Akhtar A, Giri DD, Patil S, Feigin KN, Hudis CA, Traina TA. Phase II trial of bicalutamide in patients with androgen receptor-positive, estrogen receptor-negative metastatic Breast Cancer. Clin Cancer Res 2013; 19:5505-12. [PMID: 23965901 DOI: 10.1158/1078-0432.ccr-12-3327] [Citation(s) in RCA: 487] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Patients with hormone receptor-negative breast cancer generally do not benefit from endocrine-targeted therapies. However, a subset with androgen receptor (AR) expression is predicted to respond to antiandrogen therapies. This phase II study explored bicalutamide in AR-positive, estrogen receptor (ER), and progesterone receptor (PgR)-negative metastatic breast cancer. EXPERIMENTAL DESIGN Tumors from patients with ER/PgR-negative advanced breast cancer were tested centrally for AR [immunohistochemistry (IHC) > 10% nuclear staining considered positive]. If either the primary or a metastatic site was positive, patients were eligible to receive the AR antagonist bicalutamide at a dose of 150 mg daily. Clinical benefit rate (CBR), the primary endpoint, was defined as the total number of patients who show a complete response (CR), partial response (PR), or stable disease (SD) > 6 months; secondary endpoints included progression-free survival (PFS) and toxicity. Correlative studies included measurement of circulating endocrine markers and IHC surrogates for basal-like breast cancer. RESULTS Of 424 patients with ER/PgR-negative breast cancer, 12% tested AR-positive. The 6-month CBR was 19% [95% confidence interval (CI), 7%-39%] for bicalutamide. The median PFS was 12 weeks (95% CI, 11-22 weeks). Bicalutamide was well-tolerated with no grade 4/5 treatment-related adverse events observed. CONCLUSION AR was expressed in 12% of patients with ER/PgR-negative breast cancer screened for this trial. The CBR of 19% observed with bicalutamide shows proof of principle for the efficacy of minimally toxic androgen blockade in a select group of patients with ER/PgR-negative, AR-positive breast cancer.
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Affiliation(s)
- Ayca Gucalp
- Authors' Affiliations: Breast Cancer Medicine Service, Departments of Pathology, Biostatistics, and Radiology, Memorial Sloan-Kettering Cancer Center; Weill Medical College of Cornell University, New York; Dana-Farber Cancer Institute; Massachusetts General Hospital, Boston, Massachusetts; Mayo Clinic, Rochester, Minnesota; Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia; University of North Carolina at Chapel Hill, Chapel Hill; Duke University Medical Center, Durham, North Carolina; University of California, San Francisco Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California; University of Alabama at Birmingham, Birmingham, Alabama; and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
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17
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Doane AS, Danso M, Lal P, Donaton M, Zhang L, Hudis C, Gerald WL. An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 2006; 25:3994-4008. [PMID: 16491124 DOI: 10.1038/sj.onc.1209415] [Citation(s) in RCA: 416] [Impact Index Per Article: 23.1] [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: 01/30/2023]
Abstract
Little is known of the underlying biology of estrogen receptor-negative, progesterone receptor-negative (ER(-)/PR(-)) breast cancer (BC), and few targeted therapies are available. Clinical heterogeneity of ER(-)/PR(-) tumors suggests that molecular subsets exist. We performed genome-wide expression analysis of 99 primary BC samples and eight BC cell lines in an effort to reveal distinct subsets, provide insight into their biology and potentially identify new therapeutic targets. We identified a subset of ER(-)/PR(-) tumors with paradoxical expression of genes known to be either direct targets of ER, responsive to estrogen, or typically expressed in ER(+) BC. Differentially expressed genes included SPDEF, FOXA1, XBP1, CYB5, TFF3, NAT1, APOD, ALCAM and AR (P<0.001). A classification model based on the expression signature of this tumor class identified molecularly similar BCs in an independent human BC data set and among BC cell lines (MDA-MB-453). This cell line demonstrated a proliferative response to androgen in an androgen receptor-dependent and ER-independent manner. In addition, the androgen-induced transcriptional program of MDA-MB-453 significantly overlapped the molecular signature of the unique ER(-)/PR(-) subclass of human tumors. This subset of BCs, characterized by a hormonally regulated transcriptional program and response to androgen, suggests the potential for therapeutic strategies targeting the androgen signaling pathway.
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Affiliation(s)
- A S Doane
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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