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Barisic D, Chin CR, Meydan C, Teater M, Tsialta I, Mlynarczyk C, Chadburn A, Wang X, Sarkozy M, Xia M, Carson SE, Raggiri S, Debek S, Pelzer B, Durmaz C, Deng Q, Lakra P, Rivas M, Steidl C, Scott DW, Weng AP, Mason CE, Green MR, Melnick A. ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis. Cancer Cell 2024; 42:583-604.e11. [PMID: 38458187 DOI: 10.1016/j.ccell.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/20/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. We show that ARID1A orchestrates B cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell fate toward immature IgM+CD80-PD-L2- memory B cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas (FLs) in mice. Patients with FL with ARID1A-inactivating mutations preferentially display an immature memory B cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive ARID1A-mutant lymphomas through the formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.
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Affiliation(s)
- Darko Barisic
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 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 Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt Teater
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioanna Tsialta
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Coraline Mlynarczyk
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xuehai Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Margot Sarkozy
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sandra E Carson
- Department of Biochemistry, Cell and Molecular Biology, Weill Cornell Medicine, New York, NY, USA
| | - Santo Raggiri
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sonia Debek
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Benedikt Pelzer
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Lakra
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Rivas
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA; Sylvester Comprehensive Cancer Center, University of Miami, FL, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, British Columbia, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, British Columbia, Vancouver, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ari Melnick
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Barisic D, Chin CR, Meydan C, Teater M, Tsialta I, Mlynarczyk C, Chadburn A, Wang X, Sarkozy M, Xia M, Carson SE, Raggiri S, Debek S, Pelzer B, Durmaz C, Deng Q, Lakra P, Rivas M, Steidl C, Scott DW, Weng AP, Mason CE, Green MR, Melnick A. ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis. Cancer Cell 2024; 42:720-722. [PMID: 38593783 DOI: 10.1016/j.ccell.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/11/2024]
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3
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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Jiang Y, Eagles J, Passerini V, Tang Z, Rivas MA, Weigert O, Pugh TJ, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Zappasodi R, Béguelin W, Melnick AM. Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment. Nat Commun 2024; 15:2879. [PMID: 38570506 PMCID: PMC10991284 DOI: 10.1038/s41467-024-47012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Despite regulating overlapping gene enhancers and pathways, CREBBP and KMT2D mutations recurrently co-occur in germinal center (GC) B cell-derived lymphomas, suggesting potential oncogenic cooperation. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d induces a more severe mouse lymphoma phenotype (vs either allele alone) and unexpectedly confers an immune evasive microenvironment manifesting as CD8+ T-cell exhaustion and reduced infiltration. This is linked to profound repression of immune synapse genes that mediate crosstalk with T-cells, resulting in aberrant GC B cell fate decisions. From the epigenetic perspective, we observe interaction and mutually dependent binding and function of CREBBP and KMT2D on chromatin. Their combined deficiency preferentially impairs activation of immune synapse-responsive super-enhancers, pointing to a particular dependency for both co-activators at these specialized regulatory elements. Together, our data provide an example where chromatin modifier mutations cooperatively shape and induce an immune-evasive microenvironment to facilitate lymphomagenesis.
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Affiliation(s)
- Jie Li
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Hsia-Yuan Ying
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, 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 Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew R Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Department of Pathology and Laboratorial Medicine, University of British Columbia, Vancouver, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - Chi-Shuen Chu
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Yiyue Jiang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Zhanyun Tang
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Martin A Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Robert G Roeder
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 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 Alsaud 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
| | - Roberta Zappasodi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. bioRxiv 2023:2023.07.27.550836. [PMID: 37546906 PMCID: PMC10402156 DOI: 10.1101/2023.07.27.550836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The identification of cell-type-specific 3D chromatin interactions between regulatory elements can help to decipher gene regulation and to interpret the function of disease-associated non-coding variants. However, current chromosome conformation capture (3C) technologies are unable to resolve interactions at this resolution when only small numbers of cells are available as input. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps and regulatory interactions from single-cell ATAC sequencing (scATAC-seq) data alone. ChromaFold uses pseudobulk chromatin accessibility, co-accessibility profiles across metacells, and predicted CTCF motif tracks as input features and employs a lightweight architecture to enable training on standard GPUs. Once trained on paired scATAC-seq and Hi-C data in human cell lines and tissues, ChromaFold can accurately predict both the 3D contact map and peak-level interactions across diverse human and mouse test cell types. In benchmarking against a recent deep learning method that uses bulk ATAC-seq, DNA sequence, and CTCF ChIP-seq to make cell-type-specific predictions, ChromaFold yields superior prediction performance when including CTCF ChIP-seq data as an input and comparable performance without. Finally, fine-tuning ChromaFold on paired scATAC-seq and Hi-C in a complex tissue enables deconvolution of chromatin interactions across cell subpopulations. ChromaFold thus achieves state-of-the-art prediction of 3D contact maps and regulatory interactions using scATAC-seq alone as input data, enabling accurate inference of cell-type-specific interactions in settings where 3C-based assays are infeasible.
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Affiliation(s)
- Vianne R. Gao
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Rui Yang
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Arnav Das
- University of Washington, Seattle, WA, USA
| | - Renhe Luo
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dylan R. McNally
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ioannis Karagiannidis
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Martin A. Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darko Barisic
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alireza Karbalayghareh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Yingqian A. Zhan
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Effie Apostolou
- Sanford I Weill department of Medicine, Sandra and Edward Meyer Cancer center, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Aaron D. Viny
- Departments of Medicine, Division of Hematology & Oncology, and of Genetics & Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Alexander Y. Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M. Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christina S. Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Rivas MA, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Béguelin W, Melnick AM. Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas. bioRxiv 2023:2023.02.13.528351. [PMID: 36824887 PMCID: PMC9949106 DOI: 10.1101/2023.02.13.528351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations affecting enhancer chromatin regulators CREBBP and KMT2D are highly co-occurrent in germinal center (GC)-derived lymphomas and other tumors, even though regulating similar pathways. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) indeed accelerated lymphomagenesis. C+K haploinsufficiency induced GC hyperplasia by altering cell fate decisions, skewing B cells away from memory and plasma cell differentiation. C+K deficiency particularly impaired enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for immunoregulatory and differentiation genes. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other's stable recruitment to enhancers. Notably, C+K lymphomas in mice and humans manifested significantly reduced CD8 + T-cell abundance. Hence, deficiency of C+K cooperatively induced an immune evasive phenotype due at least in part to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions. SIGNIFICANCE Although CREBBP and KMT2D have similar enhancer regulatory functions, they are paradoxically co-mutated in lymphomas. We show that their combined loss causes specific disruption of super-enhancers driving immune synapse genes. Importantly, this leads to reduction of CD8 cells in lymphomas, linking super-enhancer function to immune surveillance, with implications for immunotherapy resistance.
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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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7
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Venturutti L, Rivas MA, Pelzer BW, Flümann R, Hansen J, Karagiannidis I, Xia M, McNally DR, Isshiki Y, Lytle A, Teater M, Chin CR, Meydan C, Knittel G, Ricker E, Mason CE, Ye X, Pan-Hammarström Q, Steidl C, Scott DW, Reinhardt HC, Pernis AB, Béguelin W, Melnick AM. An Aged/Autoimmune B-cell Program Defines the Early Transformation of Extranodal Lymphomas. Cancer Discov 2023; 13:216-243. [PMID: 36264161 PMCID: PMC9839622 DOI: 10.1158/2159-8290.cd-22-0561] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/26/2022] [Accepted: 10/17/2022] [Indexed: 01/17/2023]
Abstract
A third of patients with diffuse large B-cell lymphoma (DLBCL) present with extranodal dissemination, which is associated with inferior clinical outcomes. MYD88L265P is a hallmark extranodal DLBCL mutation that supports lymphoma proliferation. Yet extranodal lymphomagenesis and the role of MYD88L265P in transformation remain mostly unknown. Here, we show that B cells expressing Myd88L252P (MYD88L265P murine equivalent) activate, proliferate, and differentiate with minimal T-cell costimulation. Additionally, Myd88L252P skewed B cells toward memory fate. Unexpectedly, the transcriptional and phenotypic profiles of B cells expressing Myd88L252P, or other extranodal lymphoma founder mutations, resembled those of CD11c+T-BET+ aged/autoimmune memory B cells (AiBC). AiBC-like cells progressively accumulated in animals prone to develop lymphomas, and ablation of T-BET, the AiBC master regulator, stripped mouse and human mutant B cells of their competitive fitness. By identifying a phenotypically defined prospective lymphoma precursor population and its dependencies, our findings pave the way for the early detection of premalignant states and targeted prophylactic interventions in high-risk patients. SIGNIFICANCE Extranodal lymphomas feature a very poor prognosis. The identification of phenotypically distinguishable prospective precursor cells represents a milestone in the pursuit of earlier diagnosis, patient stratification, and prophylactic interventions. Conceptually, we found that extranodal lymphomas and autoimmune disorders harness overlapping pathogenic trajectories, suggesting these B-cell disorders develop and evolve within a spectrum. See related commentary by Leveille et al. (Blood Cancer Discov 2023;4:8-11). This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Leandro Venturutti
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC V5Z1L3, Canada., Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z1L3, Canada., Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z7, Canada.,Corresponding authors: Leandro Venturutti, PhD. Centre for Lymphoid Cancer and Terry Fox Laboratory, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada. Phone: 604-675-8000; Fax: 604-877-0712; , Ari M. Melnick, MD. Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA. Phone: 646-962-6725; Fax: 646-962-0576;
| | - Martin A. Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Benedikt W. Pelzer
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne D-50937, Germany
| | - Ruth Flümann
- Department I of Internal Medicine, University Hospital Cologne, Cologne 50931, Germany., Max-Planck-Institute for Biology of Aging, Cologne 50931, Germany
| | - Julia Hansen
- Department I of Internal Medicine, University Hospital Cologne, Cologne 50931, Germany., Max-Planck-Institute for Biology of Aging, Cologne 50931, Germany
| | - Ioannis Karagiannidis
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dylan R. McNally
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yusuke Isshiki
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew Lytle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC V5Z1L3, Canada
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Christopher R. Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA., Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA., The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA., The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gero Knittel
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Edd Ricker
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA., The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC V5Z1L3, Canada., Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z7, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC V5Z1L3, Canada., Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T1Z7, Canada., Department of Medicine, University of British Columbia, Vancouver, BC V6T1Z7, Canada
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Alessandra B. Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,Corresponding authors: Leandro Venturutti, PhD. Centre for Lymphoid Cancer and Terry Fox Laboratory, BC Cancer Research Institute, 675 W 10th Ave, Vancouver, BC, V5Z 1L3, Canada. Phone: 604-675-8000; Fax: 604-877-0712; , Ari M. Melnick, MD. Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA. Phone: 646-962-6725; Fax: 646-962-0576;
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8
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Ferraro GB, Ali A, Luengo A, Kodack DP, Deik A, Abbott KL, Bezwada D, Blanc L, Prideaux B, Jin X, Posada JM, Chen J, Chin CR, Amoozgar Z, Ferreira R, Chen IX, Naxerova K, Ng C, Westermark AM, Duquette M, Roberge S, Lindeman NI, Lyssiotis CA, Nielsen J, Housman DE, Duda DG, Brachtel E, Golub TR, Cantley LC, Asara JM, Davidson SM, Fukumura D, Dartois VA, Clish CB, Jain RK, Vander Heiden MG. Author Correction: Fatty acid synthesis is required for breast cancer brain metastasis. Nat Cancer 2021; 2:1243. [PMID: 35122065 DOI: 10.1038/s43018-021-00283-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Gino B Ferraro
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ahmed Ali
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Alba Luengo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David P Kodack
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Amy Deik
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Divya Bezwada
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Landry Blanc
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CNRS UMR 5248, Bordeaux, France
| | - Brendan Prideaux
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, USA
| | - Xin Jin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jessica M Posada
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jiang Chen
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher R Chin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivy X Chen
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamila Naxerova
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Ng
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna M Westermark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Duquette
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sylvie Roberge
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Costas A Lyssiotis
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - David E Housman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dan G Duda
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Elena Brachtel
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Todd R Golub
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Lewis C Cantley
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lewis Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Dai Fukumura
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Véronique A Dartois
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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9
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Hamza B, Miller AB, Meier L, Stockslager M, Ng SR, King EM, Lin L, DeGouveia KL, Mulugeta N, Calistri NL, Strouf H, Bray C, Rodriguez F, Freed-Pastor WA, Chin CR, Jaramillo GC, Burger ML, Weinberg RA, Shalek AK, Jacks T, Manalis SR. Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice. Nat Commun 2021; 12:5680. [PMID: 34584084 PMCID: PMC8479082 DOI: 10.1038/s41467-021-25917-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/12/2020] [Accepted: 08/24/2021] [Indexed: 01/02/2023] Open
Abstract
Existing preclinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates, we extrapolated half-life times in the circulation of between 40 and 260 s and intravasation rates between 60 and 107,000 CTCs/hour in mouse models of small-cell lung cancer (SCLC), pancreatic ductal adenocarcinoma (PDAC), and non-small cell lung cancer (NSCLC). Additionally, direct transfer of only 1-2% of daily-shed CTCs using our blood-exchange technique from late-stage, SCLC-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.
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MESH Headings
- Animals
- Blood Transfusion/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Pancreatic Ductal/blood
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Humans
- Kinetics
- Lung Neoplasms/blood
- Lung Neoplasms/pathology
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Neoplasm Metastasis
- Neoplastic Cells, Circulating/pathology
- Pancreatic Neoplasms/blood
- Pancreatic Neoplasms/pathology
- Propensity Score
- RNA-Seq/methods
- Single-Cell Analysis/methods
- Small Cell Lung Carcinoma/blood
- Small Cell Lung Carcinoma/pathology
- Mice
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Affiliation(s)
- Bashar Hamza
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex B Miller
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lara Meier
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, Germany
- Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Max Stockslager
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sheng Rong Ng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M King
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lin Lin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey L DeGouveia
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Wentworth Institute of Technology, Boston, MA, USA
| | - Nolawit Mulugeta
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas L Calistri
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haley Strouf
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christina Bray
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Felicia Rodriguez
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christopher R Chin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Grissel C Jaramillo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan L Burger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Weinberg
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Alex K Shalek
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Department of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA
- Department of Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott R Manalis
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Ludwig Center at MIT's Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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10
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Ferraro GB, Ali A, Luengo A, Kodack DP, Deik A, Abbott KL, Bezwada D, Blanc L, Prideaux B, Jin X, Possada JM, Chen J, Chin CR, Amoozgar Z, Ferreira R, Chen I, Naxerova K, Ng C, Westermark AM, Duquette M, Roberge S, Lyssiotis CA, Duda DG, Golub TR, Davidson SM, Fukumura D, Dartois VA, Clish CB, Heiden MGV, Jain RK. Abstract 90: Fatty acid synthesis is required for breast cancer brain metastasis. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-90] [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
Brain metastases are refractory to therapies that otherwise control systemic disease in patients with human epidermal growth factor receptor 2 (HER2+) breast cancer, and the unique brain microenvironment contributes to this therapy resistance. Nutrient availability can vary across tissues, therefore metabolic adaptations required for breast cancer growth in the brain microenvironment may also introduce liabilities that can be exploited for therapy. Here, we assessed how metabolism differs between breast tumors growing in the brain versus extracranial sites and found that fatty acid synthesis is elevated in breast tumors growing in the brain. We determine that this phenotype is an adaptation to decreased lipid availability in the brain relative to other tissues, which results in a site-specific dependency on fatty acid synthesis for breast tumors growing at this site. Genetic or pharmacological inhibition of fatty acid synthase (FASN) reduces HER2+ breast tumor growth in the brain, demonstrating that differences in nutrient availability across metastatic sites can result in targetable metabolic dependencies.
Citation Format: Gino B. Ferraro, Ahmed Ali, Alba Luengo, David P. Kodack, Amy Deik, Keene L. Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica M. Possada, Jiang Chen, Christopher R. Chin, Zohreh Amoozgar, Raphael Ferreira, Ivy Chen, Kamila Naxerova, Christopher Ng, Anna M. Westermark, Mark Duquette, Sylvie Roberge, Costas A. Lyssiotis, Dan G. Duda, Todd R. Golub, Shawn M. Davidson, Dai Fukumura, Véronique A. Dartois, Clary B. Clish, Matthew G. Vander Heiden, Rakesh K. Jain. Fatty acid synthesis is required for breast cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 90.
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Affiliation(s)
- Gino B. Ferraro
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Ahmed Ali
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Alba Luengo
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - David P. Kodack
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Amy Deik
- 3Broad Institute of MIT and Harvard University, Cambridge, MA
| | - Keene L. Abbott
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Divya Bezwada
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Landry Blanc
- 4The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Brendan Prideaux
- 4The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Xin Jin
- 3Broad Institute of MIT and Harvard University, Cambridge, MA
| | | | - Jiang Chen
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Christopher R. Chin
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Zohreh Amoozgar
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Raphael Ferreira
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Ivy Chen
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Kamila Naxerova
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Christopher Ng
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Anna M. Westermark
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Mark Duquette
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Sylvie Roberge
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Costas A. Lyssiotis
- 5Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Dan G. Duda
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Todd R. Golub
- 3Broad Institute of MIT and Harvard University, Cambridge, MA
| | - Shawn M. Davidson
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Dai Fukumura
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Véronique A. Dartois
- 4The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ
| | - Clary B. Clish
- 3Broad Institute of MIT and Harvard University, Cambridge, MA
| | - Matthew G. Vander Heiden
- 2Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Rakesh K. Jain
- 1Massachusetts General Hospital/Harvard Medical School, Boston, MA
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11
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Gong B, Li D, Kusko R, Novoradovskaya N, Zhang Y, Wang S, Pabón-Peña C, Zhang Z, Lai K, Cai W, LoCoco JS, Lader E, Richmond TA, Mittal VK, Liu LC, Johann DJ, Willey JC, Bushel PR, Yu Y, Xu C, Chen G, Burgess D, Cawley S, Giorda K, Haseley N, Qiu F, Wilkins K, Arib H, Attwooll C, Babson K, Bao L, Bao W, Lucas AB, Best H, Bhandari A, Bisgin H, Blackburn J, Blomquist TM, Boardman L, Burgher B, Butler DJ, Chang CJ, Chaubey A, Chen T, Chierici M, Chin CR, Close D, Conroy J, Cooley Coleman J, Craig DJ, Crawford E, Del Pozo A, Deveson IW, Duncan D, Eterovic AK, Fan X, Foox J, Furlanello C, Ghosal A, Glenn S, Guan M, Haag C, Hang X, Happe S, Hennigan B, Hipp J, Hong H, Horvath K, Hu J, Hung LY, Jarosz M, Kerkhof J, Kipp B, Kreil DP, Łabaj P, Lapunzina P, Li P, Li QZ, Li W, Li Z, Liang Y, Liu S, Liu Z, Ma C, Marella N, Martín-Arenas R, Megherbi DB, Meng Q, Mieczkowski PA, Morrison T, Muzny D, Ning B, Parsons BL, Paweletz CP, Pirooznia M, Qu W, Raymond A, Rindler P, Ringler R, Sadikovic B, Scherer A, Schulze E, Sebra R, Shaknovich R, Shi Q, Shi T, Silla-Castro JC, Smith M, López MS, Song P, Stetson D, Strahl M, Stuart A, Supplee J, Szankasi P, Tan H, Tang LY, Tao Y, Thakkar S, Thierry-Mieg D, Thierry-Mieg J, Thodima VJ, Thomas D, Tichý B, Tom N, Garcia EV, Verma S, Walker K, Wang C, Wang J, Wang Y, Wen Z, Wirta V, Wu L, Xiao C, Xiao W, Xu S, Yang M, Ying J, Yip SH, Zhang G, Zhang S, Zhao M, Zheng Y, Zhou X, Mason CE, Mercer T, Tong W, Shi L, Jones W, Xu J. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol 2021; 22:109. [PMID: 33863344 PMCID: PMC8051090 DOI: 10.1186/s13059-021-02315-0] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/18/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. RESULTS All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. CONCLUSION This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Rebecca Kusko
- Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA
| | | | - Yifan Zhang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
- Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA
| | - Shangzi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Carlos Pabón-Peña
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA
| | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, 201114, China
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Wanshi Cai
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | | | - Eric Lader
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA
| | - Vinay K Mittal
- Thermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, 46500 Kato Rd, Fremont, CA, 94538, USA
| | - Donald J Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA
| | - James C Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, 3000 Arlington Ave, Toledo, OH, 43614, USA
| | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Chang Xu
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA
| | - Daniel Burgess
- Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd, Madison, WI, 53719, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Nathan Haseley
- Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, 201114, China
| | - Katherine Wilkins
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA
| | - Hanane Arib
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | | | - Kevin Babson
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Longlong Bao
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Wenjun Bao
- JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
| | | | - Hunter Best
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | - Halil Bisgin
- Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA
| | - James Blackburn
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
| | - Thomas M Blomquist
- Department of Pathology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
- Lucas County Coroner's Office, 2595 Arlington Ave., Toledo, OH, 43614, USA
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Blake Burgher
- OmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
| | - Alka Chaubey
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | | | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | | | - Daniel J Craig
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
| | - Erin Crawford
- Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA
| | - Angela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Duncan
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | | | | | - Sean Glenn
- OmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA
| | - Meijian Guan
- JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA
| | - Christine Haag
- Molecular Laboratory, Prof. F. Raue, Im Weiher 12, Heidelberg, Germany
| | - Xinyi Hang
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | - Scott Happe
- Agilent Technologies, 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA
| | - Brittany Hennigan
- Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Jennifer Hipp
- Department of Pathology, Strata Oncology, Inc., Ann Arbor, MI, 48103, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Kyle Horvath
- ResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
| | - Benjamin Kipp
- Division of Anatomic Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David Philip Kreil
- Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria
| | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Biotechnology, Boku University, Vienna, Austria
| | - Pablo Lapunzina
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPaz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, European Commission, Lille, France
| | - Peng Li
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Yu Liang
- Geneis, 5 Guangshun North St., Chaoyang District, Beijing, 100102, China
| | - Shaoqing Liu
- GeneSmile Ltd Co., Jiangsu Cancer Hospital, 42 Baiziting St., Xuanwu District, Nanjing, 210009, Jiangsu, China
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Charles Ma
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Narasimha Marella
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Rubén Martín-Arenas
- Genycell Biotech España, Calle Garrido Atienza, 18320 Santa Fe, Granada, Spain
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Piotr A Mieczkowski
- Department of Genetics, University of North Carolina, 250 Bell Tower Drive, Chapel Hill, NC, 27599, USA
| | - Tom Morrison
- Accugenomics, Inc., 1410 Commonwealth Drive, Suite 105, Wilmington, NC, 20403, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Barbara L Parsons
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Cloud P Paweletz
- Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wubin Qu
- iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China
| | - Amelia Raymond
- Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA
| | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, N6A3K7, Canada
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), P.O. Box 20, (Tukholmankatu 8), FI-00014 University of Helsinki, Helsinki, Finland
| | - Egbert Schulze
- Laboratory for Molecular Genetics, Endocrine Practice, Im Weiher 12, 69121, Heidelberg, Germany
| | - Robert Sebra
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Rita Shaknovich
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - Qiang Shi
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, 200241, China
| | | | - Melissa Smith
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Mario Solís López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Daniel Stetson
- Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA
| | - Maya Strahl
- Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA
| | - Alan Stuart
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, 800 Commissioners Rd E, London, Ontario, N6A5W9, Canada
| | - Julianna Supplee
- Translational Research Laboratory, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, Building C6-501, Biolake, No.666 Gaoxin Ave., East Lake High-tech Development Zone, Wuhan, 430074, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Yonghui Tao
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Shraddha Thakkar
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Venkat J Thodima
- Cancer Genetics Inc, 201 Route 17 N, Meadows Office Building, Rutherford, NJ, 07070, USA
| | - David Thomas
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Boris Tichý
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Elena Vallespin Garcia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, CIBERER Instituto de Salud Carlos III, 28046, Madrid, Spain
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands
| | - Suman Verma
- ResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA
| | - Kimbley Walker
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Division of Microbiology & Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Junwen Wang
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Department of Health Sciences, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Yexun Wang
- Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China
| | - Valtteri Wirta
- Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23B, 171 65, Solna, Sweden
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Shibei Xu
- Department of Biostatistics, Columbia Mailman School of Public Health, 722 West 168th St., New York, NY, 10032, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Shun H Yip
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA
- Center for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Guangliang Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China
| | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, 510300, Guangdong, China
| | - Meiru Zhao
- Geneplus, PKUCare Industrial Park, Changping District, Beijing, 102206, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Timothy Mercer
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, 200438, China.
| | - Wendell Jones
- Q2 Solutions - EA Genomics, 5927 S Miami Blvd, Morrisville, NC, 27560, USA.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
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Ferraro GB, Ali A, Luengo A, Kodack DP, Deik A, Abbott KL, Bezwada D, Blanc L, Prideaux B, Jin X, Posada JM, Chen J, Chin CR, Amoozgar Z, Ferreira R, Chen IX, Naxerova K, Ng C, Westermark AM, Duquette M, Roberge S, Lindeman NI, Lyssiotis CA, Nielsen J, Housman DE, Duda DG, Brachtel E, Golub TR, Cantley LC, Asara JM, Davidson SM, Fukumura D, Dartois VA, Clish CB, Jain RK, Vander Heiden MG. FATTY ACID SYNTHESIS IS REQUIRED FOR BREAST CANCER BRAIN METASTASIS. Nat Cancer 2021; 2:414-428. [PMID: 34179825 PMCID: PMC8223728 DOI: 10.1038/s43018-021-00183-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Brain metastases are refractory to therapies that control systemic disease in patients with human epidermal growth factor receptor 2 (HER2+) breast cancer, and the brain microenvironment contributes to this therapy resistance. Nutrient availability can vary across tissues, therefore metabolic adaptations required for brain metastatic breast cancer growth may introduce liabilities that can be exploited for therapy. Here, we assessed how metabolism differs between breast tumors in brain versus extracranial sites and found that fatty acid synthesis is elevated in breast tumors growing in brain. We determine that this phenotype is an adaptation to decreased lipid availability in brain relative to other tissues, resulting in a site-specific dependency on fatty acid synthesis for breast tumors growing at this site. Genetic or pharmacological inhibition of fatty acid synthase (FASN) reduces HER2+ breast tumor growth in the brain, demonstrating that differences in nutrient availability across metastatic sites can result in targetable metabolic dependencies.
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Affiliation(s)
- Gino B Ferraro
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ahmed Ali
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Alba Luengo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David P Kodack
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Amy Deik
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Keene L Abbott
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Divya Bezwada
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Landry Blanc
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CNRS UMR 5248, Bordeaux, France
| | - Brendan Prideaux
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch, Galveston, TX, USA
| | - Xin Jin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jessica M Posada
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jiang Chen
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher R Chin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivy X Chen
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kamila Naxerova
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Ng
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna M Westermark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Duquette
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sylvie Roberge
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Costas A Lyssiotis
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - David E Housman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dan G Duda
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Elena Brachtel
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Todd R Golub
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Lewis C Cantley
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Lewis Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Dai Fukumura
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Véronique A Dartois
- The Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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13
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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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14
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Duy C, Li M, Teater M, Meydan C, Garrett-Bakelman FE, Lee TC, Chin CR, Durmaz C, Kawabata KC, Dhimolea E, Mitsiades CS, Doehner H, D'Andrea RJ, Becker MW, Paietta EM, Mason CE, Carroll M, Melnick AM. Chemotherapy Induces Senescence-Like Resilient Cells Capable of Initiating AML Recurrence. Cancer Discov 2021; 11:1542-1561. [PMID: 33500244 DOI: 10.1158/2159-8290.cd-20-1375] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/28/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Patients with acute myeloid leukemia (AML) frequently relapse after chemotherapy, yet the mechanism by which AML reemerges is not fully understood. Herein, we show that primary AML cells enter a senescence-like phenotype following chemotherapy in vitro and in vivo. This is accompanied by induction of senescence/inflammatory and embryonic diapause transcriptional programs, with downregulation of MYC and leukemia stem cell genes. Single-cell RNA sequencing suggested depletion of leukemia stem cells in vitro and in vivo, and enrichment for subpopulations with distinct senescence-like cells. This senescence effect was transient and conferred superior colony-forming and engraftment potential. Entry into this senescence-like phenotype was dependent on ATR, and persistence of AML cells was severely impaired by ATR inhibitors. Altogether, we propose that AML relapse is facilitated by a senescence-like resilience phenotype that occurs regardless of their stem cell status. Upon recovery, these post-senescence AML cells give rise to relapsed AMLs with increased stem cell potential. SIGNIFICANCE: Despite entering complete remission after chemotherapy, relapse occurs in many patients with AML. Thus, there is an urgent need to understand the relapse mechanism in AML and the development of targeted treatments to improve outcome. Here, we identified a senescence-like resilience phenotype through which AML cells can survive and repopulate leukemia.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Cihangir Duy
- Cancer Signaling and Epigenetics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania. .,Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Meng Li
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Matt Teater
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Tak C Lee
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Ceyda Durmaz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Kimihito C Kawabata
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Eugen Dhimolea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | | | - Ari M Melnick
- Department of Medicine, Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York.
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15
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Malkani S, Chin CR, Cekanaviciute E, Mortreux M, Okinula H, Tarbier M, Schreurs AS, Shirazi-Fard Y, Tahimic CGT, Rodriguez DN, Sexton BS, Butler D, Verma A, Bezdan D, Durmaz C, MacKay M, Melnick A, Meydan C, Li S, Garrett-Bakelman F, Fromm B, Afshinnekoo E, Langhorst BW, Dimalanta ET, Cheng-Campbell M, Blaber E, Schisler JC, Vanderburg C, Friedländer MR, McDonald JT, Costes SV, Rutkove S, Grabham P, Mason CE, Beheshti A. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. Cell Rep 2020; 33:108448. [PMID: 33242410 PMCID: PMC8441986 DOI: 10.1016/j.celrep.2020.108448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 06/18/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents and humans in response to simulated, short-duration and long-duration spaceflight. Previous studies have identified miRNAs that regulate rodent responses to spaceflight in low-Earth orbit, and we have confirmed the expression of these proposed spaceflight-associated miRNAs in rodents reacting to simulated spaceflight conditions. Moreover, astronaut samples from the NASA Twins Study confirmed these expression signatures in miRNA sequencing, single-cell RNA sequencing (scRNA-seq), and single-cell assay for transposase accessible chromatin (scATAC-seq) data. Additionally, a subset of these miRNAs (miR-125, miR-16, and let-7a) was found to regulate vascular damage caused by simulated deep space radiation. To demonstrate the physiological relevance of key spaceflight-associated miRNAs, we utilized antagomirs to inhibit their expression and successfully rescue simulated deep-space-radiation-mediated damage in human 3D vascular constructs.
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Affiliation(s)
- Sherina Malkani
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Marie Mortreux
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hazeem Okinula
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Sofie Schreurs
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Yasaman Shirazi-Fard
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Candice G T Tahimic
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Akanksha Verma
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Ceyda Durmaz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- 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 Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Sheng Li
- The Jackson Laboratories, Farmington, CT, USA
| | - Francine Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Margareth Cheng-Campbell
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elizabeth Blaber
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, USA
| | - Jonathan C Schisler
- McAllister Heart Institute, Department of Pharmacology, and Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles Vanderburg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington DC 20007, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Seward Rutkove
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Peter Grabham
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud 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.
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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16
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Gertz ML, Chin CR, Tomoiaga D, MacKay M, Chang C, Butler D, Afshinnekoo E, Bezdan D, Schmidt MA, Mozsary C, Melnick A, Garrett-Bakelman F, Crucian B, Lee SMC, Zwart SR, Smith SM, Meydan C, Mason CE. Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. Cell Rep 2020; 33:108429. [PMID: 33242408 PMCID: PMC9444344 DOI: 10.1016/j.celrep.2020.108429] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 08/15/2020] [Revised: 10/07/2020] [Accepted: 11/03/2020] [Indexed: 12/29/2022] Open
Abstract
The National Aeronautics and Space Administration (NASA) Twins Study created an integrative molecular profile of an astronaut during NASA’s first 1-year mission on the International Space Station (ISS) and included comparisons to an identical Earth-bound twin. The unique biochemical profiles observed when landing on Earth after such a long mission (e.g., spikes in interleukin-1 [IL-1]/6/10, c-reactive protein [CRP], C-C motif chemokine ligand 2 [CCL2], IL-1 receptor antagonist [IL-1ra], and tumor necrosis factor alpha [TNF-α]) opened new questions about the human body’s response to gravity and how to plan for future astronauts, particularly around initiation or resolution of inflammation. Here, single-cell, multi-omic (100-plex epitope profile and gene expression) profiling of peripheral blood mononuclear cells (PBMCs) showed changes to blood cell composition and gene expression post-flight, specifically for monocytes and dendritic cell precursors. These were consistent with flight-induced cytokine and immune system stress, followed by skeletal muscle regeneration in response to gravity. Finally, we examined these profiles relative to 6-month missions in 28 other astronauts and detail potential pharmacological interventions for returning to gravity in future missions. Gertz et al. present a re-analysis of the landing data from the NASA Twins Study, suggesting that the biochemical signature reflects muscle regeneration after atrophy rather than a detrimental inflammatory response. This is mediated through muscle-derived IL-6 anti-inflammatory cascades. Single-cell analysis supports this role. Potential pharmacological interventions are also discussed.
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Affiliation(s)
- Monica L Gertz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, VA 22030, USA
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Delia Tomoiaga
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA; Becton Dickinson & Co., Washington, DC 20001
| | | | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, 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 10021, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tübingen 72076, Germany
| | - Michael A Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Boulder, CO 80302, USA; Sovaris Aerospace, Boulder, CO 80302, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Francine Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, Charlottesville, VA 22908, USA
| | - Brian Crucian
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX 77058, USA
| | | | - Sara R Zwart
- Department of Preventive Medicine and Population Health, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Scott M Smith
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX 77058, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, 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 10021, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, 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 10021, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA.
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17
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Lau AN, Li Z, Danai LV, Westermark AM, Darnell AM, Ferreira R, Gocheva V, Sivanand S, Lien EC, Sapp KM, Mayers JR, Biffi G, Chin CR, Davidson SM, Tuveson DA, Jacks T, Matheson NJ, Yilmaz O, Vander Heiden MG. Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma. eLife 2020; 9:56782. [PMID: 32648540 PMCID: PMC7406355 DOI: 10.7554/elife.56782] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 03/09/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023] Open
Abstract
Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between cell types within a mixed population can be challenging due to the rapid turnover of metabolites relative to the time needed to isolate cells. To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used to assess differences between cancer cell and fibroblast metabolism in murine pancreatic cancer organoid-fibroblast co-cultures and tumors. Pancreatic cancer cells exhibited increased pyruvate carboxylation relative to fibroblasts, and this flux depended on both pyruvate carboxylase and malic enzyme 1 activity. Consequently, expression of both enzymes in cancer cells was necessary for organoid and tumor growth, demonstrating that dissecting the metabolism of specific cell populations within heterogeneous systems can identify dependencies that may not be evident from studying isolated cells in culture or bulk tissue. Tumors contain a mixture of many different types of cells, including cancer cells and non-cancer cells. The interactions between these two groups of cells affect how the cancer cells use nutrients, which, in turn, affects how fast these cells grow and divide. Furthermore, different cell types may use nutrients in diverse ways to make other molecules – known as metabolites – that the cell needs to survive. Fibroblasts are a subset of non-cancer cells that are typically found in tumors and can help them form. Separating fibroblasts from cancer cells in a tumor takes a lot longer than the chemical reactions in each cell of the tumor that produce and use up nutrients, also known as the cell’s metabolism. Therefore, measuring the levels of glucose (the sugar that is the main energy source for cells) and other metabolites in each tumor cell after separating them does not necessarily provide accurate information about the tumor cell’s metabolism. This makes it difficult to study how cancer cells and fibroblasts use nutrients differently. Lau et al. have developed a strategy to study the metabolism of cancer cells and fibroblasts in tumors. Mice with tumors in their pancreas were provided glucose that had been labelled using biochemical techniques. As expected, when the cell processed the glucose, the label was transferred into metabolites that got used up very quickly. But the label also became incorporated into larger, more stable molecules, such as proteins. Unlike the small metabolites, these larger molecules do not change in the time it takes to separate the cancer cells from the fibroblasts. Lau et al. sorted cells from whole pancreatic tumors and analyzed large, stable molecules that can incorporate the label from glucose in cancer cells and fibroblasts. The experiments showed that, in cancer cells, these molecules were more likely to have labeling patterns that are characteristic of two specific enzymes called pyruvate carboxylase and malic enzyme 1. This suggests that these enzymes are more active in cancer cells. Lau et al. also found that pancreatic cancer cells needed these two enzymes to metabolize glucose and to grow into large tumors. Pancreatic cancer is one of the most lethal cancers and current therapies offer limited benefit to many patients. Therefore, it is important to develop new drugs to treat this disease. Understanding how cancer cells and non-cancer cells in pancreatic tumors use nutrients differently is important for developing drugs that only target cancer cells.
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Affiliation(s)
- Allison N Lau
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Zhaoqi Li
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, United States
| | - Anna M Westermark
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Raphael Ferreira
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vasilena Gocheva
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Sharanya Sivanand
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Evan C Lien
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Jared R Mayers
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Giulia Biffi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, United States.,Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Christopher R Chin
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States.,Department of Molecular Biology, Princeton University, Princeton, United States
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York, United States
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States
| | - Nicholas J Matheson
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Omer Yilmaz
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology at Massachusetts Institute of Technology, Cambridge, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
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18
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Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell 2020; 182:297-316.e27. [PMID: 32619424 DOI: 10.1016/j.cell.2020.05.049] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 10/28/2019] [Revised: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
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Affiliation(s)
- Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Andrew Zhai
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leena Babiker
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Daleum Kim
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Tak C Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Youngjun Kim
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael D Nissen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, and Princess Margaret Cancer Centre, Toronto, ON M5S 1A8, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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19
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Nguyen DTT, Lu Y, Chu KL, Yang X, Park SM, Choo ZN, Chin CR, Prieto C, Schurer A, Barin E, Savino AM, Gourkanti S, Patel P, Vu LP, Leslie CS, Kharas MG. HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells. Nat Commun 2020; 11:2026. [PMID: 32332729 PMCID: PMC7181745 DOI: 10.1038/s41467-020-15814-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 05/27/2019] [Accepted: 03/25/2020] [Indexed: 01/16/2023] Open
Abstract
The cell-context dependency for RNA binding proteins (RBPs) mediated control of stem cell fate remains to be defined. Here we adapt the HyperTRIBE method using an RBP fused to a Drosophila RNA editing enzyme (ADAR) to globally map the mRNA targets of the RBP MSI2 in mammalian adult normal and malignant stem cells. We reveal a unique MUSASHI-2 (MSI2) mRNA binding network in hematopoietic stem cells that changes during transition to multipotent progenitors. Additionally, we discover a significant increase in RNA binding activity of MSI2 in leukemic stem cells compared with normal hematopoietic stem and progenitor cells, resulting in selective regulation of MSI2's oncogenic targets. This provides a basis for MSI2 increased dependency in leukemia cells compared to normal cells. Moreover, our study provides a way to measure RBP function in rare cells and suggests that RBPs can achieve differential binding activity during cell state transition independent of gene expression.
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Affiliation(s)
- Diu T T Nguyen
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yuheng Lu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Blavatnik Institute of System Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sun-Mi Park
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Zi-Ning Choo
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | | | - Camila Prieto
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Angela M Savino
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Payal Patel
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, V5A 1S6, Canada
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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20
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Mayers JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM, Muir A, Chin CR, Freinkman E, Jacks T, Wolpin BM, Vitkup D, Vander Heiden MG. Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science 2017; 353:1161-5. [PMID: 27609895 DOI: 10.1126/science.aaf5171] [Citation(s) in RCA: 395] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 07/29/2016] [Indexed: 12/18/2022]
Abstract
Tumor genetics guides patient selection for many new therapies, and cell culture studies have demonstrated that specific mutations can promote metabolic phenotypes. However, whether tissue context defines cancer dependence on specific metabolic pathways is unknown. Kras activation and Trp53 deletion in the pancreas or the lung result in pancreatic ductal adenocarinoma (PDAC) or non-small cell lung carcinoma (NSCLC), respectively, but despite the same initiating events, these tumors use branched-chain amino acids (BCAAs) differently. NSCLC tumors incorporate free BCAAs into tissue protein and use BCAAs as a nitrogen source, whereas PDAC tumors have decreased BCAA uptake. These differences are reflected in expression levels of BCAA catabolic enzymes in both mice and humans. Loss of Bcat1 and Bcat2, the enzymes responsible for BCAA use, impairs NSCLC tumor formation, but these enzymes are not required for PDAC tumor formation, arguing that tissue of origin is an important determinant of how cancers satisfy their metabolic requirements.
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Affiliation(s)
- Jared R Mayers
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. These authors contributed equally to this work
| | - Margaret E Torrence
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. These authors contributed equally to this work
| | - Laura V Danai
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thales Papagiannakopoulos
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew R Bauer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Allison N Lau
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian W Ji
- Center for Computational Biology and Bioinformatics and Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Purushottam D Dixit
- Center for Computational Biology and Bioinformatics and Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Aaron M Hosios
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander Muir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher R Chin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizaveta Freinkman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA. Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tyler Jacks
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Dennis Vitkup
- Center for Computational Biology and Bioinformatics and Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA. Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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21
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Perreira JM, Aker AM, Savidis G, Chin CR, McDougall WM, Portmann JM, Meraner P, Smith MC, Rahman M, Baker RE, Gauthier A, Franti M, Brass AL. RNASEK Is a V-ATPase-Associated Factor Required for Endocytosis and the Replication of Rhinovirus, Influenza A Virus, and Dengue Virus. Cell Rep 2015. [PMID: 26212330 DOI: 10.1016/j.celrep.2015.06.076] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Human rhinovirus (HRV) causes upper respiratory infections and asthma exacerbations. We screened multiple orthologous RNAi reagents and identified host proteins that modulate HRV replication. Here, we show that RNASEK, a transmembrane protein, was needed for the replication of HRV, influenza A virus, and dengue virus. RNASEK localizes to the cell surface and endosomal pathway and closely associates with the vacuolar ATPase (V-ATPase) proton pump. RNASEK is required for endocytosis, and its depletion produces enlarged clathrin-coated pits (CCPs) at the cell surface. These enlarged CCPs contain endocytic cargo and are bound by the scissioning GTPase, DNM2. Loss of RNASEK alters the localization of multiple V-ATPase subunits and lowers the levels of the ATP6AP1 subunit. Together, our results show that RNASEK closely associates with the V-ATPase and is required for its function; its loss prevents the early events of endocytosis and the replication of multiple pathogenic viruses.
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Affiliation(s)
- Jill M Perreira
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Aaron M Aker
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - George Savidis
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Christopher R Chin
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - William M McDougall
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Jocelyn M Portmann
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Paul Meraner
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Miles C Smith
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Motiur Rahman
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Richard E Baker
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA
| | - Annick Gauthier
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Michael Franti
- Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877, USA
| | - Abraham L Brass
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, University of Massachusetts, Worcester, MA 01655, USA.
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22
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Gaiha GD, McKim KJ, Woods M, Pertel T, Rohrbach J, Barteneva N, Chin CR, Liu D, Soghoian DZ, Cesa K, Wilton S, Waring MT, Chicoine A, Doering T, Wherry EJ, Kaufmann DE, Lichterfeld M, Brass AL, Walker BD. Dysfunctional HIV-specific CD8+ T cell proliferation is associated with increased caspase-8 activity and mediated by necroptosis. Immunity 2014; 41:1001-12. [PMID: 25526311 DOI: 10.1016/j.immuni.2014.12.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [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: 05/30/2014] [Accepted: 12/04/2014] [Indexed: 02/04/2023]
Abstract
Decreased HIV-specific CD8(+) T cell proliferation is a hallmark of chronic infection, but the mechanisms of decline are unclear. We analyzed gene expression profiles from antigen-stimulated HIV-specific CD8(+) T cells from patients with controlled and uncontrolled infection and identified caspase-8 as a correlate of dysfunctional CD8(+) T cell proliferation. Caspase-8 activity was upregulated in HIV-specific CD8(+) T cells from progressors and correlated positively with disease progression and programmed cell death-1 (PD-1) expression, but negatively with proliferation. In addition, progressor cells displayed a decreased ability to upregulate membrane-associated caspase-8 activity and increased necrotic cell death following antigenic stimulation, implicating the programmed cell death pathway necroptosis. In vitro necroptosis blockade rescued HIV-specific CD8(+) T cell proliferation in progressors, as did silencing of necroptosis mediator RIPK3. Thus, chronic stimulation leading to upregulated caspase-8 activity contributes to dysfunctional HIV-specific CD8(+) T cell proliferation through activation of necroptosis and increased cell death.
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Affiliation(s)
| | | | | | - Thomas Pertel
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Natasha Barteneva
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher R Chin
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Dongfang Liu
- Center for Human Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Kevin Cesa
- Ragon Institute of MGH, Cambridge, MA 02139, USA
| | | | - Michael T Waring
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Travis Doering
- Hofstra North Shore-LIJ School of Medicine, Hempstead, NY 11549, USA
| | - E John Wherry
- Department of Microbiology and Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel E Kaufmann
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Centre de Recherche du Centre Hospitalier de l'Universite de Montreal (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Mathias Lichterfeld
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Abraham L Brass
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Department of Microbiology and Physiological Systems (MaPS), University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Bruce D Walker
- Ragon Institute of MGH, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA.
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23
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Zhu J, Davoli T, Perriera JM, Chin CR, Gaiha GD, John SP, Sigiollot FD, Gao G, Xu Q, Qu H, Pertel T, Sims JS, Smith JA, Baker RE, Maranda L, Ng A, Elledge SJ, Brass AL. Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell Rep 2014; 9:752-66. [PMID: 25373910 PMCID: PMC4926641 DOI: 10.1016/j.celrep.2014.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 05/30/2014] [Revised: 07/06/2014] [Accepted: 09/16/2014] [Indexed: 11/17/2022] Open
Abstract
RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene’s phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1–host cell interactions.
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Affiliation(s)
- Jian Zhu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Teresa Davoli
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Jill M Perriera
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher R Chin
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gaurav D Gaiha
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Sinu P John
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | | | - Geng Gao
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Qikai Xu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Hongjing Qu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
| | - Thomas Pertel
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Jennifer S Sims
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
| | - Jennifer A Smith
- ICCB-Longwood Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Richard E Baker
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Louise Maranda
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue, North Worcester, MA 01655, USA
| | - Aylwin Ng
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen J Elledge
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Abraham L Brass
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
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Desai TM, Marin M, Chin CR, Savidis G, Brass AL, Melikyan GB. IFITM3 restricts influenza A virus entry by blocking the formation of fusion pores following virus-endosome hemifusion. PLoS Pathog 2014; 10:e1004048. [PMID: 24699674 PMCID: PMC3974867 DOI: 10.1371/journal.ppat.1004048] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [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: 10/17/2013] [Accepted: 02/18/2014] [Indexed: 02/04/2023] Open
Abstract
Interferon-induced transmembrane proteins (IFITMs) inhibit infection of diverse enveloped viruses, including the influenza A virus (IAV) which is thought to enter from late endosomes. Recent evidence suggests that IFITMs block virus hemifusion (lipid mixing in the absence of viral content release) by altering the properties of cell membranes. Consistent with this mechanism, excess cholesterol in late endosomes of IFITM-expressing cells has been reported to inhibit IAV entry. Here, we examined IAV restriction by IFITM3 protein using direct virus-cell fusion assay and single virus imaging in live cells. IFITM3 over-expression did not inhibit lipid mixing, but abrogated the release of viral content into the cytoplasm. Although late endosomes of IFITM3-expressing cells accumulated cholesterol, other interventions leading to aberrantly high levels of this lipid did not inhibit virus fusion. These results imply that excess cholesterol in late endosomes is not the mechanism by which IFITM3 inhibits the transition from hemifusion to full fusion. The IFITM3's ability to block fusion pore formation at a post-hemifusion stage shows that this protein stabilizes the cytoplasmic leaflet of endosomal membranes without adversely affecting the lumenal leaflet. We propose that IFITM3 interferes with pore formation either directly, through partitioning into the cytoplasmic leaflet of a hemifusion intermediate, or indirectly, by modulating the lipid/protein composition of this leaflet. Alternatively, IFITM3 may redirect IAV fusion to a non-productive pathway, perhaps by promoting fusion with intralumenal vesicles within multivesicular bodies/late endosomes. Interferon-induced transmembrane proteins (IFITMs) block infection of many enveloped viruses, including the influenza A virus (IAV) that enters from late endosomes. IFITMs are thought to prevent virus hemifusion (merger of contacting leaflets without formation of a fusion pore) by altering the properties of cell membranes. Here we performed single IAV imaging and found that IFITM3 did not interfere with hemifusion, but prevented complete fusion. Also, contrary to a current view that excess cholesterol in late endosomes of IFITM3-expressing cells inhibits IAV entry, we show that cholesterol-laden endosomes are permissive for virus fusion. The ability of IFITM3 to block the formation of fusion pores implies that this protein stabilizes the cytoplasmic leaflet of endosomal membranes, either directly or indirectly, through altering its physical properties. IFITM3 may also redirect IAV to a non-productive pathway by promoting fusion with intralumenal vesicles of late endosomes instead of their limiting membrane.
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Affiliation(s)
- Tanay M. Desai
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
| | - Mariana Marin
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
| | - Christopher R. Chin
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - George Savidis
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Abraham L. Brass
- Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Gregory B. Melikyan
- Division of Pediatric Infectious Diseases, Emory University Children's Center, Atlanta, Georgia, United States of America
- Children's Healthcare of Atlanta, Atlanta, Georgia, United States of America
- * E-mail:
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25
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Desai TM, Marin M, Chin CR, Savidis G, Brass AL, Melikyan GB. The Viral Restriction Factor IFITM3 Promotes Hemifusion but Blocks Full Fusion of Influenza Virus. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Lin TY, Chin CR, Everitt AR, Clare S, Perreira JM, Savidis G, Aker AM, John SP, Sarlah D, Carreira EM, Elledge SJ, Kellam P, Brass AL. Amphotericin B increases influenza A virus infection by preventing IFITM3-mediated restriction. Cell Rep 2013; 5:895-908. [PMID: 24268777 PMCID: PMC3898084 DOI: 10.1016/j.celrep.2013.10.033] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [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: 02/12/2013] [Revised: 09/23/2013] [Accepted: 10/21/2013] [Indexed: 12/11/2022] Open
Abstract
The IFITMs inhibit influenza A virus (IAV) replication in vitro and in vivo. Here, we establish that the antimycotic heptaen, amphotericin B (AmphoB), prevents IFITM3-mediated restriction of IAV, thereby increasing viral replication. Consistent with its neutralization of IFITM3, a clinical preparation of AmphoB, AmBisome, reduces the majority of interferon’s protective effect against IAV in vitro. Mechanistic studies reveal that IFITM1 decreases host-membrane fluidity, suggesting both a possible mechanism for IFITM-mediated restriction and its negation by AmphoB. Notably, we reveal that mice treated with AmBisome succumbed to a normally mild IAV infection, similar to animals deficient in Ifitm3. Therefore, patients receiving antifungal therapy with clinical preparations of AmphoB may be functionally immunocompromised and thus more vulnerable to influenza, as well as other IFITM3-restricted viral infections. Amphotericin B or AmBisome prevents IFITM3-mediated restriction of IAV AmBisome overcomes the majority of IFN’s antiviral effects in vitro IFITM1 decreases membrane fluidity and inhibits membrane fusion AmBisome increases the morbidity and mortality of influenza
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Affiliation(s)
- Tsai-Yu Lin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher R Chin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA; Ragon Institute of Massachusetts General Hospital, M.I.T. and Harvard University, Charlestown, MA 02129, USA
| | - Aaron R Everitt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jill M Perreira
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George Savidis
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Aaron M Aker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sinu P John
- Ragon Institute of Massachusetts General Hospital, M.I.T. and Harvard University, Charlestown, MA 02129, USA
| | - David Sarlah
- Eidgenössische Technische Hochschule, Deutsch English Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland
| | - Erick M Carreira
- Eidgenössische Technische Hochschule, Deutsch English Department of Chemistry and Applied Biosciences, 8093 Zurich, Switzerland
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK; MRC/UCL Centre for Medical Molecular Virology, Division of Infection & Immunity, University College London, Gower Street, London W1CE 6BT, UK
| | - Abraham L Brass
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA; Ragon Institute of Massachusetts General Hospital, M.I.T. and Harvard University, Charlestown, MA 02129, USA.
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Fusco DN, Brisac C, John SP, Huang YW, Chin CR, Xie T, Zhao H, Zhang L, Chevalier S, Wambua D, Lin W, Peng L, Chung RT, Brass AL, Brass AL. A genetic screen identifies interferon-α effector genes required to suppress hepatitis C virus replication. Gastroenterology 2013; 144:1438-49, 1449.e1-9. [PMID: 23462180 PMCID: PMC3665646 DOI: 10.1053/j.gastro.2013.02.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/15/2013] [Accepted: 02/12/2013] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) infection is a leading cause of end-stage liver disease. Interferon-α (IFNα) is an important component of anti-HCV therapy; it up-regulates transcription of IFN-stimulated genes, many of which have been investigated for their antiviral effects. However, all of the genes required for the antiviral function of IFNα (IFN effector genes [IEGs]) are not known. IEGs include not only IFN-stimulated genes, but other nontranscriptionally induced genes that are required for the antiviral effect of IFNα. In contrast to candidate approaches based on analyses of messenger RNA (mRNA) expression, identification of IEGs requires a broad functional approach. METHODS We performed an unbiased genome-wide small interfering RNA screen to identify IEGs that inhibit HCV. Huh7.5.1 hepatoma cells were transfected with small interfering RNAs incubated with IFNα and then infected with JFH1 HCV. Cells were stained using HCV core antibody, imaged, and analyzed to determine the percent infection. Candidate IEGs detected in the screen were validated and analyzed further. RESULTS The screen identified 120 previously unreported IEGs. From these, we more fully evaluated the following: asparagine-linked glycosylation 10 homolog (yeast, α-1,2-glucosyltransferase); butyrylcholinesterase; dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2); glucokinase (hexokinase 4) regulator; guanylate cyclase 1, soluble, β 3; MYST histone acetyltransferase 1; protein phosphatase 3 (formerly 2B), catalytic subunit, β isoform; peroxisomal proliferator-activated receptor-γ-DBD-interacting protein 1; and solute carrier family 27 (fatty acid transporter), member 2; and demonstrated that they enabled IFNα-mediated suppression of HCV at multiple steps of its life cycle. Expression of these genes had more potent effects against flaviviridae because a subset was required for IFNα to suppress dengue virus but not influenza A virus. In addition, many of the host genes detected in this screen (92%) were not transcriptionally stimulated by IFNα; these genes represent a heretofore unknown class of non-IFN-stimulated gene IEGs. CONCLUSIONS We performed a whole-genome loss-of-function screen to identify genes that mediate the effects of IFNα against human pathogenic viruses. We found that IFNα restricts HCV via actions of general and specific IEGs.
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Affiliation(s)
- Dahlene N. Fusco
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | | | | | - Yi-Wen Huang
- Department of Internal Medicine, National Taiwan University College of, Medicine and Hospital, Liver Center, Cathay General Hospital Medical Center &, School of Medicine, Taipei Medical University, No. 280, Sec. 4, Jen-Ai Road, Taipei-10630, Taiwan
| | - Christopher R. Chin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester MA 01605
| | - Tiao Xie
- Harvard Medical School Image and Data Analysis Core, 240 Longwood Avenue, Boston, MA 02115
| | - Hong Zhao
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China, 100034
| | - Leiliang Zhang
- MOH Key Laboratory of Systems Biology of Pathogens; Institute of Pathogen Biology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing, China
| | - Stephane Chevalier
- Hospital University Henri Mondor, Department of Virology, Université Paris-Est, Créteil, France, Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Daniel Wambua
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Wenyu Lin
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Lee Peng
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Raymond T. Chung
- Correspondence: Abraham L. Brass, Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester MA 01605, Telephone: 508-856-2292, . Raymond T. Chung, Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street, Boston MA 02114, Telephone: 617-724-7562, Fax: 617-643-0446,
| | - Abraham L. Brass
- Correspondence: Abraham L. Brass, Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester MA 01605, Telephone: 508-856-2292, . Raymond T. Chung, Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street, Boston MA 02114, Telephone: 617-724-7562, Fax: 617-643-0446,
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Abstract
Reoviruses are double-stranded RNA viruses that infect the mammalian respiratory and gastrointestinal tract. Reovirus infection elicits production of type I interferons (IFNs), which trigger antiviral pathways through the induction of interferon-stimulated genes (ISGs). Although hundreds of ISGs have been identified, the functions of many of these genes are unknown. The interferon-inducible transmembrane (IFITM) proteins are one class of ISGs that restrict the cell entry of some enveloped viruses, including influenza A virus. One family member, IFITM3, localizes to late endosomes, where reoviruses undergo proteolytic disassembly; therefore, we sought to determine whether IFITM3 also restricts reovirus entry. IFITM3-expressing cell lines were less susceptible to infection by reovirus, as they exhibited significantly lower percentages of infected cells in comparison to control cells. Reovirus replication was also significantly reduced in IFITM3-expressing cells. Additionally, cells expressing an shRNA targeting IFITM3 exhibited a smaller decrease in infection after IFN treatment than the control cells, indicating that endogenous IFITM3 restricts reovirus infection. However, IFITM3 did not restrict entry of reovirus infectious subvirion particles (ISVPs), which do not require endosomal proteolysis, indicating that restriction occurs in the endocytic pathway. Proteolysis of outer capsid protein μ1 was delayed in IFITM3-expressing cells in comparison to control cells, suggesting that IFITM3 modulates the function of late endosomal compartments either by reducing the activity of endosomal proteases or delaying the proteolytic processing of virions. These data provide the first evidence that IFITM3 restricts infection by a nonenveloped virus and suggest that IFITM3 targets an increasing number of viruses through a shared requirement for endosomes during cell entry.
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Affiliation(s)
- Amanda A Anafu
- Department of Biology, Colgate University, Hamilton, New York 13346, USA
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Zhu J, Gaiha GD, John SP, Pertel T, Chin CR, Gao G, Qu H, Walker BD, Elledge SJ, Brass AL. Reactivation of latent HIV-1 by inhibition of BRD4. Cell Rep 2012; 2:807-16. [PMID: 23041316 DOI: 10.1016/j.celrep.2012.09.008] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/10/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022] Open
Abstract
HIV-1 depends on many host factors for propagation. Other host factors, however, antagonize HIV-1 and may have profound effects on viral activation. Curing HIV-1 requires the reduction of latent viral reservoirs that remain in the face of antiretroviral therapy. Using orthologous genetic screens, we identified bromodomain containing 4 (BRD4) as a negative regulator of HIV-1 replication. Antagonism of BRD4, via RNA interference or with a small molecule inhibitor, JQ1, both increased proviral transcriptional elongation and alleviated HIV-1 latency in cell-line models. In multiple instances, JQ1, when used in combination with the NF-κB activators Prostratin or PHA, enhanced the in vitro reactivation of latent HIV-1 in primary T cells. These data are consistent with a model wherein BRD4 competes with the virus for HIV-1 dependency factors (HDFs) and suggests that combinatorial therapies that activate HDFs and antagonize HIV-1 competitive factors may be useful for curing HIV-1 infection.
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Affiliation(s)
- Jian Zhu
- Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA
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30
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Chin CR, Brass AL. A genome wide RNA interference screening method to identify host factors that modulate influenza A virus replication. Methods 2012; 59:217-24. [PMID: 23036328 DOI: 10.1016/j.ymeth.2012.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/28/2012] [Accepted: 09/22/2012] [Indexed: 11/17/2022] Open
Abstract
The use of genome wide RNA interference (RNAi) screens to investigate host-virals interactions has revealed unexpected connections that have improved our understanding of viral pathogenesis and cell biology. This work describes the use of an RNAi screening method employing an immunofluorescence image-based strategy and influenza A virus. We find this approach to be readily implemented, scalable and amenable to the direct evaluation of a variety of viral lifecycles.
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Affiliation(s)
- Christopher R Chin
- Microbiology and Physiological Systems Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
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