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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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Reiss DJ, Nakayama Y, Weng AP, Stokes ME, Sehn L, Steidl C, Scott DW, Huang CC, Gandhi AK. High-plex imaging and cellular neighborhood spatial analysis reveals multiple immune escape and suppression patterns in diffuse large B-cell lymphoma. Leukemia 2024:10.1038/s41375-024-02239-1. [PMID: 38575670 DOI: 10.1038/s41375-024-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Affiliation(s)
- David J Reiss
- Informatics and Predictive Sciences, Bristol Myers Squibb, Seattle, WA, USA
| | - Yumi Nakayama
- Translational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA
| | | | - Matthew E Stokes
- Informatics and Predictive Sciences, Bristol Myers Squibb, Summit, NJ, USA
| | - Laurie Sehn
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - C Chris Huang
- Translational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA
| | - Anita K Gandhi
- Translational Medicine Hematology, Bristol Myers Squibb, Summit, NJ, USA.
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Aoki T, Jiang A, Xu A, Yin Y, Gamboa A, Milne K, Takata K, Miyata-Takata T, Chung S, Rai S, Wu S, Warren M, Strong C, Goodyear T, Morris K, Chong LC, Hav M, Colombo AR, Telenius A, Boyle M, Ben-Neriah S, Power M, Gerrie AS, Weng AP, Karsan A, Roth A, Farinha P, Scott DW, Savage KJ, Nelson BH, Merchant A, Steidl C. Spatially Resolved Tumor Microenvironment Predicts Treatment Outcomes in Relapsed/Refractory Hodgkin Lymphoma. J Clin Oncol 2024; 42:1077-1087. [PMID: 38113419 PMCID: PMC10950131 DOI: 10.1200/jco.23.01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/21/2023] Open
Abstract
PURPOSE About a third of patients with relapsed or refractory classic Hodgkin lymphoma (r/r CHL) succumb to their disease after high-dose chemotherapy followed by autologous stem-cell transplantation (HDC/ASCT). Here, we aimed to describe spatially resolved tumor microenvironment (TME) ecosystems to establish novel biomarkers associated with treatment failure in r/r CHL. PATIENTS AND METHODS We performed imaging mass cytometry (IMC) on 71 paired primary diagnostic and relapse biopsies using a marker panel specific to CHL biology. For each cell type in the TME, we calculated a spatial score measuring the distance of nearest neighbor cells to the malignant Hodgkin Reed Sternberg cells within the close interaction range. Spatial scores were used as features in prognostic model development for post-ASCT outcomes. RESULTS Highly multiplexed IMC data revealed shared TME patterns in paired diagnostic and early r/r CHL samples, whereas TME patterns were more divergent in pairs of diagnostic and late relapse samples. Integrated analysis of IMC and single-cell RNA sequencing data identified unique architecture defined by CXCR5+ Hodgkin and Reed Sternberg (HRS) cells and their strong spatial relationship with CXCL13+ macrophages in the TME. We developed a prognostic assay (RHL4S) using four spatially resolved parameters, CXCR5+ HRS cells, PD1+CD4+ T cells, CD68+ tumor-associated macrophages, and CXCR5+ B cells, which effectively separated patients into high-risk versus low-risk groups with significantly different post-ASCT outcomes. The RHL4S assay was validated in an independent r/r CHL cohort using a multicolor immunofluorescence assay. CONCLUSION We identified the interaction of CXCR5+ HRS cells with ligand-expressing CXCL13+ macrophages as a prominent crosstalk axis in relapsed CHL. Harnessing this TME biology, we developed a novel prognostic model applicable to r/r CHL biopsies, RHL4S, opening new avenues for spatial biomarker development.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Princess Margaret Cancer Centre—University Health Network, Toronto, Ontario, Canada
| | - Aixiang Jiang
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Yifan Yin
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Shanee Chung
- Leukemia/Bone Marrow Transplant Program of BC, BC Cancer, Vancouver, British Columbia, Canada
| | - Shinya Rai
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Shaocheng Wu
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Mary Warren
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Celia Strong
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Talia Goodyear
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Kayleigh Morris
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Lauren C. Chong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | | | | | - Adele Telenius
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Maryse Power
- Leukemia/Bone Marrow Transplant Program of BC, BC Cancer, Vancouver, British Columbia, Canada
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Brad H. Nelson
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | | | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Lee E, Chern K, Nissen M, Wang X, Huang C, Gandhi AK, Bouchard-Côté A, Weng AP, Roth A. SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data. Bioinformatics 2023; 39:i131-i139. [PMID: 37387130 DOI: 10.1093/bioinformatics/btad242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Recent advances in spatial proteomics technologies have enabled the profiling of dozens of proteins in thousands of single cells in situ. This has created the opportunity to move beyond quantifying the composition of cell types in tissue, and instead probe the spatial relationships between cells. However, most current methods for clustering data from these assays only consider the expression values of cells and ignore the spatial context. Furthermore, existing approaches do not account for prior information about the expected cell populations in a sample. RESULTS To address these shortcomings, we developed SpatialSort, a spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge. Our method is able to account for the affinities of cells of different types to neighbour in space, and by incorporating prior information about expected cell populations, it is able to simultaneously improve clustering accuracy and perform automated annotation of clusters. Using synthetic and real data, we show that by using spatial and prior information SpatialSort improves clustering accuracy. We also demonstrate how SpatialSort can perform label transfer between spatial and nonspatial modalities through the analysis of a real world diffuse large B-cell lymphoma dataset. AVAILABILITY AND IMPLEMENTATION Source code is available on Github at: https://github.com/Roth-Lab/SpatialSort.
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Affiliation(s)
- Eric Lee
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3, Canada
- Graduate Bioinformatics Training Program, University of British Columbia, 100-570 West 7th Avenue, Vancouver, BC V5T4S6, Canada
| | - Kevin Chern
- Department of Statistics, University of British Columbia, 2207 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Michael Nissen
- Terry Fox Laboratory, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z1L3, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z1L3, Canada
| | - Chris Huang
- Translational Medicine Hematology, Bristol Myers Squibb, 86 Morris Ave, Summit, NJ 07901, United States
| | - Anita K Gandhi
- Translational Medicine Hematology, Bristol Myers Squibb, 86 Morris Ave, Summit, NJ 07901, United States
| | - Alexandre Bouchard-Côté
- Department of Statistics, University of British Columbia, 2207 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T1Z7, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T1Z7, Canada
- Department of Computer Science, University of British Columbia, 2366 Main Mall, Vancouver, BC V6T1Z4, Canada
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Islam R, Jenkins CE, Cao Q, Wong J, Bilenky M, Carles A, Moksa M, Weng AP, Hirst M. RUNX1 colludes with NOTCH1 to reprogram chromatin in T cell acute lymphoblastic leukemia. iScience 2023; 26:106795. [PMID: 37213235 PMCID: PMC10199266 DOI: 10.1016/j.isci.2023.106795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 02/10/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including MYC, DTX1, HES4, IL7R, and NOTCH3. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.
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Affiliation(s)
- Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | | | - Qi Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jasper Wong
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Misha Bilenky
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Martin Hirst
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 2B5, Canada
- Corresponding author
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Issa N, Bjeije H, Wilson ER, Krishnan A, Dunuwille WMB, Parsons TM, Zhang CR, Han W, Young AL, Ren Z, Ge K, Wang ES, Weng AP, Cashen A, Spencer DH, Challen GA. KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress. Leukemia 2023; 37:728-740. [PMID: 36797416 PMCID: PMC10081958 DOI: 10.1038/s41375-023-01853-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematopoietic neoplasm resulting from the malignant transformation of T-cell progenitors. While activating NOTCH1 mutations are the dominant genetic drivers of T-ALL, epigenetic dysfunction plays a central role in the pathology of T-ALL and can provide alternative mechanisms to oncogenesis in lieu of or in combination with genetic mutations. The histone demethylase enzyme KDM6A (UTX) is also recurrently mutated in T-ALL patients and functions as a tumor suppressor. However, its gene paralog, KDM6B (JMJD3), is never mutated and can be significantly overexpressed, suggesting it may be necessary for sustaining the disease. Here, we used mouse and human T-ALL models to show that KDM6B is required for T-ALL development and maintenance. Using NOTCH1 gain-of-function retroviral models, mouse cells genetically deficient for Kdm6b were unable to propagate T-ALL. Inactivating KDM6B in human T-ALL patient cells by CRISPR/Cas9 showed KDM6B-targeted cells were significantly outcompeted over time. The dependence of T-ALL cells on KDM6B was proportional to the oncogenic strength of NOTCH1 mutation, with KDM6B required to prevent stress-induced apoptosis from strong NOTCH1 signaling. These studies identify a crucial role for KDM6B in sustaining NOTCH1-driven T-ALL and implicate KDM6B as a novel therapeutic target in these patients.
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Affiliation(s)
- Nancy Issa
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hassan Bjeije
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elisabeth R Wilson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aishwarya Krishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wangisa M B Dunuwille
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tyler M Parsons
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christine R Zhang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wentao Han
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Andrew L Young
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zhizhong Ren
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eunice S Wang
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Amanda Cashen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David H Spencer
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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8
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Panelli P, De Santis E, Colucci M, Tamiro F, Sansico F, Miroballo M, Murgo E, Padovano C, Gusscott S, Ciavarella M, Chavez EA, Bianchi F, Rossi G, Carella AM, Steidl C, Weng AP, Giambra V. Noncanonical β-catenin interactions promote leukemia-initiating activity in early T-cell acute lymphoblastic leukemia. Blood 2023; 141:1597-1609. [PMID: 36315912 PMCID: PMC10651788 DOI: 10.1182/blood.2022017079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a T-cell malignancy characterized by cell subsets and enriched with leukemia-initiating cells (LICs). β-Catenin modulates LIC activity in T-ALL. However, its role in maintaining established leukemia stem cells remains largely unknown. To identify functionally relevant protein interactions of β-catenin in T-ALL, we performed coimmunoprecipitation followed by liquid chromatography-mass spectrometry. Here, we report that a noncanonical functional interaction of β-catenin with the Forkhead box O3 (FOXO3) transcription factor positively regulates LIC-related genes, including the cyclin-dependent kinase 4, which is a crucial modulator of cell cycle and tumor maintenance. We also confirm the relevance of these findings using stably integrated fluorescent reporters of β-catenin and FOXO3 activity in patient-derived xenografts, which identify minor subpopulations with enriched LIC activity. In addition, gene expression data at the single-cell level of leukemic cells of primary patients at the time of diagnosis and minimal residual disease (MRD) up to 30 days after the standard treatments reveal that the expression of β-catenin- and FOXO3-dependent genes is present in the CD82+CD117+ cell fraction, which is substantially enriched with LICs in MRD as well as in early T-cell precursor ALL. These findings highlight key functional roles for β-catenin and FOXO3 and suggest novel therapeutic strategies to eradicate aggressive cell subsets in T-ALL.
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Affiliation(s)
- Patrizio Panelli
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elisabetta De Santis
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Mattia Colucci
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesco Tamiro
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Francesca Sansico
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Mattia Miroballo
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuele Murgo
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Costanzo Padovano
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Sam Gusscott
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC, Canada
| | - Michele Ciavarella
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Fabrizio Bianchi
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giovanni Rossi
- Department of Hematology and Stem Cell Transplant Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo M. Carella
- Department of Hematology and Stem Cell Transplant Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC, Canada
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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9
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Antoszewski M, Fournier N, Ruiz Buendía GA, Lourenco J, Liu Y, Sugrue T, Dubey C, Nkosi M, Pritchard CE, Huijbers IJ, Segat GC, Alonso-Moreno S, Serracanta E, Belver L, Ferrando AA, Ciriello G, Weng AP, Koch U, Radtke F. Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL. Blood 2022; 139:2483-2498. [PMID: 35020836 PMCID: PMC9710489 DOI: 10.1182/blood.2021012077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape during T-ALL initiation is unknown. Here we demonstrate an essential role for the high-mobility-group transcription factor Tcf1 in orchestrating chromatin accessibility and topology, allowing aberrant Notch1 signaling to convey its oncogenic function. Although essential, Tcf1 is not sufficient to initiate leukemia. The formation of a leukemia-prone epigenetic landscape at the distal Notch1-regulated Myc enhancer, which is fundamental to this disease, is Tcf1-dependent and occurs within the earliest progenitor stage even before cells adopt a T lymphocyte or leukemic fate. Moreover, we discovered a unique evolutionarily conserved Tcf1-regulated enhancer element in the distal Myc-enhancer, which is important for the transition of preleukemic cells to full-blown disease.
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Affiliation(s)
- Mateusz Antoszewski
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Nadine Fournier
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Gustavo A. Ruiz Buendía
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Joao Lourenco
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yuanlong Liu
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Tara Sugrue
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Botnar Research Centre for Child Health, University of Basel & ETH Zürich, Basel, Switzerland
| | - Christelle Dubey
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- INSELSPITAL, Universitätsspital Bern, Universitätsklinik für Thoraxchirurgie, Forschungsabteilung Thoraxchirurgie, Bern, Switzerland
| | - Marianne Nkosi
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Colin E.J. Pritchard
- Mouse Clinic for Cancer & Aging (MCCA)/Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ivo J. Huijbers
- Mouse Clinic for Cancer & Aging (MCCA)/Transgenic Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Laura Belver
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Catalan Institute of Oncology-Immuno Procure, Barcelona, Spain
| | - Adolfo A. Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Giovanni Ciriello
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | - Ute Koch
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Freddy Radtke
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
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10
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Wong R, Nguyen A, Wang X, Chong L, Tyshchenko K, Brown SD, Holt RA, Steidl C, Weng AP. Improved resolution of phenotypic subsets in human T-ALL by incorporation of RNA-seq based developmental profiling. Leuk Res 2021; 110:106712. [PMID: 34583126 DOI: 10.1016/j.leukres.2021.106712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Rachel Wong
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Andrew Nguyen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Lauren Chong
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | | | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Rob A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Christian Steidl
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.
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11
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Islam R, Bilenky M, Weng AP, Connors JM, Hirst M. CRIS: complete reconstruction of immunoglobulin V-D-J sequences from RNA-seq data. Bioinform Adv 2021; 1:vbab021. [PMID: 34806017 PMCID: PMC8600631 DOI: 10.1093/bioadv/vbab021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/08/2021] [Accepted: 09/06/2021] [Indexed: 01/27/2023]
Abstract
MOTIVATION B cells display remarkable diversity in producing B-cell receptors through recombination of immunoglobulin (Ig) V-D-J genes. Somatic hypermutation (SHM) of immunoglobulin heavy chain variable (IGHV) genes are used as a prognostic marker in B-cell malignancies. Clinically, IGHV mutation status is determined by targeted Sanger sequencing which is a resource-intensive and low-throughput procedure. Here, we describe a bioinformatic pipeline, CRIS (Complete Reconstruction of Immunoglobulin IGHV-D-J Sequences) that uses RNA sequencing (RNA-seq) datasets to reconstruct IGHV-D-J sequences and determine IGHV SHM status. RESULTS CRIS extracts RNA-seq reads aligned to Ig gene loci, performs assembly of Ig transcripts and aligns the resulting contigs to reference Ig sequences to enumerate and classify SHMs in the IGHV gene sequence. CRIS improves on existing tools that infer the B-cell receptor repertoire from RNA-seq data using a portion IGHV gene segment by de novo assembly. We show that the SHM status identified by CRIS using the entire IGHV gene segment is highly concordant with clinical classification in three independent chronic lymphocytic leukemia patient cohorts. AVAILABILITY AND IMPLEMENTATION The CRIS pipeline is available under the MIT License from https://github.com/Rashedul/CRIS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Rashedul Islam
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada,Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Misha Bilenky
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada,Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Joseph M Connors
- Department of Medical Oncology, BC Cancer, Vancouver, BC, V5Z 4E6, Canada
| | - Martin Hirst
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada,Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada,To whom correspondence should be addressed.
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12
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Tamiro F, Weng AP, Giambra V. Targeting Leukemia-Initiating Cells in Acute Lymphoblastic Leukemia. Cancer Res 2021; 81:4165-4173. [PMID: 33414170 DOI: 10.1158/0008-5472.can-20-2571] [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] [Received: 07/31/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022]
Abstract
The concept that different leukemias are developmentally distinct and, like in normal hematopoiesis, generated by restricted populations of cells named leukemia-initiating cells (LIC), is becoming more established. These cancer stem-like cells have been assumed to have unique properties, including the capability of self-renewing and giving rise to "differentiated" or non-LICs that make up the whole tumor. Cell populations enriched with LIC activity have been characterized in different hematopoietic malignancies, including human acute lymphoblastic leukemia (ALL). Related studies have also demonstrated that LICs are functionally distinct from bulk cells and modulated by distinct molecular signaling pathways and epigenetic mechanisms. Here we review several biological and clinical aspects related to LICs in ALL, including (i) immunophenotypic characterization of LIC-enriched subsets in human and mouse models of ALL, (ii) emerging therapeutics against regulatory signaling pathways involved in LIC progression and maintenance in T- and B-cell leukemias, (iii) novel epigenetic and age-related mechanisms of LIC propagation, and (iv) ongoing efforts in immunotherapy to eradicate LIC-enriched cell subsets in relapsed and refractory ALL cases. Current conventional treatments do not efficiently eliminate LICs. Therefore, innovative therapeutics that exclusively target LICs hold great promise for developing an effective cure for ALL.
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Affiliation(s)
- Francesco Tamiro
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Vincenzo Giambra
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.
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13
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Bulaeva E, Pellacani D, Nakamichi N, Hammond CA, Beer PA, Lorzadeh A, Moksa M, Carles A, Bilenky M, Lefort S, Shu J, Wilhelm BT, Weng AP, Hirst M, Eaves CJ. MYC-induced human acute myeloid leukemia requires a continuing IL-3/GM-CSF costimulus. Blood 2020; 136:2764-2773. [PMID: 33301029 DOI: 10.1182/blood.2020006374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/10/2020] [Indexed: 11/20/2022] Open
Abstract
Hematopoietic clones with leukemogenic mutations arise in healthy people as they age, but progression to acute myeloid leukemia (AML) is rare. Recent evidence suggests that the microenvironment may play an important role in modulating human AML population dynamics. To investigate this concept further, we examined the combined and separate effects of an oncogene (c-MYC) and exposure to interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), and stem cell factor (SCF) on the experimental genesis of a human AML in xenografted immunodeficient mice. Initial experiments showed that normal human CD34+ blood cells transduced with a lentiviral MYC vector and then transplanted into immunodeficient mice produced a hierarchically organized, rapidly fatal, and serially transplantable blast population, phenotypically and transcriptionally similar to human AML cells, but only in mice producing IL-3, GM-CSF, and SCF transgenically or in regular mice in which the cells were exposed to IL-3 or GM-CSF delivered using a cotransduction strategy. In their absence, the MYC+ human cells produced a normal repertoire of lymphoid and myeloid progeny in transplanted mice for many months, but, on transfer to secondary mice producing the human cytokines, the MYC+ cells rapidly generated AML. Indistinguishable diseases were also obtained efficiently from both primitive (CD34+CD38-) and late granulocyte-macrophage progenitor (GMP) cells. These findings underscore the critical role that these cytokines can play in activating a malignant state in normally differentiating human hematopoietic cells in which MYC expression has been deregulated. They also introduce a robust experimental model of human leukemogenesis to further elucidate key mechanisms involved and test strategies to suppress them.
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Affiliation(s)
- Elizabeth Bulaeva
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Davide Pellacani
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Naoto Nakamichi
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Colin A Hammond
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Philip A Beer
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Annaïck Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Sylvain Lefort
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jeremy Shu
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Brian T Wilhelm
- Institute for Research in Immunology and Cancer, Montreal, QC, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada; and
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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14
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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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15
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Hill AJ, Zhang C, Kusakabe M, Gowing K, Wang X, Brinkman RR, Weng AP, Craig JW. Occurrence of T-cell and NK-cell subsets with less well-recognized phenotypes in peripheral blood submitted for routine flow cytometry analysis. Cytometry B Clin Cytom 2020; 100:235-239. [PMID: 32222062 DOI: 10.1002/cyto.b.21876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/18/2020] [Accepted: 03/10/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Ainsleigh J Hill
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chaoran Zhang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Manabu Kusakabe
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Kevin Gowing
- Department of Pathology and Lab Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ryan R Brinkman
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Lab Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada.,Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jeffrey W Craig
- Department of Pathology and Lab Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada.,Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
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16
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Hoofd C, Huang SJ, Gusscott S, Lam S, Wong R, Johnston A, Ben-Neriah S, Steidl C, Scott DW, Bruyere H, Gillan TL, Toze CL, Gerrie AS, Weng AP. Ultrasensitive Detection of NOTCH1 c.7544_7545delCT Mutations in Chronic Lymphocytic Leukemia by Droplet Digital PCR Reveals High Frequency of Subclonal Mutations and Predicts Clinical Outcome in Cases with Trisomy 12. J Mol Diagn 2020; 22:571-578. [PMID: 32036086 DOI: 10.1016/j.jmoldx.2020.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/25/2019] [Accepted: 01/14/2020] [Indexed: 01/07/2023] Open
Abstract
NOTCH1 is recurrently mutated in chronic lymphocytic leukemia (CLL), most commonly as a 2-bp frameshift deletion (c.7541_7542delCT). This mutated allele encodes a truncated form of the receptor (p.P2514Rfs∗4) lacking the C-terminal proline, glutamic acid, serine, and threonine (PEST) degradation domain that increases NOTCH1 signaling duration. NOTCH1 mutation has been associated with poor clinical outcomes in CLL. We validated a highly sensitive and quantitative droplet digital PCR assay for the NOTCH1 delCT mutation, which was anticipated to perform well compared with Sanger sequencing and allele-specific PCR. Performance characteristics of this assay were tested on 126 samples from an unselected CLL cohort and a separate cohort of 85 samples from patients with trisomy 12 CLL. The delCT mutation was detected at allele frequencies as low as 0.024%; 25% of unselected cases and 55% of trisomy 12 cases were positive at the 0.024% detection threshold. Mutational burdens ≥1% were significantly associated with shorter overall survival (OS) in patients with trisomy 12+ disease in multivariate analysis (median OS, 9.1 versus 13 years, with hazard ratio of 2.34; P = 0.031). Mutational burdens <1% correlated with shorter OS in univariate, but not multivariate, analyses. These results suggest that droplet digital PCR testing for NOTCH1 delCT mutation may aid in risk stratification and/or disease monitoring in certain subsets of patients with CLL.
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Affiliation(s)
- Catherine Hoofd
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Steven J Huang
- Leukemia/Bone Marrow Transplant Program of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Samuel Gusscott
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sonya Lam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Rachel Wong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Alexa Johnston
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Helene Bruyere
- Division of Hematology and the Cytogenetics Laboratory, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Tanya L Gillan
- Division of Hematology and the Cytogenetics Laboratory, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Cynthia L Toze
- Leukemia/Bone Marrow Transplant Program of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Alina S Gerrie
- Leukemia/Bone Marrow Transplant Program of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada; Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
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17
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Aoki T, Chong LC, Takata K, Milne K, Hav M, Colombo A, Chavez EA, Nissen M, Wang X, Miyata-Takata T, Lam V, Viganò E, Woolcock BW, Telenius A, Li MY, Healy S, Ghesquiere C, Kos D, Goodyear T, Veldman J, Zhang AW, Kim J, Saberi S, Ding J, Farinha P, Weng AP, Savage KJ, Scott DW, Krystal G, Nelson BH, Mottok A, Merchant A, Shah SP, Steidl C. Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma. Cancer Discov 2019; 10:406-421. [PMID: 31857391 DOI: 10.1158/2159-8290.cd-19-0680] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Hodgkin lymphoma is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of noncancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding cross-talk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 Hodgkin lymphoma tissue specimens and 5 reactive lymph nodes, profiling for the first time the phenotype of the Hodgkin lymphoma-specific immune microenvironment at single-cell resolution. Single-cell expression profiling identified a novel Hodgkin lymphoma-associated subset of T cells with prominent expression of the inhibitory receptor LAG3, and functional analyses established this LAG3+ T-cell population as a mediator of immunosuppression. Multiplexed spatial assessment of immune cells in the microenvironment also revealed increased LAG3+ T cells in the direct vicinity of MHC class II-deficient tumor cells. Our findings provide novel insights into TME biology and suggest new approaches to immune-checkpoint targeting in Hodgkin lymphoma. SIGNIFICANCE: We provide detailed functional and spatial characteristics of immune cells in classic Hodgkin lymphoma at single-cell resolution. Specifically, we identified a regulatory T-cell-like immunosuppressive subset of LAG3+ T cells contributing to the immune-escape phenotype. Our insights aid in the development of novel biomarkers and combination treatment strategies targeting immune checkpoints.See related commentary by Fisher and Oh, p. 342.This article is highlighted in the In This Issue feature, p. 327.
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Affiliation(s)
- Tomohiro Aoki
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren C Chong
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katy Milne
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Monirath Hav
- Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Nissen
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Xuehai Wang
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Tomoko Miyata-Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Vivian Lam
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Elena Viganò
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce W Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Michael Y Li
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shannon Healy
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Chanel Ghesquiere
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Daniel Kos
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Talia Goodyear
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Johanna Veldman
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Allen W Zhang
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jubin Kim
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Gerald Krystal
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Brad H Nelson
- Deeley Research Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anja Mottok
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Akil Merchant
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Pouliot GP, Degar J, Hinze L, Kochupurakkal B, Vo CD, Burns MA, Moreau L, Ganesa C, Roderick J, Peirs S, Menten B, Loh ML, Hunger SP, Silverman LB, Harris MH, Stevenson KE, Weinstock DM, Weng AP, Van Vlierberghe P, D’Andrea AD, Gutierrez A. Fanconi-BRCA pathway mutations in childhood T-cell acute lymphoblastic leukemia. PLoS One 2019; 14:e0221288. [PMID: 31721781 PMCID: PMC6853288 DOI: 10.1371/journal.pone.0221288] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 03/27/2019] [Accepted: 08/02/2019] [Indexed: 01/03/2023] Open
Abstract
BRCA2 (also known as FANCD1) is a core component of the Fanconi pathway and suppresses transformation of immature T-cells in mice. However, the contribution of Fanconi-BRCA pathway deficiency to human T-cell acute lymphoblastic leukemia (T-ALL) remains undefined. We identified point mutations in 9 (23%) of 40 human T-ALL cases analyzed, with variant allele fractions consistent with heterozygous mutations early in tumor evolution. Two of these mutations were present in remission bone marrow specimens, suggesting germline alterations. BRCA2 was the most commonly mutated gene. The identified Fanconi-BRCA mutations encode hypomorphic or null alleles, as evidenced by their inability to fully rescue Fanconi-deficient cells from chromosome breakage, cytotoxicity and/or G2/M arrest upon treatment with DNA cross-linking agents. Disabling the tumor suppressor activity of the Fanconi-BRCA pathway is generally thought to require biallelic gene mutations. However, all mutations identified were monoallelic, and most cases appeared to retain expression of the wild-type allele. Using isogenic T-ALL cells, we found that BRCA2 haploinsufficiency induces selective hypersensitivity to ATR inhibition, in vitro and in vivo. These findings implicate Fanconi-BRCA pathway haploinsufficiency in the molecular pathogenesis of T-ALL, and provide a therapeutic rationale for inhibition of ATR or other druggable effectors of homologous recombination.
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Affiliation(s)
- Gayle P. Pouliot
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - James Degar
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Laura Hinze
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Bose Kochupurakkal
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Chau D. Vo
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Melissa A. Burns
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Lisa Moreau
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Chirag Ganesa
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Justine Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sofie Peirs
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bjorn Menten
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mignon L. Loh
- Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Stephen P. Hunger
- Division of Oncology and the Center for Childhood Cancer Research, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lewis B. Silverman
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marian H. Harris
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Kristen E. Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Andrew P. Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Alan D. D’Andrea
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Center for DNA Damage and Repair and Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail:
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19
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Nissen MD, Kusakabe M, Wang X, Simkin G, Gracias D, Tyshchenko K, Hill A, Meskas J, Hung S, Chavez EA, Ennishi D, Aoki T, Sarkozy C, Connors JM, Farinha P, Slack GW, Gascoyne RD, Brinkman RR, Scott DW, Steidl C, Weng AP. Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity. Cytometry A 2019; 97:620-629. [PMID: 31637838 DOI: 10.1002/cyto.a.23919] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common histologic subtype of non-Hodgkin lymphoma and is notorious for its clinical heterogeneity. Patient outcomes can be predicted by cell-of-origin (COO) classification, demonstrating that the underlying transcriptional signature of malignant B-cells informs biological behavior in the context of standard combination chemotherapy regimens. In the current study, we used mass cytometry (CyTOF) to examine tumor phenotypes at the protein level with single cell resolution in a collection of 27 diagnostic DLBCL biopsy specimens from treatment naïve patients. We found that malignant B-cells from each patient occupied unique regions in 37-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Interestingly, variable MHC class II expression was found to be the greatest contributor to phenotypic diversity. Within individual tumors, a subset of cases showed multiple phenotypic subpopulations, and in one case, we were able to demonstrate direct correspondence between protein-level phenotypic subsets and DNA mutation-defined subclones. In summary, CyTOF analysis can resolve both intertumoral and intratumoral heterogeneity among primary samples and reveals that each case of DLBCL is unique and may be comprised of multiple, genetically distinct subclones. © 2019 International Society for Advancement of Cytometry.
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Affiliation(s)
| | | | - Xuehai Wang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
| | | | - Deanne Gracias
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
| | | | - Ainsleigh Hill
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
| | - Justin Meskas
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada
| | - Stacy Hung
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, Canada
| | | | - Daisuke Ennishi
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, Canada
| | - Tomohiro Aoki
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, Canada
| | | | | | - Pedro Farinha
- Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, Canada
| | - Graham W Slack
- Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, Canada.,Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, Canada
| | | | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, Canada
| | | | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, Canada
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20
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Gusscott S, Tamiro F, Giambra V, Weng AP. Insulin-like growth factor (IGF) signaling in T-cell acute lymphoblastic leukemia. Adv Biol Regul 2019; 74:100652. [PMID: 31543360 DOI: 10.1016/j.jbior.2019.100652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 09/09/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer, characterized by an uncontrolled expansion and accumulation of T-cell progenitors. During leukemic progression, immature T cells grow abnormally and occupy the bone marrow compartment, thereby interfering with the production of normal blood cells. Pediatric T-ALL is curable with intensive chemotherapy, but there are significant, long-term side effects and ~20% of patients suffer relapse for which there are limited treatment options. Adult T-ALL in contrast is largely incurable and refractory/relapsed disease is common despite multi-agent chemotherapy (5-year overall survival of ~40%), and thus new therapeutic targets are needed. We have reported previously on the role of insulin-like growth factor (IGF) signaling in T-ALL, and shown that it exerts potent phenotypes in both leukemia stem cell and bulk tumor cell populations. Modulators of IGF signaling may thus prove useful in improving outcomes in patients with T-ALL. In this review, we summarize the most recent findings relating to IGF signaling in T-ALL and outline therapeutic options using clinically relevant IGF signaling modulators.
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Affiliation(s)
- Samuel Gusscott
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Francesco Tamiro
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada; Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Vincenzo Giambra
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada; Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, FG, Italy
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.
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21
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Healy S, Ennishi D, Bashashati A, Saberi S, Hother C, Mottok A, Chan FC, Chong L, Kridel R, Boyle M, Meissner B, Aoki T, Takata K, Woolcock BW, Vigano E, Abraham L, Gold M, Telenius A, Farinha P, Slack G, Ben-Neriah S, Lai D, Zhang AW, Salehi S, Shulha HP, Chiu DS, Mostafavi S, Gerrie AS, Villa D, Sehn LH, Savage KJJ, Mungall AJJ, Weng AP, Bally M, Morin RD, Freue GVC, Connors JM, Marra MA, Shah SP, Gascoyne1 RD, Scott DW, Steidl C, Steidl U. Abstract 3480: TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3480] [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
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma subtype worldwide, accounting for 40% of all non-Hodgkin lymphomas. DLBCL presents as an aggressive disease requiring immediate treatment. Although significant improvement in outcome has been achieved, ~40% of patients still experience treatment failure. Here, we characterized the recurrent genetic alterations and transcriptomic signatures in diagnostic biopsies from a population registry-based cohort of 347 patients with de novo DLBCL uniformly treated with R-CHOP. This analysis revealed bi-allelic loss of function mutations of TMEM30A that were associated with favorable treatment outcome. TMEM30A is a chaperone protein, involved in maintaining the asymmetric distribution of phosphatidylethanolamine and phosphatidylserine, an integral component of the plasma membrane and “eat-me” signal recognized by macrophages. Using TMEM30A knockout systems by CRISPR genome editing techniques, we have functionally characterized this loss-of-function mutation in representative human and mouse DLBCL cell line models. We have discovered that TMEM30A loss is associated with increased B-cell signaling following antigen stimulation, including a two-fold increase in the diffusion rate of B-cell receptor (BCR) clustering, using high resolution Single Particle Tracking (SPT) technology. In addition, we have measured three-fold increase in chemotherapeutic drug accumulation in both knockout cell lines and randomly selected patient biopsies with TMEM30A biallelic loss. This observation was validated in a xenograft mouse model, which presented improved survival and limited tumor growth following vincristine treatment in mice injected with TMEM30A null DLBCL cell lines compared with native cell lines. This phenotype explains the improved prognosis observed in DLBCL patients following R-CHOP treatment. Furthermore, we have observed over two fold higher numbers of tumor-associated macrophages in B-cell lymphoma syngeneic mouse models with Tmem30a loss-of-function, prior to any form of treatment, suggesting the existence of “hot” and primed tumors. Our data highlight a multi-faceted role for TMEM30A and plasma membrane physiology in B-cell lymphomagenesis, and characterize intrinsic and extrinsic vulnerabilities of cancer cells that can be therapeutically exploited. Characterization of these mechanisms will address a missing link in the cancer field as related insights in lymphoma will outline therapeutic approaches that can be extended to cancer therapy in general.
Citation Format: Shannon Healy, Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W. Woolcock, Elena Vigano, Libin Abraham, Michael Gold, Adele Telenius, Pedro Farinha, Graham Slack, Susana Ben-Neriah, Daniel Lai, Allen W. Zhang, Sohrab Salehi, Hennady P. Shulha, Derek S. Chiu, Sara Mostafavi, Alina S. Gerrie, Diego Villa, Laurie H. Sehn, Kerry J. J. Savage, Andrew J. J. Mungall, Andrew P. Weng, Marcel Bally, Ryan D. Morin, Gabriela V. Cohen Freue, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne1, David W. Scott, Christian Steidl, Ulrich Steidl. TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3480.
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Affiliation(s)
- Shannon Healy
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Saeed Saberi
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Anja Mottok
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fong Chun Chan
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren Chong
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Kridel
- 3University Health Network, Toronto, Ontario, Canada
| | - Merrill Boyle
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Tomohiro Aoki
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Elena Vigano
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Libin Abraham
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Gold
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Pedro Farinha
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Graham Slack
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Daniel Lai
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sohrab Salehi
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Derek S. Chiu
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara Mostafavi
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Diego Villa
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | | | - Marcel Bally
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- 4Simon Fraser University, Vancouver, British Columbia, Canada
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22
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Giambra V, Gusscott S, Gracias D, Song R, Lam SH, Panelli P, Tyshchenko K, Jenkins CE, Hoofd C, Lorzadeh A, Carles A, Hirst M, Eaves CJ, Weng AP. Epigenetic Restoration of Fetal-like IGF1 Signaling Inhibits Leukemia Stem Cell Activity. Cell Stem Cell 2018; 23:714-726.e7. [PMID: 30269902 DOI: 10.1016/j.stem.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 10/27/2017] [Revised: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022]
Abstract
Acute leukemias are aggressive malignancies of developmentally arrested hematopoietic progenitors. We sought here to explore the possibility that changes in hematopoietic stem/progenitor cells during development might alter the biology of leukemias arising from this tissue compartment. Using a mouse model of acute T cell leukemia, we found that leukemias generated from fetal liver (FL) and adult bone marrow (BM) differed dramatically in their leukemia stem cell activity with FL leukemias showing markedly reduced serial transplantability as compared to BM leukemias. We present evidence that this difference is due to NOTCH1-driven autocrine IGF1 signaling, which is active in FL cells but restrained in BM cells by EZH2-dependent H3K27 trimethylation. Further, we confirmed this mechanism is operative in human disease and show that enforced IGF1 signaling effectively limits leukemia stem cell activity. These findings demonstrate that resurrecting dormant fetal programs in adult cells may represent an alternate therapeutic approach in human cancer.
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Affiliation(s)
- Vincenzo Giambra
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy.
| | - Samuel Gusscott
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Deanne Gracias
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Raymond Song
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Sonya H Lam
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Patrizio Panelli
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | | | | | - Catherine Hoofd
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Alireza Lorzadeh
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Annaick Carles
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Martin Hirst
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
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23
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Weiswald LB, Hasan MR, Wong JCT, Pasiliao CC, Rahman M, Ren J, Yin Y, Gusscott S, Vacher S, Weng AP, Kennecke HF, Bièche I, Schaeffer DF, Yapp DT, Tai IT. Inactivation of the Kinase Domain of CDK10 Prevents Tumor Growth in a Preclinical Model of Colorectal Cancer, and Is Accompanied by Downregulation of Bcl-2. Mol Cancer Ther 2017; 16:2292-2303. [PMID: 28663269 DOI: 10.1158/1535-7163.mct-16-0666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/15/2017] [Accepted: 06/23/2017] [Indexed: 11/16/2022]
Abstract
Cyclin-dependent kinase 10 (CDK10), a CDC2-related kinase, is highly expressed in colorectal cancer. Its role in the pathogenesis of colorectal cancer is unknown. This study examines the function of CDK10 in colorectal cancer, and demonstrates its role in suppressing apoptosis and in promoting tumor growth in vitro and in vivo Modulation of CDK10 expression in colorectal cancer cell lines demonstrates that CDK10 promotes cell growth, reduces chemosensitivity and inhibits apoptosis by upregulating the expression of Bcl-2. This effect appears to depend on its kinase activity, as kinase-defective mutant colorectal cancer cell lines have an exaggerated apoptotic response and reduced proliferative capacity. In vivo, inhibiting CDK10 in colorectal cancer following intratumoral injections of lentivirus-mediated CDK10 siRNA in a patient-derived xenograft mouse model demonstrated its efficacy in suppressing tumor growth. Furthermore, using a tissue microarray of human colorectal cancer tissues, the potential for CDK10 to be a prognostic biomarker in colorectal cancer was explored. In tumors of individuals with colorectal cancer, high expression of CDK10 correlates with earlier relapse and shorter overall survival. The findings of this study indicate that CDK10 plays a role in the pathogenesis in colorectal cancer and may be a potential therapeutic target for treatment. Mol Cancer Ther; 16(10); 2292-303. ©2017 AACR.
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Affiliation(s)
- Louis-Bastien Weiswald
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mohammad R Hasan
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - John C T Wong
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Clarissa C Pasiliao
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mahbuba Rahman
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jianhua Ren
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yaling Yin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Surveillance & Outcomes, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Samuel Gusscott
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Vacher
- Department of Genetics, Institute Curie, Paris, France
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Hagen F Kennecke
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Ivan Bièche
- Department of Genetics, Institute Curie, Paris, France
| | - David F Schaeffer
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald T Yapp
- Experimental Therapeutics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Isabella T Tai
- Division of Gastroenterology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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24
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Brown SD, Hapgood G, Steidl C, Weng AP, Savage KJ, Holt RA. Defining the clonality of peripheral T cell lymphomas using RNA-seq. Bioinformatics 2017; 33:1111-1115. [PMID: 28003262 PMCID: PMC5408843 DOI: 10.1093/bioinformatics/btw810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 01/09/2023] Open
Abstract
Motivation In T-cell lymphoma, malignant T cells arising from a founding clone share an identical T cell receptor (TCR) and can be identified by the over-representation of this TCR relative to TCRs from the patient’s repertoire of normal T cells. Here, we demonstrate that TCR information extracted from RNA-seq data can provide a higher resolution view of peripheral T cell lymphomas (PTCLs) than that provided by conventional methods. Results For 60 subjects with PTCL, flow cytometry/FACS was used to identify and sort aberrant T cell populations from diagnostic lymph node cell suspensions. For samples that did not appear to contain aberrant T cell populations, T helper (TH), T follicular helper (TFH) and cytotoxic T lymphocyte (CTL) subsets were sorted. RNA-seq was performed on sorted T cell populations, and TCR alpha and beta chain sequences were extracted and quantified directly from the RNA-seq data. 96% of the immunophenotypically aberrant samples had a dominant T cell clone readily identifiable by RNA-seq. Of the samples where no aberrant population was found by flow cytometry, 80% had a dominant clone by RNA-seq. This demonstrates the increased sensitivity and diagnostic ability of RNA-seq over flow cytometry and shows that the presence of a normal immunophenotype does not exclude clonality. Availability and Implementation R scripts used in the processing of the data are available online at https://www.github.com/scottdbrown/RNAseq-TcellClonality Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Greg Hapgood
- Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, Department of Lymphoid Cancer Research, British Columbia Cancer Agency, Vancouver, Canada
| | - Andrew P Weng
- Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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25
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Sasaki T, Rivera-Mulia JC, Vera D, Zimmerman J, Das S, Padget M, Nakamichi N, Chang BH, Tyner J, Druker BJ, Weng AP, Civin CI, Eaves CJ, Gilbert DM. Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia. Exp Hematol 2017; 51:71-82.e3. [PMID: 28433605 DOI: 10.1016/j.exphem.2017.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/25/2017] [Accepted: 04/08/2017] [Indexed: 01/10/2023]
Abstract
Genome-wide DNA replication timing (RT) profiles reflect the global three-dimensional chromosome architecture of cells. They also provide a comprehensive and unique megabase-scale picture of cellular epigenetic state. Thus, normal differentiation involves reproducible changes in RT, and transformation generally perturbs these, although the potential effects of altered RT on the properties of transformed cells remain largely unknown. A major challenge to interrogating these issues in human acute lymphoid leukemia (ALL) is the low proliferative activity of most of the cells, which may be further reduced in cryopreserved samples and difficult to overcome in vitro. In contrast, the ability of many human ALL cell populations to expand when transplanted into highly immunodeficient mice is well documented. To examine the stability of DNA RT profiles of serially passaged xenografts of primary human B- and T-ALL cells, we first devised a method that circumvents the need for bromodeoxyuridine incorporation to distinguish early versus late S-phase cells. Using this and more standard protocols, we found consistently strong retention in xenografts of the original patient-specific RT features. Moreover, in a case in which genomic analyses indicated changing subclonal dynamics in serial passages, the RT profiles tracked concordantly. These results indicate that DNA RT is a relatively stable feature of human ALLs propagated in immunodeficient mice. In addition, they suggest the power of this approach for future interrogation of the origin and consequences of altered DNA RT in ALL.
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Affiliation(s)
- Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Daniel Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL
| | - Jared Zimmerman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Sunny Das
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Michelle Padget
- Departments of Pediatrics and Physiology, Center for Stem Cell Biology & Regenerative Medicine, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD
| | - Naoto Nakamichi
- Terry Fox Laboratory, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - Bill H Chang
- Division of Hematology and Oncology, Departments of Pediatrics and Medicine, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Jeff Tyner
- Department of Cell, Development, and Cancer Biology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Brian J Druker
- Department of Cell, Development, and Cancer Biology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, OR; Howard Hughes Medical Institute, Chevy Chase, MD
| | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - Curt I Civin
- Departments of Pediatrics and Physiology, Center for Stem Cell Biology & Regenerative Medicine, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency Vancouver, Vancouver, BC, Canada
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL.
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26
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Gusscott S, Jenkins CE, Lam SH, Giambra V, Pollak M, Weng AP. IGF1R Derived PI3K/AKT Signaling Maintains Growth in a Subset of Human T-Cell Acute Lymphoblastic Leukemias. PLoS One 2016; 11:e0161158. [PMID: 27532210 PMCID: PMC4988785 DOI: 10.1371/journal.pone.0161158] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 07/26/2015] [Accepted: 08/01/2016] [Indexed: 11/19/2022] Open
Abstract
Insulin-like growth factor 1 receptor (IGF1R) is a prevalent signaling pathway in human cancer that supports cell growth/survival and thus contributes to aggressive biological behavior. Much work has gone into development of IGF1R inhibitors; however, candidate agents including small molecule tyrosine kinase inhibitors and blocking antibodies have yet to fulfill their promise clinically. Understanding cellular features that define sensitivity versus resistance are important for effective patient selection and anticipation of outgrowth of a resistant clone. We previously identified an important role for IGF signaling in T-cell acute lymphoblastic leukemia (T-ALL) relying primarily upon genetically defined mouse models. We present here an assessment of IGF1R dependence in human T-ALL using a broad panel of 27 established cell lines that capture a spectrum of the genetic variation that might be encountered in clinical practice. We observed that a subset of cell lines are sensitive to IGF1R inhibition and are characterized by high levels of surface IGF1R expression and PTEN positivity. Interestingly, lentiviral expression or knock-down of PTEN in PTEN-negative/positive cell lines, respectively, had limited effects on their response to IGF1R inhibition, suggesting that PTEN contributes to, but does not define IGF dependence. Additionally, we characterize downstream PI3K/AKT signaling as dominant over RAS/RAF/MEK/ERK in mediating growth and/or survival in this context. Finally, we demonstrate that IGF and interleukin-7 (IL-7) fulfill non-overlapping roles in supporting T-ALL growth. These findings are significant in that they reveal cellular features and downstream mechanisms that may determine the response of an individual patient’s tumor to IGF1R inhibitor therapy.
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Affiliation(s)
- Samuel Gusscott
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | | | - Sonya H. Lam
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Vincenzo Giambra
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Michael Pollak
- Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- * E-mail:
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27
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Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016; 30:183. [PMID: 27479034 DOI: 10.1016/j.ccell.2016.06.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Parker JDK, Shen Y, Pleasance E, Li Y, Schein JE, Zhao Y, Moore R, Wegrzyn-Woltosz J, Savage KJ, Weng AP, Gascoyne RD, Jones S, Marra M, Laskin J, Karsan A. Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing. Cold Spring Harb Mol Case Stud 2016; 2:a000679. [PMID: 27148583 PMCID: PMC4849852 DOI: 10.1101/mcs.a000679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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] [Indexed: 11/24/2022] Open
Abstract
In an attempt to assess potential treatment options, whole-genome and transcriptome sequencing were performed on a patient with an unclassifiable small lymphoproliferative disorder. Variants from genome sequencing were prioritized using a combination of comparative variant distributions in a spectrum of lymphomas, and meta-analyses of gene expression profiling. In this patient, the molecular variants that we believe to be most relevant to the disease presentation most strongly resemble a diffuse large B-cell lymphoma (DLBCL), whereas the gene expression data are most consistent with a low-grade chronic lymphocytic leukemia (CLL). The variant of greatest interest was a predicted NOTCH2-truncating mutation, which has been recently reported in various lymphomas.
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Affiliation(s)
- Jeremy D K Parker
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yvonne Li
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Jacqueline E Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Joanna Wegrzyn-Woltosz
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Steven Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Marco Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Janessa Laskin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
| | - Aly Karsan
- Genome Sciences Centre and Department of Pathology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
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29
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Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekofer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LeBoeuf NR, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016; 29:574-586. [PMID: 27070704 PMCID: PMC5177991 DOI: 10.1016/j.ccell.2016.03.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/25/2016] [Accepted: 03/11/2016] [Indexed: 01/22/2023]
Abstract
More than 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publicly available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment, called the Public Repository of Xenografts (PRoXe). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease.
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Affiliation(s)
- Elizabeth C Townsend
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Mark A Murakami
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Alexandra Christodoulou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Amanda L Christie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Johannes Köster
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tiffany A DeSouza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Scott P Kallgren
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Huiyun Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Shuo-Chieh Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Olivia Plana
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Kristen E Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prakash Rao
- Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Raga Vadhi
- Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Michael Andreeff
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Karen K Ballen
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Patrizia Barzaghi-Rinaudo
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Sarah Cahill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vesselina G Cooke
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hilary Eaton
- Office of Research and Technology Ventures, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin L Ebert
- Department of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Julia Etchin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brant Firestone
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - David C Fisher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Arnold S Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Ilene A Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Hui Gao
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | | | - Timothy A Graubert
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ensar Halilovic
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, MA 02215, USA
| | - Zachary T Herbert
- Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven M Horwitz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Giorgio Inghirami
- Department of Pathology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Andrew M Intlekofer
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Moriko Ito
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Shai Izraeli
- Functional Genomics and Leukemia Research, Sheba Medical Center, Tel Hashomer and Tel Aviv University, Ramat Gan, 52621, Israel
| | - Eric D Jacobsen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Caron A Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Sébastien Jeay
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Irmela Jeremias
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistraße 25, 81377 Munich, Germany; Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Raphael Koch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Marina Konopleva
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadja Kopp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Steven M Kornblau
- Leukemia Division, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Thomas S Kupper
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ann S LaCasce
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Emma Lees
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Loretta S Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Masato Murakami
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Markus Muschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Samuel Y Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Oreofe O Odejide
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rachel R Paquette
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brent Shoji
- Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Jerome Tamburini
- Université Paris Descartes, Faculté de Médecine Sorbonne Paris Cité, 75005 Paris, France
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Marion Wiesmann
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Andrew P Weng
- Department of Pathology, British Columbia Cancer Research Center, Vancouver V5Z 1H8, Canada
| | - Jens U Wuerthner
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - David A Williams
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Bruce M Wollison
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Monica M Bertagnolli
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Center for Functional Cancer Epigenomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Margaret A Shipp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 450 Brookline Avenue, Dana 510B, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Belmonte M, Hoofd C, Weng AP, Giambra V. Targeting leukemia stem cells: which pathways drive self-renewal activity in T-cell acute lymphoblastic leukemia? ACTA ACUST UNITED AC 2016; 23:34-41. [PMID: 26966402 DOI: 10.3747/co.23.2806] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
T-Cell acute lymphoblastic leukemia (t-all) is a malignancy of white blood cells, characterized by an uncontrolled accumulation of T-cell progenitors. During leukemic progression, immature T cells grow abnormally and crowd into the bone marrow, preventing it from making normal blood cells and spilling out into the bloodstream. Recent studies suggest that only discrete cell populations that possess the ability to recreate the entire tumour might be responsible for the initiation and propagation of t-all. Those unique cells are commonly called "cancer stem cells" or, in the case of hematopoietic malignancies, "leukemia stem cells" (lscs). Like normal hematopoietic stem cells, lscs are thought to be capable of self-renewal, during which, by asymmetrical division, they give rise to an identical copy of themselves as well as to a daughter cell that is no longer capable of self-renewal activity and represents a more "differentiated" progeny. Here, we review the main pathways of self-renewal activity in lscs, focusing on their involvement in the maintenance and development of t-all. New stem cell-directed therapies and lsc-targeted agents are also discussed.
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Affiliation(s)
- M Belmonte
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC
| | - C Hoofd
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC
| | - A P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC
| | - V Giambra
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC
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31
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Lai CK, Moon Y, Kuchenbauer F, Starzcynowski DT, Argiropoulos B, Yung E, Beer P, Schwarzer A, Sharma A, Park G, Leung M, Lin G, Vollett S, Fung S, Eaves CJ, Karsan A, Weng AP, Humphries RK, Heuser M. Cell fate decisions in malignant hematopoiesis: leukemia phenotype is determined by distinct functional domains of the MN1 oncogene. PLoS One 2014; 9:e112671. [PMID: 25401736 PMCID: PMC4234417 DOI: 10.1371/journal.pone.0112671] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/10/2014] [Indexed: 12/02/2022] Open
Abstract
Extensive molecular profiling of leukemias and preleukemic diseases has revealed that distinct clinical entities, like acute myeloid (AML) and T-lymphoblastic leukemia (T-ALL), share similar pathogenetic mutations. It is not well understood how the cell of origin, accompanying mutations, extracellular signals or structural differences in a mutated gene determine the phenotypic identity of leukemias. We dissected the functional aspects of different protein regions of the MN1 oncogene and their effect on the leukemic phenotype, building on the ability of MN1 to induce leukemia without accompanying mutations. We found that the most C-terminal region of MN1 was required to block myeloid differentiation at an early stage, and deletion of an extended C-terminal region resulted in loss of myeloid identity and cell differentiation along the T-cell lineage in vivo. Megakaryocytic/erythroid lineage differentiation was blocked by the N-terminal region. In addition, the N-terminus was required for proliferation and leukemogenesis in vitro and in vivo through upregulation of HoxA9, HoxA10 and Meis2. Our results provide evidence that a single oncogene can modulate cellular identity of leukemic cells based on its active gene regions. It is therefore likely that different mutations in the same oncogene may impact cell fate decisions and phenotypic appearance of malignant diseases.
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Affiliation(s)
- Courteney K. Lai
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yeonsook Moon
- Department of Laboratory Medicine, Medical School of Inha University, Incheon, Korea
| | - Florian Kuchenbauer
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
- Institute of Experimental Cancer Research, Comprehensive Cancer Centre, University Hospital of Ulm, Ulm, Germany
| | - Daniel T. Starzcynowski
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Bob Argiropoulos
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Eric Yung
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Philip Beer
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Amit Sharma
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Gyeongsin Park
- Department of Hospital Pathology, Catholic University of Korea, Seoul, Korea
| | - Malina Leung
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Grace Lin
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Sarah Vollett
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Stephen Fung
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
| | - Connie J. Eaves
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Aly Karsan
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - R. Keith Humphries
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC, Canada
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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32
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Gutierrez A, Pan L, Groen R, Baleydier F, Kentsis A, Marineau J, Grebliunaite R, Kozakewich E, Reed C, Pflumio F, Poglio S, Uzan B, Clemons P, Verplank L, An F, Burbank J, Norton S, Tolliday N, Steen H, Weng AP, Yuan H, Bradner JE, Mitsiades C, Look AT, Aster JC. Abstract IA8: A new class of drugs active in T-ALL is revealed in a zebrafish screen. Mol Cancer Res 2014. [DOI: 10.1158/1557-3125.modorg-ia8] [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
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer frequently associated with activating NOTCH1 mutations and dysregulation of MYC. We performed two complementary screens to identify novel agents with activity against T-ALL: i) a zebrafish screen for small molecules toxic to MYC-overexpressing thymocytes, and ii) a human T-ALL cell line screen for small molecules that synergize with Notch inhibitors. “Hits” common to both screens included perphenazine, a phenothiazine antipsychotic that induced apoptosis of fish, mouse, and human T-ALL cells. Using ligand-affinity chromatography coupled to mass spectrometry, we identified protein phosphatase 2A (PP2A) as the critical perphenazine target. In line with this finding, T-ALL cell lines treated with perphenazine underwent apoptosis associated with rapid dephosphorylation of multiple PP2A substrates, indicating that perphenazine binds and activates the PP2A tumor supressor. Moreover, shRNA knockdown of the scaffolding or catalytic subunits of PP2A attenuated the activity of perphenazine, indicating that PP2A is required for its antileukemic activity. Finally, treatment of primary human T-ALLs with pherphenazine suppressed cell growth and caused dephosphorylated of PP2A targets in vitro and in vivo. Our findings provide a mechanistic explanation for the recurrent “rediscovery” of phenothiazines as a class of drugs with anti-cancer effects and highlight the therapeutic potential of pharmacologic PP2A activation in T-ALL and other cancers driven by hyperphosphorylated PP2A substrates.
Citation Format: Alejandro Gutierrez, Li Pan, Richard Groen, Frederic Baleydier, Alex Kentsis, Jason Marineau, Ruta Grebliunaite, Elena Kozakewich, Casie Reed, Francoise Pflumio, Sandrine Poglio, Benjamin Uzan, Paul Clemons, Lynn Verplank, Frank An, Jason Burbank, Stephanie Norton, Nicola Tolliday, Hanno Steen, Andrew P. Weng, Huipin Yuan, James E. Bradner, Constantine Mitsiades, A. Thomas Look, Jon C. Aster. A new class of drugs active in T-ALL is revealed in a zebrafish screen. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr IA8.
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Affiliation(s)
- Alejandro Gutierrez
- 1Dana-Farber Cancer Institute, Boston, MA,
- 5Boston Children's Hospital, Boston, MA,
| | - Li Pan
- 2Brigham & Women's Hospital, Boston, MA,
| | - Richard Groen
- 1Dana-Farber Cancer Institute, Boston, MA,
- 8University of Utrecht, Utrecht, Netherlands,
| | - Frederic Baleydier
- 2Brigham & Women's Hospital, Boston, MA,
- 9Hospices Civils de Lyon, Lyon, France,
| | - Alex Kentsis
- 1Dana-Farber Cancer Institute, Boston, MA,
- 5Boston Children's Hospital, Boston, MA,
| | | | | | | | - Casie Reed
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Francoise Pflumio
- 3Institut National de la Santé et de la Recherche Médicale, Fontenay-aux-Roses and Université Paris-Sud, Fontenay-aux-Roses, France,
- 10Université Paris-Diderot, Paris, France
| | - Sandrine Poglio
- 3Institut National de la Santé et de la Recherche Médicale, Fontenay-aux-Roses and Université Paris-Sud, Fontenay-aux-Roses, France,
- 10Université Paris-Diderot, Paris, France
| | - Benjamin Uzan
- 3Institut National de la Santé et de la Recherche Médicale, Fontenay-aux-Roses and Université Paris-Sud, Fontenay-aux-Roses, France,
- 10Université Paris-Diderot, Paris, France
| | | | | | - Frank An
- 4Broad Institute, Cambridge, MA,
| | | | | | | | | | | | - Huipin Yuan
- 7University of Twente, Enschede, Netherlands,
| | | | | | - A. Thomas Look
- 1Dana-Farber Cancer Institute, Boston, MA,
- 5Boston Children's Hospital, Boston, MA,
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Bentley VL, Veinotte CJ, Corkery DP, Pinder JB, LeBlanc MA, Bedard K, Weng AP, Berman JN, Dellaire G. Focused chemical genomics using zebrafish xenotransplantation as a pre-clinical therapeutic platform for T-cell acute lymphoblastic leukemia. Haematologica 2014; 100:70-6. [PMID: 25281505 DOI: 10.3324/haematol.2014.110742] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer therapeutics is evolving to precision medicine, with the goal of matching targeted compounds with molecular aberrations underlying a patient's cancer. While murine models offer a pre-clinical tool, associated costs and time are not compatible with actionable patient-directed interventions. Using the paradigm of T-cell acute lymphoblastic leukemia, a high-risk disease with defined molecular underpinnings, we developed a zebrafish human cancer xenotransplantation model to inform therapeutic decisions. Using a focused chemical genomic approach, we demonstrate that xenografted cell lines harboring mutations in the NOTCH1 and PI3K/AKT pathways respond concordantly to their targeted therapies, patient-derived T-cell acute lymphoblastic leukemia can be successfully engrafted in zebrafish and specific drug responses can be quantitatively determined. Using this approach, we identified a mutation sensitive to γ-secretase inhibition in a xenograft from a child with T-cell acute lymphoblastic leukemia, confirmed by Sanger sequencing and validated as a gain-of-function NOTCH1 mutation. The zebrafish xenotransplantation platform provides a novel cost-effective means of tailoring leukemia therapy in real time.
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Affiliation(s)
| | | | - Dale P Corkery
- Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS
| | | | | | | | - Andrew P Weng
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC
| | - Jason N Berman
- IWK Health Centre, Halifax, NS Pediatrics and Microbiology & Immunology Dalhousie University, Halifax, NS, Canada
| | - Graham Dellaire
- Pathology, Dalhousie University, Halifax, NS Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS
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34
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Gutierrez A, Pan L, Groen RWJ, Baleydier F, Kentsis A, Marineau J, Grebliunaite R, Kozakewich E, Reed C, Pflumio F, Poglio S, Uzan B, Clemons P, VerPlank L, An F, Burbank J, Norton S, Tolliday N, Steen H, Weng AP, Yuan H, Bradner JE, Mitsiades C, Look AT, Aster JC. Phenothiazines induce PP2A-mediated apoptosis in T cell acute lymphoblastic leukemia. J Clin Invest 2014; 124:644-55. [PMID: 24401270 DOI: 10.1172/jci65093] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/30/2013] [Indexed: 12/15/2022] Open
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer that is frequently associated with activating mutations in NOTCH1 and dysregulation of MYC. Here, we performed 2 complementary screens to identify FDA-approved drugs and drug-like small molecules with activity against T-ALL. We developed a zebrafish system to screen small molecules for toxic activity toward MYC-overexpressing thymocytes and used a human T-ALL cell line to screen for small molecules that synergize with Notch inhibitors. We identified the antipsychotic drug perphenazine in both screens due to its ability to induce apoptosis in fish, mouse, and human T-ALL cells. Using ligand-affinity chromatography coupled with mass spectrometry, we identified protein phosphatase 2A (PP2A) as a perphenazine target. T-ALL cell lines treated with perphenazine exhibited rapid dephosphorylation of multiple PP2A substrates and subsequent apoptosis. Moreover, shRNA knockdown of specific PP2A subunits attenuated perphenazine activity, indicating that PP2A mediates the drug's antileukemic activity. Finally, human T-ALLs treated with perphenazine exhibited suppressed cell growth and dephosphorylation of PP2A targets in vitro and in vivo. Our findings provide a mechanistic explanation for the recurring identification of phenothiazines as a class of drugs with anticancer effects. Furthermore, these data suggest that pharmacologic PP2A activation in T-ALL and other cancers driven by hyperphosphorylated PP2A substrates has therapeutic potential.
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35
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Sanda T, Tyner JW, Gutierrez A, Ngo VN, Glover J, Chang BH, Yost A, Ma W, Fleischman AG, Zhou W, Yang Y, Kleppe M, Ahn Y, Tatarek J, Kelliher MA, Neuberg DS, Levine RL, Moriggl R, Müller M, Gray NS, Jamieson CHM, Weng AP, Staudt LM, Druker BJ, Look AT. TYK2-STAT1-BCL2 pathway dependence in T-cell acute lymphoblastic leukemia. Cancer Discov 2013; 3:564-77. [PMID: 23471820 DOI: 10.1158/2159-8290.cd-12-0504] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
UNLABELLED Targeted molecular therapy has yielded remarkable outcomes in certain cancers, but specific therapeutic targets remain elusive for many others. As a result of two independent RNA interference (RNAi) screens, we identified pathway dependence on a member of the Janus-activated kinase (JAK) tyrosine kinase family, TYK2, and its downstream effector STAT1, in T-cell acute lymphoblastic leukemia (T-ALL). Gene knockdown experiments consistently showed TYK2 dependence in both T-ALL primary specimens and cell lines, and a small-molecule inhibitor of JAK activity induced T-ALL cell death. Activation of this TYK2-STAT1 pathway in T-ALL cell lines occurs by gain-of-function TYK2 mutations or activation of interleukin (IL)-10 receptor signaling, and this pathway mediates T-ALL cell survival through upregulation of the antiapoptotic protein BCL2. These findings indicate that in many T-ALL cases, the leukemic cells are dependent upon the TYK2-STAT1-BCL2 pathway for continued survival, supporting the development of molecular therapies targeting TYK2 and other components of this pathway. SIGNIFICANCE In recent years, "pathway dependence" has been revealed in specific types of human cancer, which can be important because they pinpoint proteins that are particularly vulnerable to antitumor-targeted inhibition (so-called Achilles’ heel proteins). Here, we use RNAi technology to identify a novel oncogenic pathway that involves aberrant activation of the TYK2 tyrosine kinase and its downstream substrate, STAT1, which ultimately promotes T-ALL cell survival through the upregulation of BCL2 expression
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Affiliation(s)
- Takaomi Sanda
- Department of Pediatric Oncology, Children's Hospital, Boston, MA, USA
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Giambra V, Jenkins CR, Wang H, Lam SH, Shevchuk OO, Nemirovsky O, Wai C, Gusscott S, Chiang MY, Aster JC, Humphries RK, Eaves C, Weng AP. NOTCH1 promotes T cell leukemia-initiating activity by RUNX-mediated regulation of PKC-θ and reactive oxygen species. Nat Med 2012; 18:1693-8. [PMID: 23086478 PMCID: PMC3738873 DOI: 10.1038/nm.2960] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [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: 09/10/2010] [Accepted: 08/29/2012] [Indexed: 12/19/2022]
Abstract
Reactive oxygen species (ROS), a by-product of cellular metabolism, damage intracellular macromolecules and, in excess, can promote normal hematopoietic stem cell differentiation and exhaustion1–3. However, mechanisms that regulate ROS levels in leukemia-initiating cells (LICs) and the biological role of ROS in these cells remain largely unknown. We show here the ROSlow subset of CD44+ cells in T-cell acute lymphoblastic leukemia (T-ALL), a malignancy of immature T-cell progenitors, to be highly enriched in the most aggressive LICs, and that ROS are maintained at low levels by downregulation of protein kinase C theta (PKCθ). Strikingly, primary mouse T-ALLs lacking PKCθ show improved LIC activity whereas enforced PKCθ expression in both mouse and human primary T-ALLs compromised LIC activity. We also demonstrate that PKCθ is positively regulated by RUNX1, and that NOTCH1, which is frequently activated by mutation in T-ALL4–6 and required for LIC activity in both mouse and human models7,8, downregulates PKCθ and ROS via a novel pathway involving induction of RUNX3 and subsequent repression of RUNX1. These results reveal key functional roles for PKCθ and ROS in T-ALL and suggest that aggressive biological behavior in vivo could be limited by therapeutic strategies that promote PKCθ expression/activity or ROS accumulation.
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Affiliation(s)
- Vincenzo Giambra
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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37
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Jenkins CE, Shevchuk OO, Giambra V, Lam SH, Carboni JM, Gottardis MM, Holzenberger M, Pollak M, Humphries RK, Weng AP. IGF signaling contributes to malignant transformation of hematopoietic progenitors by the MLL-AF9 oncoprotein. Exp Hematol 2012; 40:715-723.e6. [PMID: 22613471 DOI: 10.1016/j.exphem.2012.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 12/14/2022]
Abstract
Malignant transformation of normal hematopoietic progenitors is a multistep process that likely requires interaction between collaborating oncogenic signals at critical junctures. For instance, the MLL-AF9 fusion oncogene is thought to contribute to myeloid leukemogenesis by driving a hematopoietic stem cell-like "self-renewal" gene expression signature in committed myeloid progenitors. In addition, insulin-like growth factor (IGF) signaling has been implicated in self-renewal/pluripotency in hematopoietic and embryonic stem cell contexts and supports cell growth/survival by activation of downstream pathways, including phosphatidylinositol 3-kinase/Akt and Ras/Raf/extracellular signal-regulated kinase. We hypothesized that IGF signaling could be an important contributor in the process of cellular transformation and/or clonal propagation. Utilizing an MLL-AF9 mouse bone marrow transplantation model of acute myelogenous leukemia, we discovered that committed myeloid progenitor cells with genetically reduced levels of IGF1R were less susceptible to leukemogenic transformation due, at least in part, to a cell-autonomous defect in clonogenic activity. Rather unexpectedly, genetic deletion of IGF1R by inducible Cre recombinase had no effect on growth/survival of established leukemia cells. These findings suggest that IGF1R signaling contributes to transformation of normal myeloid progenitor cells, but is not required for propagation of the leukemic clone once it has become established. We also show that treatment of mouse MLL-AF9 acute myelogenous leukemia cells with BMS-536924, an IGF1R/insulin receptor-selective tyrosine kinase inhibitor, blocked cell growth, suggesting its efficacy in this model may be due to inhibition of insulin receptor and/or related tyrosine kinases, and raising the possibility that similar IGF1R inhibitors in clinical development may be acting through alternate/related pathways.
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Affiliation(s)
- Catherine E Jenkins
- Terry Fox Laboratory/Department of Pathology, BC Cancer Agency, Vancouver, BC, Canada
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38
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Bashashati A, Johnson NA, Khodabakhshi AH, Whiteside MD, Zare H, Scott DW, Lo K, Gottardo R, Brinkman FS, Connors JM, Slack GW, Gascoyne RD, Weng AP, Brinkman RR. B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma. Am J Clin Pathol 2012; 137:805-14. [PMID: 22523221 DOI: 10.1309/ajcpgr8bg4jdvowr] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Despite advances in the understanding of diffuse large B-cell lymphoma (DLBCL) biology, only the clinically based International Prognostic Index (IPI) is used routinely for risk stratification at diagnosis. To find novel prognostic markers, we analyzed flow cytometric data from 229 diagnostic DLBCL samples using an automated multiparameter data analysis approach developed in our laboratory. By using the developed automated data analysis pipeline, we identified 71 of 229 cases as having more than 35% B cells with a high side scatter (SSC) profile, a parameter reflecting internal cellular complexity. This high SSC B-cell feature was associated with inferior overall and progression-free survival (P = .001 and P = .01, respectively) and remained a significant predictor of overall survival in multivariate Cox regression analysis (IPI, P = .001; high SSC, P = .004; rituximab, P = .53). This study suggests that high SSC among B cells may serve as a useful biomarker to identify patients with DLBCL at high risk for relapse. This is of particular interest because this biomarker is readily available in most clinical laboratories without significant alteration to existing routine diagnostic strategies or incurring additional costs.
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39
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Gusscott S, Kuchenbauer F, Humphries RK, Weng AP. Notch-mediated repression of miR-223 contributes to IGF1R regulation in T-ALL. Leuk Res 2012; 36:905-11. [PMID: 22424712 DOI: 10.1016/j.leukres.2012.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/12/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
Abstract
To identify microRNAs regulated by oncogenic Notch signaling, we performed microarray-based miRNA profiling of T-cell acute lymphoblastic leukemia (T-ALL) cells before and after treatment with γ-secretase inhibitor (GSI) to block Notch signaling. We show miR-223 levels increase after GSI treatment suggesting that active Notch signaling represses miR-223 expression. We also demonstrate that insulin-like growth factor-1 receptor (IGF1R) is regulated by miR-223 in this context, but observe no apparent effects on cell growth by overexpression or knock-down of miR-223 alone. We conclude that miR-223 contributes to IGF1R regulation, but may act in concert with other genes and/or microRNAs to alter T-ALL biology.
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Affiliation(s)
- Samuel Gusscott
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
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40
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Kridel R, Meissner B, Rogic S, Boyle M, Telenius A, Woolcock B, Gunawardana J, Jenkins CE, Cochrane C, Ben-Neriah S, Tan K, Morin RD, Opat S, Sehn LH, Connors JM, Marra MA, Weng AP, Steidl C, Gascoyne RD. Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma. Blood 2012; 119:1963-71. [PMID: 22210878 DOI: 10.1182/blood-2011-11-391474] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma, is characterized by the hallmark translocation t(11;14)(q13;q32) and the resulting overexpression of cyclin D1 (CCND1). Our current knowledge of this disease encompasses frequent secondary cytogenetic aberrations and the recurrent mutation of a handful of genes, such as TP53, ATM, and CCND1. However, these findings insufficiently explain the biologic underpinnings of MCL. Here, we performed whole transcriptome sequencing on a discovery cohort of 18 primary tissue MCL samples and 2 cell lines. We found recurrent mutations in NOTCH1, a finding that we confirmed in an extension cohort of 108 clinical samples and 8 cell lines. In total, 12% of clinical samples and 20% of cell lines harbored somatic NOTCH1 coding sequence mutations that clustered in the PEST domain and predominantly consisted of truncating mutations or small frame-shifting indels. NOTCH1 mutations were associated with poor overall survival (P = .003). Furthermore, we showed that inhibition of the NOTCH pathway reduced proliferation and induced apoptosis in 2 MCL cell lines. In summary, we have identified recurrent NOTCH1 mutations that provide the preclinical rationale for therapeutic inhibition of the NOTCH pathway in a subset of patients with MCL.
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Affiliation(s)
- Robert Kridel
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, 675 W.10th Ave.,Vancouver, BC, Canada
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41
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Zare H, Bashashati A, Kridel R, Aghaeepour N, Haffari G, Connors JM, Gascoyne RD, Gupta A, Brinkman RR, Weng AP. Automated analysis of multidimensional flow cytometry data improves diagnostic accuracy between mantle cell lymphoma and small lymphocytic lymphoma. Am J Clin Pathol 2012; 137:75-85. [PMID: 22180480 DOI: 10.1309/ajcpmmlq67yomgew] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Mantle cell lymphoma (MCL) and small lymphocytic lymphoma (SLL) exhibit similar but distinct immunophenotypic profiles. Many cases can be diagnosed readily by flow cytometry (FCM) alone; however, ambiguous cases are frequently encountered and necessitate additional studies, including immunohistochemical staining for cyclin D1 and fluorescence in situ hybridization for IgH-CCND1 rearrangement. To determine if greater diagnostic accuracy could be achieved from FCM data alone, we developed an unbiased, machine-based algorithm to identify features that best distinguish between the 2 diseases. By applying conventional diagnostic criteria to the flow cytometry data, we were able to assign 28 of 44 (64%) MCL and 48 of 70 (69%) SLL cases correctly. In contrast, we were able to assign all 44 (100%) MCL and 68 of 70 (97%) SLL cases correctly using a novel set of criteria, as identified by our automated approach. The most discriminating feature was the CD20/CD23 mean fluorescence intensity ratio, and we found unexpectedly that inclusion of FMC7 expression in the diagnostic algorithm actually reduced its accuracy. This study demonstrates that computational methods can be used on existing clinical FCM data to improve diagnostic accuracy and suggests similar computational approaches could be used to identify novel prognostic markers and perhaps subdivide existing or define new diagnostic entities.
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42
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Dakappagari N, Ho SN, Gascoyne RD, Ranuio J, Weng AP, Tangri S. CD80 (B7.1) is expressed on both malignant B cells and nonmalignant stromal cells in non-Hodgkin lymphoma. Cytometry B Clin Cytom 2011; 82:112-9. [PMID: 22076940 DOI: 10.1002/cyto.b.20631] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 11/06/2022]
Abstract
BACKGROUND CD80 is a member of the B7 family of immune coregulatory proteins that mediate both immune activation and suppression. CD80 in particular has recently been shown to play an important role in supporting immune suppression through interactions with B7-H1. CD80 has been identified as a therapeutic target in non-Hodgkin lymphoma (NHL) based on limited immunohistochemical studies of CD80 expression. Clinical studies have shown that the anti-CD80 antibody galiximab is safe and clinically efficacious in follicular NHL. However, the mechanisms through which targeting CD80 inhibits tumor progression remain poorly understood. METHODS To further define the potential of CD80 as a therapeutic target in NHL, CD80 expression was evaluated by multicolor flow cytometric analysis of primary lymphoma cell suspensions generated from 241 diagnostic biopsies of patients with NHL. RESULTS CD80 was expressed on malignant B cells in essentially all cases of follicular lymphoma (97%; n = 115), the majority of cases of diffuse large B-cell lymphoma (90%; n = 69), marginal zone lymphoma (91%; n = 22), mantle cell lymphoma (75%; n = 12), and in about half of small lymphocytic lymphoma cases (43%; n = 23). CD80 was also present on tumor-infiltrating T lymphocytes in nearly all cases. Additionally, CD80 was expressed by non-B, non-T cells in 68 and 44% of cases of follicular and diffuse large B-cell NHL, respectively. CONCLUSIONS CD80 is expressed on both malignant cells and the nonmalignant cells in NHL. Therapeutic targeting of CD80 will therefore modulate the complex intercellular interactions that define the tumor microenvironment in NHL.
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Affiliation(s)
- Naveen Dakappagari
- Global Clinical Assay Group, Pfizer, Inc, San Diego, California 92121, USA
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43
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Medyouf H, Gusscott S, Wang H, Tseng JC, Wai C, Nemirovsky O, Trumpp A, Pflumio F, Carboni J, Gottardis M, Pollak M, Kung AL, Aster JC, Holzenberger M, Weng AP. High-level IGF1R expression is required for leukemia-initiating cell activity in T-ALL and is supported by Notch signaling. J Biophys Biochem Cytol 2011. [DOI: 10.1083/jcb1943oia8] [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: 11/22/2022] Open
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44
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Medyouf H, Gusscott S, Wang H, Tseng JC, Wai C, Nemirovsky O, Trumpp A, Pflumio F, Carboni J, Gottardis M, Pollak M, Kung AL, Aster JC, Holzenberger M, Weng AP. High-level IGF1R expression is required for leukemia-initiating cell activity in T-ALL and is supported by Notch signaling. ACTA ACUST UNITED AC 2011; 208:1809-22. [PMID: 21807868 PMCID: PMC3171095 DOI: 10.1084/jem.20110121] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Notch-driven expression of IGF1R promotes the growth, viability, and transplantability of T-ALL cells. T cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer of immature T cells that often shows aberrant activation of Notch1 and PI3K–Akt pathways. Although mutations that activate PI3K–Akt signaling have previously been identified, the relative contribution of growth factor-dependent activation is unclear. We show here that pharmacologic inhibition or genetic deletion of insulin-like growth factor 1 receptor (IGF1R) blocks the growth and viability of T-ALL cells, whereas moderate diminution of IGF1R signaling compromises leukemia-initiating cell (LIC) activity as defined by transplantability in syngeneic/congenic secondary recipients. Furthermore, IGF1R is a Notch1 target, and Notch1 signaling is required to maintain IGF1R expression at high levels in T-ALL cells. These findings suggest effects of Notch on LIC activity may be mediated in part by enhancing the responsiveness of T-ALL cells to ambient growth factors, and provide strong rationale for use of IGF1R inhibitors to improve initial response to therapy and to achieve long-term cure of patients with T-ALL.
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Affiliation(s)
- Hind Medyouf
- Terry Fox Laboratory/Department of Pathology, BC Cancer Agency, Vancouver, BC, V52 1L3 Canada.
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45
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Hahne F, Khodabakhshi AH, Bashashati A, Wong CJ, Gascoyne RD, Weng AP, Seyfert-Margolis V, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR. Per-channel basis normalization methods for flow cytometry data. Cytometry A 2010; 77:121-31. [PMID: 19899135 DOI: 10.1002/cyto.a.20823] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Between-sample variation in high-throughput flow cytometry data poses a significant challenge for analysis of large-scale data sets, such as those derived from multicenter clinical trials. It is often hard to match biologically relevant cell populations across samples because of technical variation in sample acquisition and instrumentation differences. Thus, normalization of data is a critical step before analysis, particularly in large-scale data sets from clinical trials, where group-specific differences may be subtle and patient-to-patient variation common. We have developed two normalization methods that remove technical between-sample variation by aligning prominent features (landmarks) in the raw data on a per-channel basis. These algorithms were tested on two independent flow cytometry data sets by comparing manually gated data, either individually for each sample or using static gating templates, before and after normalization. Our results show a marked improvement in the overlap between manual and static gating when the data are normalized, thereby facilitating the use of automated analyses on large flow cytometry data sets. Such automated analyses are essential for high-throughput flow cytometry.
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Affiliation(s)
- Florian Hahne
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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46
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Chan SM, Weng AP, Tibshirani R, Aster JC, Utz PJ. Notch signals positively regulate activity of the mTOR pathway in T-cell acute lymphoblastic leukemia. Blood 2007; 110:278-86. [PMID: 17363738 PMCID: PMC1896117 DOI: 10.1182/blood-2006-08-039883] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Constitutive Notch activation is required for the proliferation of a subgroup of T-cell acute lymphoblastic leukemia (T-ALL). Downstream pathways that transmit pro-oncogenic signals are not well characterized. To identify these pathways, protein microarrays were used to profile the phosphorylation state of 108 epitopes on 82 distinct signaling proteins in a panel of 13 T-cell leukemia cell lines treated with a gamma-secretase inhibitor (GSI) to inhibit Notch signals. The microarray screen detected GSI-induced hypophosphorylation of multiple signaling proteins in the mTOR pathway. This effect was rescued by expression of the intracellular domain of Notch and mimicked by dominant negative MAML1, confirming Notch specificity. Withdrawal of Notch signals prevented stimulation of the mTOR pathway by mitogenic factors. These findings collectively suggest that the mTOR pathway is positively regulated by Notch in T-ALL cells. The effect of GSI on the mTOR pathway was independent of changes in phosphatidylinositol-3 kinase and Akt activity, but was rescued by expression of c-Myc, a direct transcriptional target of Notch, implicating c-Myc as an intermediary between Notch and mTOR. T-ALL cell growth was suppressed in a highly synergistic manner by simultaneous treatment with the mTOR inhibitor rapamycin and GSI, which represents a rational drug combination for treating this aggressive human malignancy.
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Affiliation(s)
- Steven M Chan
- Division of Immunology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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47
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Rodig SJ, Savage KJ, LaCasce AS, Weng AP, Harris NL, Shipp MA, Hsi ED, Gascoyne RD, Kutok JL. Expression of TRAF1 and Nuclear c-Rel Distinguishes Primary Mediastinal Large Cell Lymphoma From Other Types of Diffuse Large B-cell Lymphoma. Am J Surg Pathol 2007; 31:106-12. [PMID: 17197926 DOI: 10.1097/01.pas.0000213334.40358.0e] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Primary mediastinal large B-cell lymphoma (PMLBCL) is a recently identified subtype of diffuse large B-cell lymphoma (DLBCL) that is difficult to distinguish from other types of DLBCL on the basis of histologic features alone. We recently identified a molecular signature of PMLBCL that is distinct from other forms of DLBCL but shares features with classical Hodgkin lymphoma. This signature includes activation of the nuclear factor kappaB (NFkappaB) signaling pathway, which in part, acts through nuclear translocation of c-Rel containing NFkappaB transcriptional complexes, and subsequent expression of NFkappaB target genes such as tumor necrosis factor receptor-associated factor-1 (TRAF1). Using standard immunohistochemical techniques, we examined 251 large B-cell lymphomas (78 cases of PMLBCL and 173 cases of other types of DLBCL) to determine whether the expression patterns of c-Rel and TRAF1 could reliably distinguish between PMLBCL and other types of DLBCL. Robust nuclear c-Rel was present in 31 of 48 (65%) cases of PMLBCL and 28 of 160 (18%) cases of DLBCL. In addition, cytoplasmic TRAF1 expression was seen in 48 of 78 (62%) cases of PMLBCL, but only 20 of 173 (12%) cases of DLBCL. Finally, the combined expression of nuclear c-Rel and TRAF1 was seen in 24 of 45 cases (53%) of PMLBCL, but in only 3 of 156 cases (2%) of other types of DLBCL. Thus, the combined nuclear localization of c-Rel and the cellular expression of TRAF1 is a highly specific (specificity=98%) means to distinguish PMLBCL from DLBCL that is readily applicable to routine surgical pathology practice.
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Affiliation(s)
- Scott J Rodig
- Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
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48
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Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, Look AT, Young RA, Califano A, Ferrando AA. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A 2006; 103:18261-6. [PMID: 17114293 PMCID: PMC1838740 DOI: 10.1073/pnas.0606108103] [Citation(s) in RCA: 629] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The NOTCH1 signaling pathway directly links extracellular signals with transcriptional responses in the cell nucleus and plays a critical role during T cell development and in the pathogenesis over 50% of human T cell lymphoblastic leukemia (T-ALL) cases. However, little is known about the transcriptional programs activated by NOTCH1. Using an integrative systems biology approach we show that NOTCH1 controls a feed-forward-loop transcriptional network that promotes cell growth. Inhibition of NOTCH1 signaling in T-ALL cells led to a reduction in cell size and elicited a gene expression signature dominated by down-regulated biosynthetic pathway genes. By integrating gene expression array and ChIP-on-chip data, we show that NOTCH1 directly activates multiple biosynthetic routes and induces c-MYC gene expression. Reverse engineering of regulatory networks from expression profiles showed that NOTCH1 and c-MYC govern two directly interconnected transcriptional programs containing common target genes that together regulate the growth of primary T-ALL cells. These results identify c-MYC as an essential mediator of NOTCH1 signaling and integrate NOTCH1 activation with oncogenic signaling pathways upstream of c-MYC.
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Affiliation(s)
| | - Wei Keat Lim
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
| | | | | | | | - Adam Margolin
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
| | | | | | - Donna Neuberg
- Biostatistics, Dana–Farber Cancer Institute, Boston, MA 02115
| | - Andrew P. Weng
- Terry Fox Laboratory, BC Cancer Research Centre, Vancouver, BC, Canada V5Z 1L3
| | - Jon C. Aster
- **Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115; and
| | - Francois Sigaux
- Genome Rearrangements and Cancer Group, Institut National de la Santé et de la Recherche Médicale U728, Saint-Louis Hospital, 75010 Paris, France
| | - Jean Soulier
- Genome Rearrangements and Cancer Group, Institut National de la Santé et de la Recherche Médicale U728, Saint-Louis Hospital, 75010 Paris, France
| | | | | | - Andrea Califano
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
| | - Adolfo A. Ferrando
- *Institute for Cancer Genetics and
- Whitehead Institute, Cambridge, MA 02142
- To whom correspondence should be addressed. E-mail:
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49
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Weng AP, Millholland JM, Yashiro-Ohtani Y, Arcangeli ML, Lau A, Wai C, Del Bianco C, Rodriguez CG, Sai H, Tobias J, Li Y, Wolfe MS, Shachaf C, Felsher D, Blacklow SC, Pear WS, Aster JC. c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev 2006; 20:2096-109. [PMID: 16847353 PMCID: PMC1536060 DOI: 10.1101/gad.1450406] [Citation(s) in RCA: 660] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Accepted: 06/06/2006] [Indexed: 02/06/2023]
Abstract
Human acute T-cell lymphoblastic leukemias and lymphomas (T-ALL) are commonly associated with gain-of-function mutations in Notch1 that contribute to T-ALL induction and maintenance. Starting from an expression-profiling screen, we identified c-myc as a direct target of Notch1 in Notch-dependent T-ALL cell lines, in which Notch accounts for the majority of c-myc expression. In functional assays, inhibitors of c-myc interfere with the progrowth effects of activated Notch1, and enforced expression of c-myc rescues multiple Notch1-dependent T-ALL cell lines from Notch withdrawal. The existence of a Notch1-c-myc signaling axis was bolstered further by experiments using c-myc-dependent murine T-ALL cells, which are rescued from withdrawal of c-myc by retroviral transduction of activated Notch1. This Notch1-mediated rescue is associated with the up-regulation of endogenous murine c-myc and its downstream transcriptional targets, and the acquisition of sensitivity to Notch pathway inhibitors. Additionally, we show that primary murine thymocytes at the DN3 stage of development depend on ligand-induced Notch signaling to maintain c-myc expression. Together, these data implicate c-myc as a developmentally regulated direct downstream target of Notch1 that contributes to the growth of T-ALL cells.
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Affiliation(s)
- Andrew P Weng
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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50
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Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a form of pediatric leukemia that is thought to be caused by approximately 12 distinct chromosomal translocations that lead to aberrant expression of as many different cellular genes. Development of novel, rational therapies against such a diverse set of mechanistic targets has thus been a formidable challenge. Recent studies, however, have identified a large fraction of T-ALL cases carrying mutations in one of these genes, Notch1, suggesting for the first time that many cases may share a common pathogenic etiology, and perhaps may allow the development of targeted therapies that benefit the majority of patients with this disease.
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Affiliation(s)
- Andrew P Weng
- British Columbia Cancer Agency, Department of Pathology, British Columbia Cancer Research Centre, Terry Fox Laboratory, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
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