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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Jiang Y, Eagles J, Passerini V, Tang Z, Rivas MA, Weigert O, Pugh TJ, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Zappasodi R, Béguelin W, Melnick AM. Loss of CREBBP and KMT2D cooperate to accelerate lymphomagenesis and shape the lymphoma immune microenvironment. Nat Commun 2024; 15:2879. [PMID: 38570506 PMCID: PMC10991284 DOI: 10.1038/s41467-024-47012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024] Open
Abstract
Despite regulating overlapping gene enhancers and pathways, CREBBP and KMT2D mutations recurrently co-occur in germinal center (GC) B cell-derived lymphomas, suggesting potential oncogenic cooperation. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d induces a more severe mouse lymphoma phenotype (vs either allele alone) and unexpectedly confers an immune evasive microenvironment manifesting as CD8+ T-cell exhaustion and reduced infiltration. This is linked to profound repression of immune synapse genes that mediate crosstalk with T-cells, resulting in aberrant GC B cell fate decisions. From the epigenetic perspective, we observe interaction and mutually dependent binding and function of CREBBP and KMT2D on chromatin. Their combined deficiency preferentially impairs activation of immune synapse-responsive super-enhancers, pointing to a particular dependency for both co-activators at these specialized regulatory elements. Together, our data provide an example where chromatin modifier mutations cooperatively shape and induce an immune-evasive microenvironment to facilitate lymphomagenesis.
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Affiliation(s)
- Jie Li
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Hsia-Yuan Ying
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew R Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Department of Pathology and Laboratorial Medicine, University of British Columbia, Vancouver, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - Chi-Shuen Chu
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Yiyue Jiang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Verena Passerini
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Zhanyun Tang
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Martin A Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Oliver Weigert
- Department of Medicine III, Laboratory for Experimental Leukemia and Lymphoma Research (ELLF), Ludwig-Maximilians University (LMU) Hospital, Munich, Germany
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Robert G Roeder
- The Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Roberta Zappasodi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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Li J, Chin CR, Ying HY, Meydan C, Teater MR, Xia M, Farinha P, Takata K, Chu CS, Rivas MA, Chadburn A, Steidl C, Scott DW, Roeder RG, Mason CE, Béguelin W, Melnick AM. Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas. bioRxiv 2023:2023.02.13.528351. [PMID: 36824887 PMCID: PMC9949106 DOI: 10.1101/2023.02.13.528351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Mutations affecting enhancer chromatin regulators CREBBP and KMT2D are highly co-occurrent in germinal center (GC)-derived lymphomas and other tumors, even though regulating similar pathways. Herein, we report that combined haploinsufficiency of Crebbp and Kmt2d (C+K) indeed accelerated lymphomagenesis. C+K haploinsufficiency induced GC hyperplasia by altering cell fate decisions, skewing B cells away from memory and plasma cell differentiation. C+K deficiency particularly impaired enhancer activation for immune synapse genes involved in exiting the GC reaction. This effect was especially severe at super-enhancers for immunoregulatory and differentiation genes. Mechanistically, CREBBP and KMT2D formed a complex, were highly co-localized on chromatin, and were required for each-other's stable recruitment to enhancers. Notably, C+K lymphomas in mice and humans manifested significantly reduced CD8 + T-cell abundance. Hence, deficiency of C+K cooperatively induced an immune evasive phenotype due at least in part to failure to activate key immune synapse super-enhancers, associated with altered immune cell fate decisions. SIGNIFICANCE Although CREBBP and KMT2D have similar enhancer regulatory functions, they are paradoxically co-mutated in lymphomas. We show that their combined loss causes specific disruption of super-enhancers driving immune synapse genes. Importantly, this leads to reduction of CD8 cells in lymphomas, linking super-enhancer function to immune surveillance, with implications for immunotherapy resistance.
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Xia M, David L, Teater MR, Gutierrez J, Wang X, Meydan C, Lytle A, Slack G, Scott D, Onder O, Elenitoba-Johnson K, Zamponi N, Cerchietti L, Lu T, Philippar U, Fontan L, Wu H, Melnick A. Abstract A28: BCL10 mutations define distinct dependencies guiding precision therapy for DLBCL. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy and the activated B cell-like subtype (ABC-DLBCL) is the most aggressive form and harbors frequent mutations of immune signaling pathways that culminate in constitutive activation of CARD11-MALT1-BCL10 (CBM) complex and downstream NF-κB pathway. CBM complexes form large macromolecular structures due to signal-induced polymerization of the BCL10 subunit, which is affected by recurrent somatic mutations in ABC-DLBCLs. Through biochemical, structural and functional dissection of these mutations, we find that BCL10 mutations fall into two functionally distinct classes: missense mutations of the BCL10 CARD domain (hotspot R58Q) and truncation of its C-terminal tail (hotspot E140X). To explore the functional consequences of BCL10 mutations, we established reporter systems to evaluate their impact on MALT1 and NF-𝜅B activities which are BCL10 downstream signaling cascades. We found that almost all mutants induced aberrantly strong NF-𝜅B and MALT1 activities in lymphoma cells as compared to WT BCL10, indicating the gain-of-function effect of BCL10 mutations. By performing immunohistochemistry staining of p65 in a set of tumor tissue microarray from DLBCL patients (n=298), we revealed that BCL10 mutant tumors have significantly (Mann-Whitney p<0.0001) increased p65 nuclear staining score compared to BCL10 WT tumors, suggesting enhanced NF-𝜅B activity. To investigate the biochemical impact of BCL10 mutants on CBM complex formation, we performed fluorescence polarization and filamentation formation assays with purified WT and mutant BCL10 proteins and found that both BCL10R58Q and BCL10E140X manifested faster and more spontaneous polarization compared to BCL10WT. Surprisingly, through mapping the BCL10-MALT1 interaction, we found that truncating mutation (E140X) abrogated a novel protein interaction motif through which MALT1 inhibits BCL10 polymerization, thus unleashing spontaneous CBM filament formation and inducing addiction to MALT1 activity. In marked contrast, the CARD missense mutation (R58Q) on BCL10 filament interface not only does not disrupt but enhances filament formation and it also alters CBM complex kinetics forming glutamine network structures that stabilize BCL10 filaments, but this still may require the upstream signal to activate MALT1. Importantly, we found that BCL10 mutant cells were less dependent on upstream CARD11 activation in MALT1 activation, NF-𝜅B signaling and cell growth assays performed in ABC-DLBCL lines. Furthermore, in vitro and in vivo xenograft studies revealed that BCL10 mutant lymphomas are resistant to BTK inhibitors, whereas BCL10 truncating (E140X) but not missense CARD (R58Q) mutants were hypersensitive to MALT1 protease inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL and further precision can be achieved by tailoring therapy (e.g. MALT1 inhibitors that are currently being tested in clinical trials) according to specific biochemical effects of distinct mutation classes.
Citation Format: Min Xia, Liron David, Matthew R Teater, Johana Gutierrez, Xiang Wang, Cem Meydan, Andrew Lytle, Graham Slack, David Scott, Ozlem Onder, Kojo Elenitoba-Johnson, Nahuel Zamponi, Leandro Cerchietti, Tianbao Lu, Ulrike Philippar, Lorena Fontan, Hao Wu, Ari Melnick. BCL10 mutations define distinct dependencies guiding precision therapy for DLBCL [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A28.
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Affiliation(s)
- Min Xia
- 1Weill Cornell Medicine, New York, NY,
| | | | | | | | | | | | | | | | | | - Ozlem Onder
- 4University of Pennsylvania, Philadelphia, PA,
| | | | | | | | - Tianbao Lu
- 5Janssen Research & Development, Springhouse, PA,
| | | | - Lorena Fontan
- 6Janssen Research & Development, Beerse, AR, Belgium
| | - Hao Wu
- 2Harvard Medical School, Boston, MA,
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Li M, Teater MR, Hong JY, Park NR, Duy C, Shen H, Wang L, Chen Z, Cerchietti L, Davidson SM, Lin H, Melnick AM. Translational Activation of ATF4 through Mitochondrial Anaplerotic Metabolic Pathways Is Required for DLBCL Growth and Survival. Blood Cancer Discov 2022; 3:50-65. [PMID: 35019856 PMCID: PMC9789686 DOI: 10.1158/2643-3230.bcd-20-0183] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/01/2021] [Accepted: 11/03/2021] [Indexed: 12/09/2022] Open
Abstract
Diffuse large B-cell lymphomas (DLBCL) are broadly dependent on anaplerotic metabolism regulated by mitochondrial SIRT3. Herein we find that translational upregulation of ATF4 is coupled with anaplerotic metabolism in DLBCLs due to nutrient deprivation caused by SIRT3 driving rapid flux of glutamine into the tricarboxylic acid (TCA) cycle. SIRT3 depletion led to ATF4 downregulation and cell death, which was rescued by ectopic ATF4 expression. Mechanistically, ATF4 translation is inhibited in SIRT3-deficient cells due to the increased pools of amino acids derived from compensatory autophagy and decreased glutamine consumption by the TCA cycle. Absence of ATF4 further aggravates this state through downregulation of its target genes, including genes for amino acid biosynthesis and import. Collectively, we identify a SIRT3-ATF4 axis required to maintain survival of DLBCL cells by enabling them to optimize amino acid uptake and utilization. Targeting ATF4 translation can potentiate the cytotoxic effect of SIRT3 inhibitor to DLBCL cells. SIGNIFICANCE: We discovered the link between SIRT3 and ATF4 in DLBCL cells, which connected lymphoma amino acid metabolism with ATF4 translation via metabolic stress signals. SIRT3-ATF4 axis is required in DLBCL cells regardless of subtype, which indicates a common metabolic vulnerability in DLBCLs and can serve as a therapeutic target.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Meng Li
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Matthew R. Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Jun Young Hong
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Cornell University, Ithaca, New York
| | - Noel R. Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Cihangir Duy
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Hao Shen
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Ling Wang
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, New York
| | - Leandro Cerchietti
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Shawn M. Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Cornell University, Ithaca, New York.,Corresponding Authors: Ari M. Melnick, Departments of Medicine and Pharmacology, Weill Cornell Medicine, 413 E. 69th Street, BB-1430, New York, NY 10021. Phone: 212-746-7643; E-mail: ; and Hening Lin, Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Phone: 607-255-4650; E-mail:
| | - Ari M. Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, New York.,Corresponding Authors: Ari M. Melnick, Departments of Medicine and Pharmacology, Weill Cornell Medicine, 413 E. 69th Street, BB-1430, New York, NY 10021. Phone: 212-746-7643; E-mail: ; and Hening Lin, Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Phone: 607-255-4650; E-mail:
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Li M, Teater MR, Hong JY, Duy C, Shen H, Wang L, Chen Z, Cerchietti L, Lin H, Melnick A. Abstract LB014: Translational activation of ATF4 through mitochondrial anaplerotic metabolic pathways is required for DLBCL growth and survival. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb014] [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 lymphomas (DLBCLs) tolerate various forms of cellular stress associated with their rapid proliferation and depletion of nutrients in their microenvironment. Our previous finding discovered that DLBCLs are broadly dependent mitochondrial SIRT3 as a critical source of non-oncogene addiction in DLBCL. SIRT3 promotes tumorigenesis in DLBCL, where it is required for glutamine fueled anaplerosis, and its loss of function leads to tumor suppressive autophagy. However, it is not known why SIRT3 deficient DLBCL cells are so vulnerable to such metabolic changes and autophagy, which points to potentially novel and critical nutrient regulatory circuits occurring in this disease.
We set out to identify downstream signals induced by SIRT3 deficiency in DLBCL cells in order to gain insight into how SIRT3 could interface with nutrient flux stress response pathways to support tumorigenesis of DLBCLs. First, we carried out RNA sequencing study in three DLBCL cell lines representing different subtypes of DLBCLs. The data showed that all SIRT3 deficient DLBCL cells experienced transcriptional inhibitions of ATF4 target genes. We further observed that ATF4 protein was decreased due to the translational inhibition in SIRT3 deficient DLBCL cells, which indicates that ATF4 may play a role downstream of SIRT3 contributing to DLBCL cell proliferation. Secondly, we proved that ATF4 is indeed required to DLBCL cells' proliferation. ATF4 target genes are more expressed in DLBCL tumor cells than normal germinal center B cells. Loss of ATF4 induced proliferation arrest as SIRT3 depletion and over-expression of ATF4 can partially rescue the proliferation and viability inhibited by SIRT3 deficiency. Consistently, we observed that loss of SIRT3 led to ATF4 reduction in the vavP-Bcl2 mouse lymphoma model. Mechanistically, we identified that ATF4 functions downstream of SIRT3 through the metabolic cascade of GDH-TCA cycle-autophagy. GDH and DMKG can rescue the ATF4 protein decreased by SIRT3 depletion. Blockage of autophagy with chloroquine or knocking down ATG5 can also neutralize SIRT3's inhibition on ATF4. Furthermore, we discovered that
ATF4's translation is highly sensitive to nutrient/amino acid levels in DLBCL cells as a stress signal for cell survival. However, ATF4 translation failed to respond to glutamine starvation in SIRT3 depleted DLBCL cells. SIRT3 deficiency underwent drastic changes of amino acid levels because of the TCA cycle inhibition and autophagy activation, which interfered the ATF4's translation and can lead to deleterious metabolic stresses. Collectively, we identify a novel SIRT3-ATF4 axis required to maintain survival of DLBCL cells by enabling them to optimize amino acid utilization. Lack of this coordination is lethal to DLBCL cells, exposing a critical and exploitable metabolic vulnerability.
Citation Format: Meng Li, Matthew R. Teater, Jun Young Hong, Cihangir Duy, Hao Shen, Ling Wang, Zhengming Chen, Leandro Cerchietti, Hening Lin, Ari Melnick. Translational activation of ATF4 through mitochondrial anaplerotic metabolic pathways is required for DLBCL growth and survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB014.
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Affiliation(s)
- Meng Li
- 1Weill Cornell Medical College, New York, NY
| | | | | | | | - Hao Shen
- 1Weill Cornell Medical College, New York, NY
| | - Ling Wang
- 1Weill Cornell Medical College, New York, NY
| | | | | | | | - Ari Melnick
- 1Weill Cornell Medical College, New York, NY
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Fontan L, Goldstein R, Casalena G, Durant M, Teater MR, Wilson J, Phillip J, Xia M, Shah S, Us I, Shinglot H, Singh A, Inghirami G, Melnick A. Identification of MALT1 feedback mechanisms enables rational design of potent antilymphoma regimens for ABC-DLBCL. Blood 2021; 137:788-800. [PMID: 32785655 PMCID: PMC7885826 DOI: 10.1182/blood.2019004713] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 12/26/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
MALT1 inhibitors are promising therapeutic agents for B-cell lymphomas that are dependent on constitutive or aberrant signaling pathways. However, a potential limitation for signal transduction-targeted therapies is the occurrence of feedback mechanisms that enable escape from the full impact of such drugs. Here, we used a functional genomics screen in activated B-cell-like (ABC) diffuse large B-cell lymphoma (DLBCL) cells treated with a small molecule irreversible inhibitor of MALT1 to identify genes that might confer resistance or enhance the activity of MALT1 inhibition (MALT1i). We find that loss of B-cell receptor (BCR)- and phosphatidylinositol 3-kinase (PI3K)-activating proteins enhanced sensitivity, whereas loss of negative regulators of these pathways (eg, TRAF2, TNFAIP3) promoted resistance. These findings were validated by knockdown of individual genes and a combinatorial drug screen focused on BCR and PI3K pathway-targeting drugs. Among these, the most potent combinatorial effect was observed with PI3Kδ inhibitors against ABC-DLBCLs in vitro and in vivo, but that led to an adaptive increase in phosphorylated S6 and eventual disease progression. Along these lines, MALT1i promoted increased MTORC1 activity and phosphorylation of S6K1-T389 and S6-S235/6, an effect that was only partially blocked by PI3Kδ inhibition in vitro and in vivo. In contrast, simultaneous inhibition of MALT1 and MTORC1 prevented S6 phosphorylation, yielded potent activity against DLBCL cell lines and primary patient specimens, and resulted in more profound tumor regression and significantly improved survival of ABC-DLBCLs in vivo compared with PI3K inhibitors. These findings provide a basis for maximal therapeutic impact of MALT1 inhibitors in the clinic, by disrupting feedback mechanisms that might otherwise limit their efficacy.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Drug Design
- Drug Resistance, Neoplasm
- Drug Synergism
- Feedback, Physiological/drug effects
- Female
- Humans
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors
- Mechanistic Target of Rapamycin Complex 1/metabolism
- Mice
- Mice, Inbred NOD
- Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/antagonists & inhibitors
- Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein/physiology
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/physiology
- Organoids/drug effects
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphorylation/drug effects
- Protein Processing, Post-Translational/drug effects
- RNA, Small Interfering/genetics
- Receptors, Antigen, B-Cell/immunology
- Ribosomal Protein S6 Kinases/metabolism
- Signal Transduction/drug effects
- Toll-Like Receptors/immunology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Lorena Fontan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Rebecca Goldstein
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Gabriella Casalena
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Matthew Durant
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Matthew R Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Jimmy Wilson
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Jude Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Shivem Shah
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY; and
| | - Ilkay Us
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Himaly Shinglot
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Ankur Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY; and
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
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7
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Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
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Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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Scholze H, Stephenson RE, Reynolds R, Shah S, Puri R, Teater MR, van Besien H, Gibbs-Curtis D, Ueno H, Parvin S, Letai AG, Mathew S, Singh A, Cesarman E, Melnick A, Giulino-Roth L. Abstract PO-53: Combined EZH2 and BCL2 inhibitors as precision therapy for genetically defined DLBCL subtypes. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Molecular alterations in the histone methyltransferase EZH2 and the antiapoptotic protein BCL2 frequently co-occur in diffuse large B-cell lymphoma (DLBCL). We hypothesized that EZH2 inhibition and BCL2 inhibition would be synergistic in DLBCL. To test this, we evaluated the EZH2 inhibitor tazemetostat and the BCL2 inhibitor venetoclax in DLBCL cells, 3D lymphoma organoids, and patient-derived xenografts (PDXs). We found that tazemetostat and venetoclax are synergistic in DLBCL cells that harbor both an EZH2 mutation and a BCL2/IGH translocation, as demonstrated by CI values <1 (CI: 0.034, 0.259 and 0.074 in SUDHL-6, WSU-DLCL2, and OCI-Ly1 respectively), but not in wild-type cells. Since cell lines in suspension do not reflect lymph node architecture, we developed a 3D lymphoma organoid culture system that consists of extracellular matrix, lymphoma cells, and stromal cells (Tian et al., Biomaterials 2015). We observed synergy between the two agents in two organoid model systems: 1) OCI-LY1; 2) PDX derived from a DLBCL with BCL2/IGH translocation and EZH2 mutation. To investigate mechanisms of synergy, we evaluated previously published RNA-seq profiles of DLBCL cell lines (n=26) treated with vehicle or tazemetostat to investigate changes in BCL2 family members (Brach et al., Mol Can Ther 2017). Tazemetostat-treated cells showed enhanced expression of proapoptotic BCL2 family members including BCL2L11 (p=0.012), BMF (p<0.001), and BCL2L14 (p=0.002), suggesting that these may be direct or indirect EZH2 target genes that are de-repressed upon EZH2 inhibition. To assess mitochondrial priming to apoptosis as a result of EZH2 inhibition, we performed BH3 profiling of DLBCL PDX organoids treated with vehicle vs. tazemetostat. Tazemetostat-treated cells had increased priming as evidenced by cytochrome c release in response to general apoptotic signaling peptides BIM and PUMA (p<0.0001) and to the BCL2 specific peptide BAD (p<0.0001), suggesting that pretreatment with tazemetostat increases mitochondrial sensitivity to BCL2 inhibition. We next evaluated combination therapy in vivo. In SUDHL-6 xenografts, the combination resulted in attenuation of tumor growth compared to either drug alone (combination vs. venetoclax p<0.0001, combination vs. tazemetostat p=0.0004) and improved overall survival. In DLBCL PDXs, combination therapy resulted in complete resolutions of tumors, which were durable over time and associated with improved overall survival. Strikingly, after 197 days of follow-up there was no detectable disease in any combination-treated animal. In summary, we demonstrate that combined BCL2 and EZH2 inhibition results in synergistic anti-lymphoma effects. We expect this combination to be especially effective as precision therapy for the newly identified cluster 3/EZB DLBCL subtype, which frequently harbors both EZH2 and BCL2 alterations. A clinical trial of this combination is currently in development.
Citation Format: Hanna Scholze, Regan E. Stephenson, Raymond Reynolds, Shivem Shah, Rishi Puri, Matthew R. Teater, Herman van Besien, Destini Gibbs-Curtis, Hideki Ueno, Salma Parvin, Anthony G. Letai, Susan Mathew, Ankur Singh, Ethel Cesarman, Ari Melnick, Lisa Giulino-Roth. Combined EZH2 and BCL2 inhibitors as precision therapy for genetically defined DLBCL subtypes [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-53.
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Affiliation(s)
- Hanna Scholze
- 1Department of Pediatrics, Weill Cornell Medical College, New York, NY,
| | | | - Raymond Reynolds
- 3Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY,
| | - Shivem Shah
- 2School of Biomedical Engineering, Cornell University, Ithaca, NY,
| | - Rishi Puri
- 4School of Mechanical Engineering, Cornell University, Ithaca, NY,
| | - Matthew R. Teater
- 5Department of Medicine, Weill Cornell Medical College, New York, NY,
| | - Herman van Besien
- 3Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY,
| | - Destini Gibbs-Curtis
- 3Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY,
| | - Hideki Ueno
- 6Department of Microbiology, Mount Sinai School of Medicine, New York, NY,
| | - Salma Parvin
- 7Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,
| | - Anthony G. Letai
- 7Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA,
| | - Susan Mathew
- 3Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY,
| | - Ankur Singh
- 8School of Biomedical Engineering, Cornell University; School of Mechanical Engineering, Cornell University, Ithaca, NY,
| | - Ethel Cesarman
- 3Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY,
| | - Ari Melnick
- 5Department of Medicine, Weill Cornell Medical College, New York, NY,
| | - Lisa Giulino-Roth
- 9Department of Pediatrics, Weill Cornell Medical College; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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9
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Li M, Chiang YL, Lyssiotis CA, Teater MR, Hong JY, Shen H, Wang L, Hu J, Jing H, Chen Z, Jain N, Duy C, Mistry SJ, Cerchietti L, Cross JR, Cantley LC, Green MR, Lin H, Melnick AM. Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis. Cancer Cell 2019; 35:916-931.e9. [PMID: 31185214 PMCID: PMC7534582 DOI: 10.1016/j.ccell.2019.05.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 02/05/2019] [Accepted: 05/07/2019] [Indexed: 12/14/2022]
Abstract
Diffuse large B cell lymphomas (DLBCLs) are genetically heterogeneous and highly proliferative neoplasms derived from germinal center (GC) B cells. Here, we show that DLBCLs are dependent on mitochondrial lysine deacetylase SIRT3 for proliferation, survival, self-renewal, and tumor growth in vivo regardless of disease subtype and genetics. SIRT3 knockout attenuated B cell lymphomagenesis in VavP-Bcl2 mice without affecting normal GC formation. Mechanistically, SIRT3 depletion impaired glutamine flux to the TCA cycle via glutamate dehydrogenase and reduction in acetyl-CoA pools, which in turn induce autophagy and cell death. We developed a mitochondrial-targeted class I sirtuin inhibitor, YC8-02, which phenocopied the effects of SIRT3 depletion and killed DLBCL cells. SIRT3 is thus a metabolic non-oncogene addiction and therapeutic target for DLBCLs.
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MESH Headings
- Acetyl Coenzyme A/metabolism
- Animals
- Antineoplastic Agents/pharmacology
- Autophagic Cell Death/drug effects
- Cell Proliferation/drug effects
- Citric Acid Cycle/drug effects
- Energy Metabolism/drug effects
- Female
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Neoplastic
- Glutamine/metabolism
- HEK293 Cells
- Histone Deacetylase Inhibitors/pharmacology
- Humans
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/enzymology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- MCF-7 Cells
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Molecular Targeted Therapy
- Signal Transduction
- Sirtuin 3/antagonists & inhibitors
- Sirtuin 3/deficiency
- Sirtuin 3/genetics
- Sirtuin 3/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Meng Li
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ying-Ling Chiang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jun Young Hong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Hao Shen
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ling Wang
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jing Hu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Neeraj Jain
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77005, USA
| | - Cihangir Duy
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sucharita J Mistry
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leandro Cerchietti
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Justin R Cross
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Michael R Green
- Department of Lymphoma/Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77005, USA
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
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Cardenas MG, Yu W, Beguelin W, Teater MR, Geng H, Goldstein RL, Oswald E, Hatzi K, Yang SN, Cohen J, Shaknovich R, Vanommeslaeghe K, Cheng H, Liang D, Cho HJ, Abbott J, Tam W, Du W, Leonard JP, Elemento O, Cerchietti L, Cierpicki T, Xue F, MacKerell AD, Melnick AM. Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest 2016; 126:3351-62. [PMID: 27482887 DOI: 10.1172/jci85795] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/03/2016] [Indexed: 12/17/2022] Open
Abstract
Diffuse large B cell lymphomas (DLBCLs) arise from proliferating B cells transiting different stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of DLBCLs that respond poorly to current therapies, chromosomal translocations and amplification lead to constitutive expression of the B cell lymphoma 6 (BCL6) oncogene. The role of BCL6 in maintaining these lymphomas has not been investigated. Here, we designed small-molecule inhibitors that display higher affinity for BCL6 than its endogenous corepressor ligands to evaluate their therapeutic efficacy for targeting ABC-DLBCL. We used an in silico drug design functional-group mapping approach called SILCS to create a specific BCL6 inhibitor called FX1 that has 10-fold greater potency than endogenous corepressors and binds an essential region of the BCL6 lateral groove. FX1 disrupted formation of the BCL6 repression complex, reactivated BCL6 target genes, and mimicked the phenotype of mice engineered to express BCL6 with corepressor binding site mutations. Low doses of FX1 induced regression of established tumors in mice bearing DLBCL xenografts. Furthermore, FX1 suppressed ABC-DLBCL cells in vitro and in vivo, as well as primary human ABC-DLBCL specimens ex vivo. These findings indicate that ABC-DLBCL is a BCL6-dependent disease that can be targeted by rationally designed inhibitors that exceed the binding affinity of natural BCL6 ligands.
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