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Qiu Z, Khalife J, Ethiraj P, Jaafar C, Lin AP, Holder KN, Ritter JP, Chiou L, Huelgas-Morales G, Aslam S, Zhang Z, Liu Z, Arya S, Gupta YK, Dahia PLM, Aguiar RC. IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHCII complexes. SCIENCE ADVANCES 2024; 10:eadk2091. [PMID: 38996030 PMCID: PMC11244530 DOI: 10.1126/sciadv.adk2091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/06/2024] [Indexed: 07/14/2024]
Abstract
The mechanism by which interferon regulatory factor 8 (IRF8) mutation contributes to lymphomagenesis is unknown. We modeled IRF8 variants in B cell lymphomas and found that they affected the expression of regulators of antigen presentation. Expression of IRF8 mutants in murine B cell lymphomas suppressed CD4, but not CD8, activation elicited by antigen presentation and downmodulated CD74 and human leukocyte antigen (HLA) DM, intracellular regulators of antigen peptide processing/loading in the major histocompatibility complex (MHC) II. Concordantly, mutant IRF8 bound less efficiently to the promoters of these genes. Mice harboring IRF8 mutant lymphomas displayed higher tumor burden and remodeling of the tumor microenvironment, typified by depletion of CD4, CD8, and natural killer cells, increase in regulatory T cells and T follicular helper cells. Deconvolution of bulk RNA sequencing data from IRF8-mutant human diffuse large B cell lymphoma (DLBCL) recapitulated part of the immune remodeling detected in mice. We concluded that IRF8 mutations contribute to DLBCL biology by facilitating immune escape.
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MESH Headings
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/metabolism
- Animals
- Antigen Presentation/immunology
- Antigen Presentation/genetics
- Humans
- Mice
- Mutation
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/metabolism
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Tumor Microenvironment/immunology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Cell Line, Tumor
- Tumor Escape/genetics
- Gene Expression Regulation, Neoplastic
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Affiliation(s)
- Zhijun Qiu
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jihane Khalife
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Purushoth Ethiraj
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Carine Jaafar
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - An-Ping Lin
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Kenneth N. Holder
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jacob P. Ritter
- Department of Pathology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Lilly Chiou
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gabriela Huelgas-Morales
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Sadia Aslam
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Zhao Zhang
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Zhijie Liu
- Department of Molecular Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patricia L. M. Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Ricardo C.T. Aguiar
- Division of Hematology and Medical Oncology, Department of Medicine, Mays Cancer Center, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
- South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, TX 78229, USA
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2
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Li B, Adam Eichhorn PJ, Chng WJ. Targeting the ubiquitin pathway in lymphoid malignancies. Cancer Lett 2024; 594:216978. [PMID: 38795760 DOI: 10.1016/j.canlet.2024.216978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
Ubiquitination and related cellular processes control a variety of aspects in human cell biology, and defects in these processes contribute to multiple illnesses. In recent decades, our knowledge about the pathological role of ubiquitination in lymphoid cancers and therapeutic strategies to target the modified ubiquitination system has evolved tremendously. Here we review the altered signalling mechanisms mediated by the aberrant expression of cancer-associated E2s/E3s and deubiquitinating enzymes (DUBs), which result in the hyperactivation of oncoproteins or the frequently allied downregulation of tumour suppressors. We discuss recent highlights pertaining to the several different therapeutic interventions which are currently being evaluated to effectively block abnormal ubiquitin-proteasome pathway and the use of heterobifunctional molecules which recruit the ubiquitination system to degrade or stabilize non-cognate substrates. This review aids in comprehension of ubiquitination aberrance in lymphoid cancers and current targeting strategies and elicits further investigations to deeply understand the link between cellular ubiquitination and lymphoid pathogenesis as well as to ameliorate corresponding treatment interventions.
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Affiliation(s)
- Boheng Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Pieter Johan Adam Eichhorn
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia; Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Singapore, Singapore; Department of Haematology-Oncology, National University Cancer Institute of Singapore, Singapore, Singapore; Department of Medicine, School of Medicine, National University of Singapore, Singapore, Singapore.
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3
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Hamilton MP, Craig E, Gentille Sanchez C, Mina A, Tamaresis J, Kirmani N, Ehlinger Z, Syal S, Good Z, Sworder B, Schroers-Martin J, Lu Y, Muffly L, Negrin RS, Arai S, Lowsky R, Meyer E, Rezvani AR, Shizuru J, Weng WK, Shiraz P, Sidana S, Bharadwaj S, Smith M, Dahiya S, Sahaf B, Kurtz DM, Mackall CL, Tibshirani R, Alizadeh AA, Frank MJ, Miklos DB. CAR19 monitoring by peripheral blood immunophenotyping reveals histology-specific expansion and toxicity. Blood Adv 2024; 8:3314-3326. [PMID: 38498731 PMCID: PMC11258628 DOI: 10.1182/bloodadvances.2024012637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
ABSTRACT Chimeric antigen receptor (CAR) T cells directed against CD19 (CAR19) are a revolutionary treatment for B-cell lymphomas (BCLs). CAR19 cell expansion is necessary for CAR19 function but is also associated with toxicity. To define the impact of CAR19 expansion on patient outcomes, we prospectively followed a cohort of 236 patients treated with CAR19 (brexucabtagene autoleucel or axicabtagene ciloleucel) for mantle cell lymphoma (MCL), follicular lymphoma, and large BCL (LBCL) over the course of 5 years and obtained CAR19 expansion data using peripheral blood immunophenotyping for 188 of these patients. CAR19 expansion was higher in patients with MCL than other lymphoma histologic subtypes. Notably, patients with MCL had increased toxicity and required fourfold higher cumulative steroid doses than patients with LBCL. CAR19 expansion was associated with the development of cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, and the requirement for granulocyte colony-stimulating factor 14 days after infusion. Younger patients and those with elevated lactate dehydrogenase (LDH) had significantly higher CAR19 expansion. In general, no association between CAR19 expansion and LBCL treatment response was observed. However, when controlling for tumor burden, we found that lower CAR19 expansion in conjunction with low LDH was associated with improved outcomes in LBCL. In sum, this study finds CAR19 expansion principally associates with CAR-related toxicity. Additionally, CAR19 expansion as measured by peripheral blood immunophenotyping may be dispensable to favorable outcomes in LBCL.
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Affiliation(s)
- Mark P. Hamilton
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Erin Craig
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Cesar Gentille Sanchez
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Alain Mina
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - John Tamaresis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Nadia Kirmani
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Zachary Ehlinger
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Shriya Syal
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Zinaida Good
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Brian Sworder
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Joseph Schroers-Martin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Ying Lu
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Lori Muffly
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Robert S. Negrin
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Sally Arai
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Robert Lowsky
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Everett Meyer
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Andrew R. Rezvani
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Judith Shizuru
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Wen-Kai Weng
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Parveen Shiraz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Surbhi Sidana
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Sushma Bharadwaj
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Melody Smith
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Saurabh Dahiya
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Bita Sahaf
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - David M. Kurtz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Crystal L. Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Robert Tibshirani
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Ash A. Alizadeh
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University, Stanford, CA
| | - Matthew J. Frank
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - David B. Miklos
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University School of Medicine, Stanford, CA
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Lou SY, Zheng FL, Tang YM, Zheng YN, Lu J, An H, Zhang EJ, Cui SL, Zhao HJ. TYM-3-98, a novel selective inhibitor of PI3Kδ, demonstrates promising preclinical antitumor activity in B-cell lymphomas. Life Sci 2024; 347:122662. [PMID: 38670450 DOI: 10.1016/j.lfs.2024.122662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/07/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
AIMS PI3Kδ is expressed predominately in leukocytes and is commonly found to be aberrantly activated in human B-cell lymphomas. Although PI3Kδ has been intensively targeted for discovering anti-lymphoma drugs, the application of currently approved PI3Kδ inhibitors has been limited due to unwanted systemic toxicities, thus warranting the development of novel PI3Kδ inhibitors with new scaffolds. MAIN METHODS We designed TYM-3-98, an indazole derivative, and evaluated its selectivity for all four PI3K isoforms, as well as its efficacy against various B-cell lymphomas both in vitro and in vivo. KEY FINDINGS We identified TYM-3-98 as a highly selective PI3Kδ inhibitor over other PI3K isoforms at both molecular and cellular levels. It showed superior antiproliferative activity in several B-lymphoma cell lines compared with the approved first-generation PI3Kδ inhibitor idelalisib. TYM-3-98 demonstrated a concentration-dependent PI3K/AKT/mTOR signaling blockage followed by apoptosis induction. In vivo, TYM-3-98 showed good pharmaceutical properties and remarkably reduced tumor growth in a human lymphoma xenograft model and a mouse lymphoma model. SIGNIFICANCE Our findings establish TYM-3-98 as a promising PI3Kδ inhibitor for the treatment of B-cell lymphoma.
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Affiliation(s)
- Si-Yue Lou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China; Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Binwen Rd, Hangzhou, Zhejiang 310053, China
| | - Fan-Li Zheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong-Mei Tang
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ya-Nan Zheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Jun Lu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Hai An
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Binwen Rd, Hangzhou, Zhejiang 310053, China
| | - En-Jun Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China
| | - Sun-Liang Cui
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Hua-Jun Zhao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311403, China; Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Binwen Rd, Hangzhou, Zhejiang 310053, China.
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5
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Sánchez-Beato M, Méndez M, Guirado M, Pedrosa L, Sequero S, Yanguas-Casás N, de la Cruz-Merino L, Gálvez L, Llanos M, García JF, Provencio M. A genetic profiling guideline to support diagnosis and clinical management of lymphomas. Clin Transl Oncol 2024; 26:1043-1062. [PMID: 37672206 PMCID: PMC11026206 DOI: 10.1007/s12094-023-03307-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
The new lymphoma classifications (International Consensus Classification of Mature Lymphoid Neoplasms, and 5th World Health Organization Classification of Lymphoid Neoplasms) include genetics as an integral part of lymphoma diagnosis, allowing better lymphoma subclassification, patient risk stratification, and prediction of treatment response. Lymphomas are characterized by very few recurrent and disease-specific mutations, and most entities have a heterogenous genetic landscape with a long tail of recurrently mutated genes. Most of these occur at low frequencies, reflecting the clinical heterogeneity of lymphomas. Multiple studies have identified genetic markers that improve diagnostics and prognostication, and next-generation sequencing is becoming an essential tool in the clinical laboratory. This review provides a "next-generation sequencing" guide for lymphomas. It discusses the genetic alterations of the most frequent mature lymphoma entities with diagnostic, prognostic, and predictive potential and proposes targeted sequencing panels to detect mutations and copy-number alterations for B- and NK/T-cell lymphomas.
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Affiliation(s)
- Margarita Sánchez-Beato
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain.
| | - Miriam Méndez
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - María Guirado
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital General Universitario de Elche, Alicante, Spain
| | - Lucía Pedrosa
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Silvia Sequero
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario San Cecilio, Granada, Spain
| | - Natalia Yanguas-Casás
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Luis de la Cruz-Merino
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Facultad de Medicina, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBID)/CSIC, Seville, Spain
| | - Laura Gálvez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Marta Llanos
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario de Canarias, La Laguna, Sta. Cruz de Tenerife, Spain
| | - Juan Fernando García
- Servicio de Anatomía Patológica, Hospital MD Anderson Cancer Center, Madrid, Spain
| | - Mariano Provencio
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Departamento de Medicina, Facultad de Medicina, Hospital Universitario Puerta de Hierro-Majadahonda, Universidad Autónoma de Madrid, IDIPHISA, Madrid, Spain
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6
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Carreras J, Hamoudi R, Nakamura N. Artificial intelligence and classification of mature lymphoid neoplasms. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:332-348. [PMID: 38745770 PMCID: PMC11090685 DOI: 10.37349/etat.2024.00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/07/2023] [Indexed: 05/16/2024] Open
Abstract
Hematologists, geneticists, and clinicians came to a multidisciplinary agreement on the classification of lymphoid neoplasms that combines clinical features, histological characteristics, immunophenotype, and molecular pathology analyses. The current classification includes the World Health Organization (WHO) Classification of tumours of haematopoietic and lymphoid tissues revised 4th edition, the International Consensus Classification (ICC) of mature lymphoid neoplasms (report from the Clinical Advisory Committee 2022), and the 5th edition of the proposed WHO Classification of haematolymphoid tumours (lymphoid neoplasms, WHO-HAEM5). This article revises the recent advances in the classification of mature lymphoid neoplasms. Artificial intelligence (AI) has advanced rapidly recently, and its role in medicine is becoming more important as AI integrates computer science and datasets to make predictions or classifications based on complex input data. Summarizing previous research, it is described how several machine learning and neural networks can predict the prognosis of the patients, and classified mature B-cell neoplasms. In addition, new analysis predicted lymphoma subtypes using cell-of-origin markers that hematopathologists use in the clinical routine, including CD3, CD5, CD19, CD79A, MS4A1 (CD20), MME (CD10), BCL6, IRF4 (MUM-1), BCL2, SOX11, MNDA, and FCRL4 (IRTA1). In conclusion, although most categories are similar in both classifications, there are also conceptual differences and differences in the diagnostic criteria for some diseases. It is expected that AI will be incorporated into the lymphoma classification as another bioinformatics tool.
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Affiliation(s)
- Joaquim Carreras
- Department of Pathology, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Rifat Hamoudi
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, WC1E 6BT London, UK
| | - Naoya Nakamura
- Department of Pathology, Tokai University School of Medicine, Isehara 259-1193, Japan
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7
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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] [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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8
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Deng Q, Lakra P, Gou P, Yang H, Meydan C, Teater M, Chin C, Zhang W, Dinh T, Hussein U, Li X, Rojas E, Liu W, Reville PK, Kizhakeyil A, Barisic D, Parsons S, Wilson A, Henderson J, Scull B, Gurumurthy C, Vega F, Chadburn A, Cuglievan B, El-Mallawany NK, Allen C, Mason C, Melnick A, Green MR. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions. Cancer Cell 2024; 42:605-622.e11. [PMID: 38458188 PMCID: PMC11003852 DOI: 10.1016/j.ccell.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/30/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including ∼30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-κB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt lymphoma cells. SMARCA4 therefore facilitates chromatin accessibility for TFs that shape centrocyte trajectories, and loss of fine-control of these programs biases toward centroblast cell-fate, GC hyperplasia and lymphoma.
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Affiliation(s)
- Qing Deng
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priya Lakra
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Panhong Gou
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Haopeng Yang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cem Meydan
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matthew Teater
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Chin
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wenchao Zhang
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tommy Dinh
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Usama Hussein
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xubin Li
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Estela Rojas
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiguang Liu
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick K Reville
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atish Kizhakeyil
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Darko Barisic
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sydney Parsons
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashley Wilson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared Henderson
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brooks Scull
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | | | - Francisco Vega
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Branko Cuglievan
- Department of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nader Kim El-Mallawany
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Carl Allen
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX, USA
| | - Christopher Mason
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Department of Medicine and Weill Cornell Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Michael R Green
- Department of Lymphoma & Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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9
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Sievers Q, Abdel-Wahab O. SWI/SNF regulation of germinal center fate and lymphomagenesis. Cancer Cell 2024; 42:507-509. [PMID: 38458185 DOI: 10.1016/j.ccell.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
The mSWI/SNF subunits ARID1A and SMARCA4 are mutated in B cell lymphomas. Now, Barisic et al. and Deng et al. find that loss of ARID1A or SMARCA4 contributes to lymphomagenesis by causing B cells to aberrantly re-enter germinal centers where they undergo repeated rounds of proliferation and somatic hypermutation.
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Affiliation(s)
- Quinlan Sievers
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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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] [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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11
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Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024; 5:101443. [PMID: 38428430 PMCID: PMC10983045 DOI: 10.1016/j.xcrm.2024.101443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin, which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies, combined with machine-learning approaches, we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed, proliferative, and chromatin-modifying states, with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling, we find that each state was associated with a combination of mutations in chromatin modifiers, copy-number alterations to TNFAIP3, and T follicular helper cells (Tfh) cell interactions, or primarily by a microenvironment rich in activated T cells. Altogether, these data define FL B cell transcriptional states across a large cohort of patients, contribute to our understanding of FL heterogeneity at the tumor cell level, and provide a foundation for guiding therapeutic intervention.
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Matthew J Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - ZhiZhang Yang
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Brian K Link
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Rebecca L King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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12
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Gordon MJ, Feng L, Strati P, Lee HJ, Hagemeister FB, Westin JR, Samaniego F, Marques-Piubelli ML, Parra Cuentas ER, Solis-Soto LM, Ma W, Wang J, Claret L, Averill B, Ibanez K, Fayad LE, Flowers CR, Green MR, Davis RE, Neelapu SS, Fowler NH, Nastoupil LJ. Safety and efficacy of ibrutinib in combination with rituximab and lenalidomide in previously untreated follicular and marginal zone lymphoma: An open label, phase 2 study. Cancer 2024; 130:876-885. [PMID: 37985359 PMCID: PMC10922670 DOI: 10.1002/cncr.35114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 08/08/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Follicular lymphoma (FL) and marginal zone lymphoma (MZL) are indolent non-Hodgkin lymphomas (iNHL). Median survival for iNHL is approximately 20 years. Because standard treatments are not curative, patients often receive multiple lines of therapy with associated toxicity-rationally designed, combination therapies with curative potential are needed. The immunomodulatory drug lenalidomide was evaluated in combination with rituximab for the frontline treatment of FL in the phase 3 RELEVANCE study. Ibrutinib, an oral Bruton tyrosine kinase inhibitor, is active in NHL and was evaluated in combination with lenalidomide, rituximab, and ibrutinib (IRR) in a phase 1 study. METHODS The authors conducted an open-label, phase 2 clinical trial of IRR for previously untreated FL and MZL. The primary end point was progression-free survival (PFS) at 24 months. RESULTS This study included 48 participants with previously untreated FL grade 1-3a (N = 38), or MZL (N = 10). Participants received 12, 28-day cycles of lenalidomide (15 mg, days 1-21 cycle 1; 20 mg, cycles 2-12), rituximab (375 mg/m2 weekly in cycle 1; day 1 cycles 2-12), and ibrutinib 560 mg daily. With a median follow-up of 65.3 months, the estimated PFS at 24 months was 78.8% (95% confidence interval [CI], 68.0%-91.4%) and 60-month PFS was 59.7% (95% CI, 46.6%-76.4%). One death occurred unrelated to disease progression. Grade 3-4 adverse events were observed in 64.6%, including 50% with grade 3-4 rash. CONCLUSIONS IRR is highly active as frontline therapy for FL and MZL. Compared to historical results with lenalidomide and rituximab, PFS is similar with higher grade 3-4 toxicity, particularly rash. The study was registered with ClinicalTrials.gov (NCT02532257).
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Affiliation(s)
- Max J. Gordon
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Paolo Strati
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Hun Ju Lee
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Fredrick B. Hagemeister
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jason R. Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Felipe Samaniego
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Mario L. Marques-Piubelli
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Edwin R Parra Cuentas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Luisa M Solis-Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Linda Claret
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Barbara Averill
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Karina Ibanez
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Luis E. Fayad
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christopher R. Flowers
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Michael R. Green
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - R. Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Sattva S. Neelapu
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Nathan H. Fowler
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Loretta J. Nastoupil
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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13
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Xu D, Bewicke-Copley F, Close K, Okosun J, Gale RP, Apperley J, Weinstock DM, Wendel HG, Fitzgibbon J. Targeting lysine demethylase 5 (KDM5) in mantle cell lymphoma. Blood Cancer J 2024; 14:29. [PMID: 38351059 PMCID: PMC10864367 DOI: 10.1038/s41408-024-00999-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Affiliation(s)
- Danmei Xu
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK.
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK.
- Centre for Haematology, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK.
- Oxford Cancer and Haematology centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK.
| | - Findlay Bewicke-Copley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
| | - Karina Close
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
| | - Robert Peter Gale
- Centre for Haematology, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK
| | - Jane Apperley
- Centre for Haematology, Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Merck and Co., Rahway, NJ, USA
| | - Hans-Guido Wendel
- Memorial Sloan-Kettering Cancer Center, Cancer Biology & Genetics, New York, NY, 10065, USA
| | - Jude Fitzgibbon
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Sq, London, UK
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14
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Castejón-Griñán M, Albers E, Simón-Carrasco L, Aguilera P, Sbroggio M, Pladevall-Morera D, Ingham A, Lim E, Guillen-Benitez A, Pietrini E, Lisby M, Hickson ID, Lopez-Contreras AJ. PICH deficiency limits the progression of MYC-induced B-cell lymphoma. Blood Cancer J 2024; 14:16. [PMID: 38253636 PMCID: PMC10803365 DOI: 10.1038/s41408-024-00979-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Plk1-interacting checkpoint helicase (PICH) is a DNA translocase involved in resolving ultrafine anaphase DNA bridges and, therefore, is important to safeguard chromosome segregation and stability. PICH is overexpressed in various human cancers, particularly in lymphomas such as Burkitt lymphoma, which is caused by MYC translocations. To investigate the relevance of PICH in cancer development and progression, we have combined novel PICH-deficient mouse models with the Eμ-Myc transgenic mouse model, which recapitulates B-cell lymphoma development. We have observed that PICH deficiency delays the onset of MYC-induced lymphomas in Pich heterozygous females. Moreover, using a Pich conditional knockout mouse model, we have found that Pich deletion in adult mice improves the survival of Eμ-Myc transgenic mice. Notably, we show that Pich deletion in healthy adult mice is well tolerated, supporting PICH as a suitable target for anticancer therapies. Finally, we have corroborated these findings in two human Burkitt lymphoma cell lines and we have found that the death of cancer cells was accompanied by chromosomal instability. Based on these findings, we propose PICH as a potential therapeutic target for Burkitt lymphoma and for other cancers where PICH is overexpressed.
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Affiliation(s)
- María Castejón-Griñán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eliene Albers
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lucía Simón-Carrasco
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain
| | - Paula Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mauro Sbroggio
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David Pladevall-Morera
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Ingham
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ernest Lim
- Center for Chromosome Stability, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alba Guillen-Benitez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain
| | - Elena Pietrini
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain
| | - Michael Lisby
- Center for Chromosome Stability, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Andres J Lopez-Contreras
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla - Universidad Pablo de Olavide, Seville, Spain.
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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15
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Tkachenko A, Kupcova K, Havranek O. B-Cell Receptor Signaling and Beyond: The Role of Igα (CD79a)/Igβ (CD79b) in Normal and Malignant B Cells. Int J Mol Sci 2023; 25:10. [PMID: 38203179 PMCID: PMC10779339 DOI: 10.3390/ijms25010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
B-cell receptor (BCR) is a B cell hallmark surface complex regulating multiple cellular processes in normal as well as malignant B cells. Igα (CD79a)/Igβ (CD79b) are essential components of BCR that are indispensable for its functionality, signal initiation, and signal transduction. CD79a/CD79b-mediated BCR signaling is required for the survival of normal as well as malignant B cells via a wide signaling network. Recent studies identified the great complexity of this signaling network and revealed the emerging role of CD79a/CD79b in signal integration. In this review, we have focused on functional features of CD79a/CD79b, summarized signaling consequences of CD79a/CD79b post-translational modifications, and highlighted specifics of CD79a/CD79b interactions within BCR and related signaling cascades. We have reviewed the complex role of CD79a/CD79b in multiple aspects of normal B cell biology and how is the normal BCR signaling affected by lymphoid neoplasms associated CD79A/CD79B mutations. We have also summarized important unresolved questions and highlighted issues that remain to be explored for better understanding of CD79a/CD79b-mediated signal transduction and the eventual identification of additional therapeutically targetable BCR signaling vulnerabilities.
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Affiliation(s)
- Anton Tkachenko
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Kristyna Kupcova
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
- First Department of Internal Medicine–Hematology, General University Hospital and First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Ondrej Havranek
- BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, 252 50 Vestec, Czech Republic
- First Department of Internal Medicine–Hematology, General University Hospital and First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
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16
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Decombis S, Bellanger C, Le Bris Y, Madiot C, Jardine J, Santos JC, Boulet D, Dousset C, Menard A, Kervoelen C, Douillard E, Moreau P, Minvielle S, Moreau-Aubry A, Tessoulin B, Roue G, Bidère N, Le Gouill S, Pellat-Deceunynck C, Chiron D. CARD11 gain of function upregulates BCL2A1 expression and promotes resistance to targeted therapies combination in B-cell lymphoma. Blood 2023; 142:1543-1555. [PMID: 37562004 DOI: 10.1182/blood.2023020211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
A strategy combining targeted therapies is effective in B-cell lymphomas (BCL), such as mantle cell lymphoma (MCL), but acquired resistances remain a recurrent issue. In this study, we performed integrative longitudinal genomic and single-cell RNA-sequencing analyses of patients with MCL who were treated with targeted therapies against CD20, BCL2, and Bruton tyrosine kinase (OAsIs trial). We revealed the emergence of subclones with a selective advantage against OAsIs combination in vivo and showed that resistant cells were characterized by B-cell receptor (BCR)-independent overexpression of NF-κB1 target genes, especially owing to CARD11 mutations. Functional studies demonstrated that CARD11 gain of function not only resulted in BCR independence but also directly increased the transcription of the antiapoptotic BCL2A1, leading to resistance against venetoclax and OAsIs combination. Based on the transcriptional profile of OAsIs-resistant subclones, we designed a 16-gene resistance signature that was also predictive for patients with MCL who were treated with conventional chemotherapy, underlying a common escape mechanism. Among druggable strategies to inhibit CARD11-dependent NF-κB1 transduction, we evaluated the selective inhibition of its essential partner MALT1. We demonstrated that MALT1 protease inhibition led to a reduction in the expression of genes involved in OAsIs resistance, including BCL2A1. Consequently, MALT1 inhibition induced synergistic cell death in combination with BCL2 inhibition, irrespective of CARD11 mutational status, both in vitro and in vivo. Taken together, our study identified mechanisms of resistance to targeted therapies and provided a novel strategy to overcome resistance in aggressive BCL. The OAsIs trial was registered at www.clinicaltrials.gov #NCT02558816.
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Affiliation(s)
- Salomé Decombis
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Celine Bellanger
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Yannick Le Bris
- Hematology Department, Nantes Université, Centre Hospitalier Universitaire de Nantes, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Candice Madiot
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Jane Jardine
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | | | - Delphine Boulet
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Christelle Dousset
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Audrey Menard
- Hematology Department, Nantes Université, Centre Hospitalier Universitaire de Nantes, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Charlotte Kervoelen
- Therassay (Onco-Hemato) Core Facility, Nantes Université, Capacités, Nantes, France
| | - Elise Douillard
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Philippe Moreau
- Hematology Department, Nantes Université, Centre Hospitalier Universitaire de Nantes, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Stephane Minvielle
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Agnes Moreau-Aubry
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Benoit Tessoulin
- Hematology Department, Nantes Université, Centre Hospitalier Universitaire de Nantes, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | - Gael Roue
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Nicolas Bidère
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
| | | | | | - David Chiron
- Hematology Department, Nantes Université, INSERM, CNRS, Université d'Angers, CRCI2NA, Nantes, France
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17
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Gao F, Liu H, Meng X, Liu J, Wang J, Yu J, Liu X, Liu X, Li L, Qiu L, Qian Z, Zhou S, Gong W, Meng B, Ren X, Golchehre Z, Chavoshzadeh Z, He J, Zhang H, Wang X. Integrative genomic and transcriptomic analysis reveals genetic alterations associated with the early progression of follicular lymphoma. Br J Haematol 2023; 202:1151-1164. [PMID: 37455019 DOI: 10.1111/bjh.18974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Follicular lymphoma (FL), the most common indolent lymphoma, is a clinically and genetically heterogeneous disease. However, the prognostic value of driver gene mutations and copy number alterations has not been systematically assessed. Here, we analysed the clinical-biological features of 415 FL patients to identify variables associated with disease progression within 24 months of first-line therapy (POD24). Patients with B symptoms, elevated lactate dehydrogenase and β2-microglobulin levels, unfavourable baseline haemoglobin levels, advanced stage, and high-risk FL International Prognostic Index (FLIPI) scores had an increased risk of POD24, with FLIPI being the most important factor in logistic regression. HIST1H1D, identified as a driver mutation, was correlated with POD24. Gains of 6p22.2 (HIST1H1D) and 18q21.33 (BCL2) and loss of 1p36.13 (NBPF1) predicted POD24 independent of FLIPI. Gene expression profiling of FL samples showed that the POD24 cohort was significantly enriched in the inflammatory response (mediated by interferon and tumour necrosis factor), cell cycle regulation (transcription, replication and proliferation) sets and PI3K-AKT-mTOR signalling. This result was further validated with transcriptome-wide information provided by RNA-seq at single-cell resolution. Our study, performed on a large cohort of FL patients, highlights the importance of distinctive genetic alterations and gene expression relevant to disease diagnosis and early progression.
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Affiliation(s)
- Fenghua Gao
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Hengqi Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xiangrui Meng
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jing Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Jiesong Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
- Department of Lymphoma & Head and Neck Oncology, College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, China
| | - Jingwei Yu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xia Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianming Liu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lanfang Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Lihua Qiu
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Zhengzi Qian
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Shiyong Zhou
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Wenchen Gong
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Bin Meng
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiubao Ren
- Department of Immunology/Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Zahra Golchehre
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Department of Immunology/Allergy, Pediatric Infections Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jin He
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, the Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
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18
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Lees J, Hay J, Moles MW, Michie AM. The discrete roles of individual FOXO transcription factor family members in B-cell malignancies. Front Immunol 2023; 14:1179101. [PMID: 37275916 PMCID: PMC10233034 DOI: 10.3389/fimmu.2023.1179101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Forkhead box (FOX) class O (FOXO) proteins are a dynamic family of transcription factors composed of four family members: FOXO1, FOXO3, FOXO4 and FOXO6. As context-dependent transcriptional activators and repressors, the FOXO family regulates diverse cellular processes including cell cycle arrest, apoptosis, metabolism, longevity and cell fate determination. A central pathway responsible for negative regulation of FOXO activity is the phosphatidylinositol-3-kinase (PI3K)-AKT signalling pathway, enabling cell survival and proliferation. FOXO family members can be further regulated by distinct kinases, both positively (e.g., JNK, AMPK) and negatively (e.g., ERK-MAPK, CDK2), with additional post-translational modifications further impacting on FOXO activity. Evidence has suggested that FOXOs behave as 'bona fide' tumour suppressors, through transcriptional programmes regulating several cellular behaviours including cell cycle arrest and apoptosis. However, an alternative paradigm has emerged which indicates that FOXOs operate as mediators of cellular homeostasis and/or resistance in both 'normal' and pathophysiological scenarios. Distinct FOXO family members fulfil discrete roles during normal B cell maturation and function, and it is now clear that FOXOs are aberrantly expressed and mutated in discrete B-cell malignancies. While active FOXO function is generally associated with disease suppression in chronic lymphocytic leukemia for example, FOXO expression is associated with disease progression in diffuse large B cell lymphoma, an observation also seen in other cancers. The opposing functions of the FOXO family drives the debate about the circumstances in which FOXOs favour or hinder disease progression, and whether targeting FOXO-mediated processes would be effective in the treatment of B-cell malignancies. Here, we discuss the disparate roles of FOXO family members in B lineage cells, the regulatory events that influence FOXO function focusing mainly on post-translational modifications, and consider the potential for future development of therapies that target FOXO activity.
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Affiliation(s)
| | | | | | - Alison M. Michie
- Paul O’Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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19
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Thus YJ, De Rooij MFM, Swier N, Beijersbergen RL, Guikema JEJ, Kersten MJ, Eldering E, Pals ST, Kater AP, Spaargaren M. Inhibition of casein kinase 2 sensitizes mantle cell lymphoma to venetoclax through MCL-1 downregulation. Haematologica 2023; 108:797-810. [PMID: 36226498 PMCID: PMC9973496 DOI: 10.3324/haematol.2022.281668] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
BCL-2 family proteins are frequently aberrantly expressed in mantle cell lymphoma (MCL). Recently, the BCL-2-specific inhibitor venetoclax has been approved by the US Food and Drug Administration for chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML). In MCL, venetoclax has shown promising efficacy in early clinical trials; however, a significant subset of patients is resistant. By conducting a kinome-centered CRISPR-Cas9 knockout sensitizer screen, we identified casein kinase 2 (CK2) as a major regulator of venetoclax resistance in MCL. Interestingly, CK2 is over-expressed in MCL and high CK2 expression is associated with poor patient survival. Targeting of CK2, either by inducible short hairpin RNA (shRNA)-mediated knockdown of CK2 or by the CK2-inhibitor silmitasertib, did not affect cell viability by itself, but strongly synergized with venetoclax in both MCL cell lines and primary samples, also if combined with ibrutinib. Furthermore, targeting of CK2 reduced MCL-1 levels, which involved impaired MCL-1 translation by inhibition of eIF4F complex assembly, without affecting BCL-2 and BCL-XL expression. Combined, this results in enhanced BCL-2 dependence and, consequently, venetoclax sensitization. In cocultures, targeting of CK2 overcame stroma-mediated venetoclax resistance of MCL cells. Taken together, our findings indicate that targeting of CK2 sensitizes MCL cells to venetoclax through downregulation of MCL-1. These novel insights provide a strong rationale for combining venetoclax with CK2 inhibition as therapeutic strategy for MCL patients.
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Affiliation(s)
- Yvonne J Thus
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Martin F M De Rooij
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Nathalie Swier
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands; The NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam
| | - Jeroen E J Guikema
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Marie-José Kersten
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Eric Eldering
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam, The Netherlands; Department of Experimental Immunology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Steven T Pals
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam
| | - Arnon P Kater
- Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam, The Netherlands; Department of Hematology, Amsterdam UMC location University of Amsterdam, Amsterdam
| | - Marcel Spaargaren
- Department of Pathology, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, The Netherlands; Cancer Center Amsterdam (CCA), Cancer Biology and Immunology - Target and Therapy Discovery, Amsterdam.
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20
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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21
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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22
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Targeting Pim kinases in hematological cancers: molecular and clinical review. Mol Cancer 2023; 22:18. [PMID: 36694243 PMCID: PMC9875428 DOI: 10.1186/s12943-023-01721-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Decades of research has recognized a solid role for Pim kinases in lymphoproliferative disorders. Often up-regulated following JAK/STAT and tyrosine kinase receptor signaling, Pim kinases regulate cell proliferation, survival, metabolism, cellular trafficking and signaling. Targeting Pim kinases represents an interesting approach since knock-down of Pim kinases leads to non-fatal phenotypes in vivo suggesting clinical inhibition of Pim may have less side effects. In addition, the ATP binding site offers unique characteristics that can be used for the development of small inhibitors targeting one or all Pim isoforms. This review takes a closer look at Pim kinase expression and involvement in hematopoietic cancers. Current and past clinical trials and in vitro characterization of Pim kinase inhibitors are examined and future directions are discussed. Current studies suggest that Pim kinase inhibition may be most valuable when accompanied by multi-drug targeting therapy.
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23
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Mlynarczyk C, Teater M, Pae J, Chin CR, Wang L, Arulraj T, Barisic D, Papin A, Hoehn KB, Kots E, Ersching J, Bandyopadhyay A, Barin E, Poh HX, Evans CM, Chadburn A, Chen Z, Shen H, Isles HM, Pelzer B, Tsialta I, Doane AS, Geng H, Rehman MH, Melnick J, Morgan W, Nguyen DTT, Elemento O, Kharas MG, Jaffrey SR, Scott DW, Khelashvili G, Meyer-Hermann M, Victora GD, Melnick A. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science 2023; 379:eabj7412. [PMID: 36656933 PMCID: PMC10515739 DOI: 10.1126/science.abj7412] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/12/2022] [Indexed: 01/21/2023]
Abstract
Multicellular life requires altruistic cooperation between cells. The adaptive immune system is a notable exception, wherein germinal center B cells compete vigorously for limiting positive selection signals. Studying primary human lymphomas and developing new mouse models, we found that mutations affecting BTG1 disrupt a critical immune gatekeeper mechanism that strictly limits B cell fitness during antibody affinity maturation. This mechanism converted germinal center B cells into supercompetitors that rapidly outstrip their normal counterparts. This effect was conferred by a small shift in MYC protein induction kinetics but resulted in aggressive invasive lymphomas, which in humans are linked to dire clinical outcomes. Our findings reveal a delicate evolutionary trade-off between natural selection of B cells to provide immunity and potentially dangerous features that recall the more competitive nature of unicellular organisms.
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Affiliation(s)
- Coraline Mlynarczyk
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matt Teater
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juhee Pae
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Christopher R. Chin
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biomedicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ling Wang
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Darko Barisic
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Antonin Papin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonatan Ersching
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Arnab Bandyopadhyay
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ersilia Barin
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hui Xian Poh
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chiara M. Evans
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Hao Shen
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Hannah M. Isles
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Benedikt Pelzer
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ioanna Tsialta
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S. Doane
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Muhammad Hassan Rehman
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Medicine–Qatar, Doha, Qatar
| | - Jonah Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Wyatt Morgan
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Diu T. T. Nguyen
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael G. Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, and Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samie R. Jaffrey
- Department of Pharmacology and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - George Khelashvili
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Ari Melnick
- Division of Hematology and Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
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24
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Perrett M, Edmondson C, Okosun J. Biology of follicular lymphoma: insights and windows of clinical opportunity. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2022; 2022:688-694. [PMID: 36485095 PMCID: PMC9820323 DOI: 10.1182/hematology.2022000361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Follicular lymphoma (FL) is a heterogeneous disease, both clinically and biologically. The biological behavior and development of FL is a culmination of complex multistep processes underpinned by genetic and nongenetic determinants. Epigenetic deregulation through recurrent genetic alterations is now a recognized major biological hallmark of FL, alongside the t(14;18) translocation. In parallel, there is a strong interplay between the lymphoma B cells and the immune microenvironment, with the microenvironment serving as a critical enabler by creating a tumor-supportive niche and modulating the immune response to favor survival of the malignant B cells. A further layer of complexity arises from the biological heterogeneity that occurs between patients and within an individual, both over the course of the disease and at different sites of disease involvement. Altogether, taking the first steps to bridge the understanding of these various biological components and how to evaluate these clinically may aid and inform future strategies, including logical therapeutic interventions, risk stratification, therapy selection, and disease monitoring.
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Affiliation(s)
- Megan Perrett
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carina Edmondson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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25
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Fahrmann JF, Saini NY, Chia-Chi C, Irajizad E, Strati P, Nair R, Fayad LE, Ahmed S, Lee HJ, Iyer S, Steiner R, Vykoukal J, Wu R, Dennison JB, Nastoupil L, Jain P, Wang M, Green M, Westin J, Blumenberg V, Davila M, Champlin R, Shpall EJ, Kebriaei P, Flowers CR, Jain M, Jenq R, Stein-Thoeringer CK, Subklewe M, Neelapu SS, Hanash S. A polyamine-centric, blood-based metabolite panel predictive of poor response to CAR-T cell therapy in large B cell lymphoma. Cell Rep Med 2022; 3:100720. [PMID: 36384092 PMCID: PMC9729795 DOI: 10.1016/j.xcrm.2022.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/06/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022]
Abstract
Anti-CD19 chimeric antigen receptor (CAR) T cell therapy for relapsed or refractory (r/r) large B cell lymphoma (LBCL) results in durable response in only a subset of patients. MYC overexpression in LBCL tumors is associated with poor response to treatment. We tested whether an MYC-driven polyamine signature, as a liquid biopsy, is predictive of response to anti-CD19 CAR-T therapy in patients with r/r LBCL. Elevated plasma acetylated polyamines were associated with non-durable response. Concordantly, increased expression of spermidine synthase, a key enzyme that regulates levels of acetylated spermidine, was prognostic for survival in r/r LBCL. A broad metabolite screen identified additional markers that resulted in a 6-marker panel (6MetP) consisting of acetylspermidine, diacetylspermidine, and lysophospholipids, which was validated in an independent set from another institution as predictive of non-durable response to CAR-T therapy. A polyamine centric metabolomics liquid biopsy panel has predictive value for response to CAR-T therapy in r/r LBCL.
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Affiliation(s)
- Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Neeraj Y. Saini
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA,Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chang Chia-Chi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ehsan Irajizad
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Luis E. Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Hun Ju Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Swaminathan Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Raphael Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jody Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Ranran Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Loretta Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Preetesh Jain
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Michael Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jason Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Viktoria Blumenberg
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany,National Center for Tumor Diseases (NCT), Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Marco Davila
- Department of Blood and Marrow Transplant and Cellular Therapy, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Richard Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Christopher R. Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Michael Jain
- Department of Blood and Marrow Transplant and Cellular Therapy, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Robert Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Christoph K. Stein-Thoeringer
- National Center for Tumor Diseases (NCT), Neuenheimer Feld 460, 69120 Heidelberg, Germany,German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, LMU Munich, 81377 Munich, Germany,German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany,Laboratory for Translational Cancer Immunology, Gene Center of the LMU Munich, Munich, Germany,Corresponding author
| | - Sattva S. Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA,Corresponding author
| | - Sam Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX 77030, USA,Corresponding author
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26
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Crouch S, Painter D, Barrans SL, Roman E, Beer PA, Cooke SL, Glover P, Van Hoppe SJ, Webster N, Lacy SE, Ruiz C, Campbell PJ, Hodson DJ, Patmore R, Burton C, Smith A, Tooze RM. Molecular subclusters of follicular lymphoma: a report from the United Kingdom's Haematological Malignancy Research Network. Blood Adv 2022; 6:5716-5731. [PMID: 35363872 PMCID: PMC9619185 DOI: 10.1182/bloodadvances.2021005284] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/06/2022] [Indexed: 11/20/2022] Open
Abstract
Follicular lymphoma (FL) is morphologically and clinically diverse, with mutations in epigenetic regulators alongside t(14;18) identified as disease-initiating events. Identification of additional mutational entities confirms this cancer's heterogeneity, but whether mutational data can be resolved into mechanistically distinct subsets remains an open question. Targeted sequencing was applied to an unselected population-based FL cohort (n = 548) with full clinical follow-up (n = 538), which included 96 diffuse large B-cell lymphoma (DLBCL) transformations. We investigated whether molecular subclusters of FL can be identified and whether mutational data provide predictive information relating to transformation. DNA extracted from FL samples was sequenced with a 293-gene panel representing genes frequently mutated in DLBCL and FL. Three clusters were resolved using mutational data alone, independent of translocation status: FL_aSHM, with high burden of aberrant somatic hypermutation (aSHM) targets; FL_STAT6, with high STAT6 & CREBBP mutation and low aSHM; and FL_Com, with the absence of features of other subtypes and enriched KMT2D mutation. Analysis of mutation signatures demonstrated differential enrichment of predicted mutation signatures between subgroups and a dominant preference in the FL_aSHM subgroup for G(C>T)T and G(C>T)C transitions consistent with previously defined aSHM-like patterns. Of transformed cases with paired samples, 17 of 26 had evidence of branching evolution. Poorer overall survival (OS) in the aSHM group (P = .04) was associated with older age; however, overall tumor genetics provided limited information to predict individual patient risk. Our approach identifies 3 molecular subclusters of FL linked to differences in underlying mechanistic pathways. These clusters, which may be further resolved by the inclusion of translocation status and wider mutation profiles, have implications for understanding pathogenesis as well as improving treatment strategies in the future.
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Affiliation(s)
- Simon Crouch
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Daniel Painter
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Sharon L. Barrans
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Philip A. Beer
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Susanna L. Cooke
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Paul Glover
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Suzan J.L. Van Hoppe
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Nichola Webster
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Stuart E. Lacy
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Camilo Ruiz
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Daniel J. Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Russell Patmore
- Queen’s Centre for Oncology and Haematology, Castle Hill Hospital, Cottingham, United Kingdom
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Alexandra Smith
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Reuben M. Tooze
- Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
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27
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Carreras J, Roncador G, Hamoudi R. Artificial Intelligence Predicted Overall Survival and Classified Mature B-Cell Neoplasms Based on Immuno-Oncology and Immune Checkpoint Panels. Cancers (Basel) 2022; 14:5318. [PMID: 36358737 PMCID: PMC9657332 DOI: 10.3390/cancers14215318] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 08/01/2023] Open
Abstract
Artificial intelligence (AI) can identify actionable oncology biomarkers. This research integrates our previous analyses of non-Hodgkin lymphoma. We used gene expression and immunohistochemical data, focusing on the immune checkpoint, and added a new analysis of macrophages, including 3D rendering. The AI comprised machine learning (C5, Bayesian network, C&R, CHAID, discriminant analysis, KNN, logistic regression, LSVM, Quest, random forest, random trees, SVM, tree-AS, and XGBoost linear and tree) and artificial neural networks (multilayer perceptron and radial basis function). The series included chronic lymphocytic leukemia, mantle cell lymphoma, follicular lymphoma, Burkitt, diffuse large B-cell lymphoma, marginal zone lymphoma, and multiple myeloma, as well as acute myeloid leukemia and pan-cancer series. AI classified lymphoma subtypes and predicted overall survival accurately. Oncogenes and tumor suppressor genes were highlighted (MYC, BCL2, and TP53), along with immune microenvironment markers of tumor-associated macrophages (M2-like TAMs), T-cells and regulatory T lymphocytes (Tregs) (CD68, CD163, MARCO, CSF1R, CSF1, PD-L1/CD274, SIRPA, CD85A/LILRB3, CD47, IL10, TNFRSF14/HVEM, TNFAIP8, IKAROS, STAT3, NFKB, MAPK, PD-1/PDCD1, BTLA, and FOXP3), apoptosis (BCL2, CASP3, CASP8, PARP, and pathway-related MDM2, E2F1, CDK6, MYB, and LMO2), and metabolism (ENO3, GGA3). In conclusion, AI with immuno-oncology markers is a powerful predictive tool. Additionally, a review of recent literature was made.
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Affiliation(s)
- Joaquim Carreras
- Department of Pathology, School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan
| | - Giovanna Roncador
- Monoclonal Antibodies Unit, Spanish National Cancer Research Center (Centro Nacional de Investigaciones Oncologicas, CNIO), Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Rifat Hamoudi
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, Gower Street, London WC1E 6BT, UK
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28
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Denizot Y, Braza MS, Amin R. Editorial: B Cell Non-Hodgkin’s Lymphoma & Tumor Microenvironment Crosstalk: An Epigenetic Matter? Front Genet 2022; 13:912737. [PMID: 35664310 PMCID: PMC9161633 DOI: 10.3389/fgene.2022.912737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Y Denizot
- UMR CNRS 7276, INSERM U1262, Equipe Labellise LIGUE 2018, Universite de Limoges, CBRS, Limoges, France
| | - MS Braza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - R Amin
- Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
- *Correspondence: R Amin,
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29
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Freile JÁ, Ustyanovska Avtenyuk N, Corrales MG, Lourens HJ, Huls G, van Meerten T, Cendrowicz E, Bremer E. CD24 Is a Potential Immunotherapeutic Target for Mantle Cell Lymphoma. Biomedicines 2022; 10:1175. [PMID: 35625912 PMCID: PMC9138264 DOI: 10.3390/biomedicines10051175] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 01/05/2023] Open
Abstract
CD24 and its ligand Siglec-10 were described as an innate immune checkpoint in carcinoma. Here, we investigated this axis in B-cell lymphoma by assessing CD24 expression and evaluating pro-phagocytic effects of CD24 antibody treatment in comparison to hallmark immune checkpoint CD47. In mantle cell lymphoma (MCL) and follicular lymphoma patients, high mRNA expression of CD24 correlated with poor overall survival, whereas CD47 expression did not. Conversely, CD24 expression did not correlate with survival in diffuse large B-cell lymphoma (DLBCL), whereas CD47 did. CD24 was also highly expressed on MCL cell lines, where treatment with CD24 antibody clones SN3 or ML5 potently induced phagocytosis, with SN3 yielding >90% removal of MCL cells and triggering phagocytosis of primary patient-derived MCL cells by autologous macrophages. Treatment with CD24 mAb was superior to CD47 mAb in MCL and was comparable in magnitude to the effect observed in carcinoma lines. Reversely, CD24 mAb treatment was less effective than CD47 mAb treatment in DLBCL. Finally, phagocytic activity of clone SN3 appeared at least partly independent of antibody-dependent cellular phagocytosis (ADCP), suggesting CD24/Siglec-10 checkpoint activity, whereas clone ML5 solely induced ADCP. In conclusion, CD24 is an immunotherapeutic target of potential clinical relevance for MCL, but not DLBCL.
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Affiliation(s)
- Jimena Álvarez Freile
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Natasha Ustyanovska Avtenyuk
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Macarena González Corrales
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Harm Jan Lourens
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Gerwin Huls
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Tom van Meerten
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
| | - Ewa Cendrowicz
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
- Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Edwin Bremer
- Department of Hematology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (J.Á.F.); (N.U.A.); (M.G.C.); (H.J.L.); (G.H.); (T.v.M.)
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Neoantigens – the next frontier in precision immunotherapy for B-cell lymphoproliferative disorders. Blood Rev 2022; 56:100969. [DOI: 10.1016/j.blre.2022.100969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022]
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Marino D, Pizzi M, Kotova I, Schmidt R, Schröder C, Guzzardo V, Talli I, Peroni E, Finotto S, Scapinello G, Dei Tos AP, Piazza F, Trentin L, Zagonel V, Piovan E. High ETV6 Levels Support Aggressive B Lymphoma Cell Survival and Predict Poor Outcome in Diffuse Large B-Cell Lymphoma Patients. Cancers (Basel) 2022; 14:cancers14020338. [PMID: 35053500 PMCID: PMC8774128 DOI: 10.3390/cancers14020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022] Open
Abstract
The identification of prognostic factors for aggressive B-cell lymphomas still represents an unmet clinical need. We used forward phase protein arrays (FFPA) to identify proteins associated with overall survival (OS) from diagnostic formalin-fixed paraffin-embedded material of diffuse large B-cell lymphoma (DLBCL) patients (n = 47). Univariate Cox regression analysis identified numerous proteins, including immune check-point molecules (PDCD1, PDCD2 and PD1L2) and BCL2 to be significantly associated with OS. However, only ETV6 and PIM2 proteins persisted following multivariate Cox analysis. Independent validation studies by immunohistochemistry and analysis of public gene expression profiles of DLBCL confirmed a prognostic role for high ETV6 and ETV6/PIM2 ratios in DLBCL. ETV6 is a recurrently mutated/deleted gene in DLBCL for which its function in this disease entity is currently unknown. We find that ETV6 is upregulated during oncogenic transformation of germinal center B-cells and that it regulates DLBCL survival, as its acute loss results in marked apoptosis. Fluctuations in survivin (BIRC5) expression levels were associated with this phenomenon. Furthermore, an inverse correlation between ETV6 and BIRC5 expression levels was found and correlated with a response to the BIRC5 inhibitor, YM155. In conclusion, we present evidence for an oncogenic function of ETV6 in DLBCL.
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Affiliation(s)
- Dario Marino
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Marco Pizzi
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Iuliia Kotova
- Sciomics GmbH, 69151 Neckargemünd, Germany; (I.K.); (R.S.); (C.S.)
| | - Ronny Schmidt
- Sciomics GmbH, 69151 Neckargemünd, Germany; (I.K.); (R.S.); (C.S.)
| | | | - Vincenza Guzzardo
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Ilaria Talli
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy;
| | - Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy;
| | - Silvia Finotto
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Greta Scapinello
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Angelo Paolo Dei Tos
- Surgical Pathology & Cytopathology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (M.P.); (V.G.); (A.P.D.T.)
| | - Francesco Piazza
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Livio Trentin
- Hematology Unit, Department of Medicine—DIMED, University of Padova, 35128 Padova, Italy; (G.S.); (F.P.); (L.T.)
| | - Vittorina Zagonel
- Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy; (D.M.); (S.F.); (V.Z.)
| | - Erich Piovan
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35128 Padova, Italy;
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy;
- Correspondence: ; Tel.: +39-(049)-8215895
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Watanabe T. Approaches of the Innate Immune System to Ameliorate Adaptive Immunotherapy for B-Cell Non-Hodgkin Lymphoma in Their Microenvironment. Cancers (Basel) 2021; 14:cancers14010141. [PMID: 35008305 PMCID: PMC8750340 DOI: 10.3390/cancers14010141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022] Open
Abstract
A dominant paradigm being developed in immunotherapy for hematologic malignancies is of adaptive immunotherapy that involves chimeric antigen receptor (CAR) T cells and bispecific T-cell engagers. CAR T-cell therapy has yielded results that surpass those of the existing salvage immunochemotherapy for patients with relapsed/refractory diffuse large B-cell lymphoma (DLBCL) after first-line immunochemotherapy, while offering a therapeutic option for patients with follicular lymphoma (FL) and mantle cell lymphoma (MCL). However, the role of the innate immune system has been shown to prolong CAR T-cell persistence. Cluster of differentiation (CD) 47-blocking antibodies, which are a promising therapeutic armamentarium for DLBCL, are novel innate immune checkpoint inhibitors that allow macrophages to phagocytose tumor cells. Intratumoral Toll-like receptor 9 agonist CpG oligodeoxynucleotide plays a pivotal role in FL, and vaccination may be required in MCL. Additionally, local stimulator of interferon gene agonists, which induce a systemic anti-lymphoma CD8+ T-cell response, and the costimulatory molecule 4-1BB/CD137 or OX40/CD134 agonistic antibodies represent attractive agents for dendritic cell activations, which subsequently, facilitates initiation of productive T-cell priming and NK cells. This review describes the exploitation of approaches that trigger innate immune activation for adaptive immune cells to operate maximally in the tumor microenvironment of these lymphomas.
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Affiliation(s)
- Takashi Watanabe
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, 2-174, Edobashi, Tsu City 514-8507, Japan
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Soshnev AA, Allis CD, Cesarman E, Melnick AM. Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer. Cancer Res 2021; 81:6061-6070. [PMID: 34580064 PMCID: PMC8678342 DOI: 10.1158/0008-5472.can-21-2619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
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Affiliation(s)
- Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology & Medical Oncology, Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.
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Wilson WH, Wright GW, Huang DW, Hodkinson B, Balasubramanian S, Fan Y, Vermeulen J, Shreeve M, Staudt LM. Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL. Cancer Cell 2021; 39:1643-1653.e3. [PMID: 34739844 PMCID: PMC8722194 DOI: 10.1016/j.ccell.2021.10.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022]
Abstract
In diffuse large B cell lymphoma (DLBCL), tumors belonging to the ABC but not GCB gene expression subgroup rely upon chronic active B cell receptor signaling for viability, a dependency that is targetable by ibrutinib. A phase III trial ("Phoenix;" ClinicalTrials.gov: NCT01855750) showed a survival benefit of ibrutinib addition to R-CHOP chemotherapy in younger patients with non-GCB DLBCL, but the molecular basis for this benefit was unclear. Analysis of biopsies from Phoenix trial patients revealed three previously characterized genetic subtypes of DLBCL: MCD, BN2, and N1. The 3-year event-free survival of younger patients (age ≤60 years) treated with ibrutinib plus R-CHOP was 100% in the MCD and N1 subtypes while the survival of patients with these subtypes treated with R-CHOP alone was significantly inferior (42.9% and 50%, respectively). This work provides a mechanistic understanding of the benefit of ibrutinib addition to chemotherapy, supporting its use in younger patients with non-GCB DLBCL.
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Affiliation(s)
- Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brendan Hodkinson
- Johnson & Johnson, 1 Johnson & Johnson Plaza, New Brunswick, NJ 08933, USA
| | | | - Yue Fan
- Johnson & Johnson, 1 Johnson & Johnson Plaza, New Brunswick, NJ 08933, USA
| | - Jessica Vermeulen
- Johnson & Johnson, 1 Johnson & Johnson Plaza, New Brunswick, NJ 08933, USA
| | - Martin Shreeve
- Johnson & Johnson, 1 Johnson & Johnson Plaza, New Brunswick, NJ 08933, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Artificial Neural Network Analysis of Gene Expression Data Predicted Non-Hodgkin Lymphoma Subtypes with High Accuracy. MACHINE LEARNING AND KNOWLEDGE EXTRACTION 2021. [DOI: 10.3390/make3030036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Predictive analytics using artificial intelligence is a useful tool in cancer research. A multilayer perceptron neural network used gene expression data to predict the lymphoma subtypes of 290 cases of non-Hodgkin lymphoma (GSE132929). The input layer included both the whole array of 20,863 genes and a cancer transcriptome panel of 1769 genes. The output layer was lymphoma subtypes, including follicular lymphoma, mantle cell lymphoma, diffuse large B-cell lymphoma, Burkitt lymphoma, and marginal zone lymphoma. The neural networks successfully classified the cases consistent with the lymphoma subtypes, with an area under the curve (AUC) that ranged from 0.87 to 0.99. The most relevant predictive genes were LCE2B, KNG1, IGHV7_81, TG, C6, FGB, ZNF750, CTSV, INGX, and COL4A6 for the whole set; and ARG1, MAGEA3, AKT2, IL1B, S100A7A, CLEC5A, WIF1, TREM1, DEFB1, and GAGE1 for the cancer panel. The characteristic predictive genes for each lymphoma subtypes were also identified with high accuracy (AUC = 0.95, incorrect predictions = 6.2%). Finally, the topmost relevant 30 genes of the whole set, which belonged to apoptosis, cell proliferation, metabolism, and antigen presentation pathways, not only predicted the lymphoma subtypes but also the overall survival of diffuse large B-cell lymphoma (series GSE10846, n = 414 cases), and most relevant cancer subtypes of The Cancer Genome Atlas (TCGA) consortium including carcinomas of breast, colorectal, lung, prostate, and gastric, melanoma, etc. (7441 cases). In conclusion, neural networks predicted the non-Hodgkin lymphoma subtypes with high accuracy, and the highlighted genes also predicted the survival of a pan-cancer series.
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