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Mosquera Orgueira A, Ferreiro Ferro R, Díaz Arias JÁ, Aliste Santos C, Antelo Rodríguez B, Bao Pérez L, Alonso Vence N, Bendaña López Á, Abuin Blanco A, Melero Valentín P, Peleteiro Raindo A, Cid López M, Pérez Encinas MM, González Pérez MS, Fraga Rodríguez MF, Bello López JL. Detection of new drivers of frequent B-cell lymphoid neoplasms using an integrated analysis of whole genomes. PLoS One 2021; 16:e0248886. [PMID: 33945543 PMCID: PMC8096002 DOI: 10.1371/journal.pone.0248886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
B-cell lymphoproliferative disorders exhibit a diverse spectrum of diagnostic entities with heterogeneous behaviour. Multiple efforts have focused on the determination of the genomic drivers of B-cell lymphoma subtypes. In the meantime, the aggregation of diverse tumors in pan-cancer genomic studies has become a useful tool to detect new driver genes, while enabling the comparison of mutational patterns across tumors. Here we present an integrated analysis of 354 B-cell lymphoid disorders. 112 recurrently mutated genes were discovered, of which KMT2D, CREBBP, IGLL5 and BCL2 were the most frequent, and 31 genes were putative new drivers. Mutations in CREBBP, TNFRSF14 and KMT2D predominated in follicular lymphoma, whereas those in BTG2, HTA-A and PIM1 were more frequent in diffuse large B-cell lymphoma. Additionally, we discovered 31 significantly mutated protein networks, reinforcing the role of genes such as CREBBP, EEF1A1, STAT6, GNA13 and TP53, but also pointing towards a myriad of infrequent players in lymphomagenesis. Finally, we report aberrant expression of oncogenes and tumor suppressors associated with novel noncoding mutations (DTX1 and S1PR2), and new recurrent copy number aberrations affecting immune check-point regulators (CD83, PVR) and B-cell specific genes (TNFRSF13C). Our analysis expands the number of mutational drivers of B-cell lymphoid neoplasms, and identifies several differential somatic events between disease subtypes.
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Affiliation(s)
- Adrián Mosquera Orgueira
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Roi Ferreiro Ferro
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - José Ángel Díaz Arias
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Carlos Aliste Santos
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Pathology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Beatriz Antelo Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Pathology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Laura Bao Pérez
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Natalia Alonso Vence
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Ággeles Bendaña López
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Aitor Abuin Blanco
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Paula Melero Valentín
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - And´res Peleteiro Raindo
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Miguel Cid López
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Manuel Mateo Pérez Encinas
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Marta Sonia González Pérez
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - Máximo Francisco Fraga Rodríguez
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
- Department of Pathology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
| | - José Luis Bello López
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
- Department of Hematology, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago de Compostela, Galicia, Spain
- University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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Afaghani J, Taylor J. A Moving Target: Inactivating BTK Mutations as Drivers of Follicular Lymphoma. Clin Cancer Res 2021; 27:2123-2125. [PMID: 33579791 PMCID: PMC11305113 DOI: 10.1158/1078-0432.ccr-21-0140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 11/16/2022]
Abstract
Drugs that target Bruton tyrosine kinase (BTK) have been highly successful and changed the landscape of therapies in B-cell lymphomas. However, their lower rates of effectiveness in follicular lymphoma are unexplained. Recent work describes inactivating BTK mutations that show that at least some follicular lymphomas do not require BTK.See related article by Hu et al., p. 2301.
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Affiliation(s)
- Jumana Afaghani
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Justin Taylor
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida.
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, Florida
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Hu N, Wang F, Sun T, Xu Z, Zhang J, Bernard D, Xu S, Wang S, Kaminski M, Devata S, Phillips T, Malek SN. Follicular Lymphoma-associated BTK Mutations are Inactivating Resulting in Augmented AKT Activation. Clin Cancer Res 2021; 27:2301-2313. [PMID: 33419778 DOI: 10.1158/1078-0432.ccr-20-3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/29/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE On the basis of the recent discovery of mutations in Bruton tyrosine kinase (BTK) in follicular lymphoma, we studied their functional properties. EXPERIMENTAL DESIGN We identified novel somatic BTK mutations in 7% of a combined total of 139 follicular lymphoma and 11 transformed follicular lymphoma cases, none of which had received prior treatment with B-cell receptor (BCR) targeted drugs. We reconstituted wild-type (WT) and mutant BTK into various engineered lymphoma cell lines. We measured BCR-induced signal transduction events in engineered cell lines and primary human follicular lymphoma B cells. RESULTS We uncovered that all BTK mutants destabilized the BTK protein and some created BTK kinase-dead mutants. The phospholipase C gamma 2 (PLCγ2) is a substrate of BTK but the BTK mutants did not alter PLCγ2 phosphorylation. Instead, we discovered that BTK mutants induced an exaggerated AKT phosphorylation phenotype in anti-Ig-treated recombinant lymphoma cell lines. The short hairpin RNA-mediated knockdown of BTK expression in primary human nonmalignant lymph node-derived B cells resulted in strong anti-Ig-induced AKT activation, as did the degradation of BTK protein in cell lines using ibrutinib-based proteolysis targeting chimera. Finally, through analyses of primary human follicular lymphoma B cells carrying WT or mutant BTK, we detected elevated AKT phosphorylation following surface Ig crosslinking in all follicular lymphoma B cells, including all BTK-mutant follicular lymphoma. The augmented AKT phosphorylation following BCR crosslinking could be abrogated by pretreatment with a PI3Kδ inhibitor. CONCLUSIONS Altogether, our data uncover novel unexpected properties of follicular lymphoma-associated BTK mutations with direct implications for targeted therapy development in follicular lymphoma.See related commentary by Afaghani and Taylor, p. 2123.
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Affiliation(s)
- Nan Hu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Fangyang Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Tianyu Sun
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Zhengfan Xu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Jing Zhang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Denzil Bernard
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Shilin Xu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Shaomeng Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Mark Kaminski
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Suma Devata
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Tycel Phillips
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | - Sami N Malek
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan.
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Clinical Applications of Genomic Alterations in ATLL: Predictive Markers and Therapeutic Targets. Cancers (Basel) 2021; 13:cancers13081801. [PMID: 33918793 PMCID: PMC8068906 DOI: 10.3390/cancers13081801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary In this review paper, we aim to summarize recent findings of genomic alterations found in adult T-cell leukemia/lymphoma (ATLL), which is an incurable disease induced by a virus; human T-cell leukemia virus type 1 (HTLV-1). Genomic alterations of ATLL have been comprehensively analyzed and the identified alterations and HTLV-1 infection synergistically act for ATLL development. As HTLV-1 is an endemic disease, ATLL frequently occurs in the endemic areas. Current clinicogenomic analyses suggest the existence of regional difference in ATLL pathophysiology. From a clinical perspective, several studies identified alterations that act as predictive markers and that a part of the alterations can be targetable in ATLL. The alterations can be leveraged to improve ATLL prognosis. Abstract Adult T-cell leukemia/lymphoma (ATLL) is a peripheral T-cell lymphoma (PTCL) caused by human T-cell leukemia virus type 1 (HTLV-1). Recent comprehensive genomic analyses have revealed the genomic landscape. One of the important findings of genomic alterations in ATLL is that almost all alterations are subclonal, suggesting that therapeutic strategies targeting a genomic alteration will result in partial effects. Among the identified alterations, genes involved in T-cell receptor signaling and immune escape mechanisms, such as PLCG1, CARD11, and PD-L1 (also known as CD274), are characteristic of ATLL alterations. From a geographic perspective, ATLL patients in Caribbean islands tend to be younger than those in Japan and the landscape differs between the two areas. Additionally, young Japanese ATLL patients frequently have CD28 fusions, compared with unselected Japanese cases. From a clinical perspective, PD-L1 amplification is an independent prognostic factor among every subtype of ATLL case. Recently, genomic analysis using deep sequencing identified a pre-ATLL clone with ATLL-common mutations in HTLV-1 carriers before development, indicating that genomic analysis can stratify cases based on the risks of development and mortality. In addition to genomic alterations, targetable super-enhancers have been identified in ATLL. These data can be leveraged to improve the prognosis of ATLL.
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Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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Chen Q, Qiu B, Zeng X, Hu L, Huang D, Chen K, Qiu X. Identification of a tumor microenvironment-related gene signature to improve the prediction of cervical cancer prognosis. Cancer Cell Int 2021; 21:182. [PMID: 33766042 PMCID: PMC7992856 DOI: 10.1186/s12935-021-01867-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Previous studies have found that the microenvironment of cervical cancer (CESC) affects the progression and treatment of this disease. Thus, we constructed a multigene model to assess the survival of patients with cervical cancer. Methods We scored 307 CESC samples from The Cancer Genome Atlas (TCGA) and divided them into high and low matrix and immune scores using the ESTIMATE algorithm for differential gene analysis. Cervical cancer patients were randomly divided into a training group, testing group and combined group. The multigene signature prognostic model was constructed by Cox analyses. Multivariate Cox analysis was applied to evaluate the significance of the multigene signature for cervical cancer prognosis. Prognosis was assessed by Kaplan–Meier curves comparing the different groups, and the accuracy of the prognostic model was analyzed by receiver operating characteristic-area under the curve (ROC-AUC) analysis and calibration curve. The Tumor Immune Estimation Resource (TIMER) database was used to analyze the relationship between the multigene signature and immune cell infiltration. Results We obtained 420 differentially expressed genes in the tumor microenvironment from 307 patients with cervical cancer. A three-gene signature (SLAMF1, CD27, SELL) model related to the tumor microenvironment was constructed to assess patient survival. Kaplan–Meier analysis showed that patients with high risk scores had a poor prognosis. The ROC-AUC value indicated that the model was an accurate predictor of cervical cancer prognosis. Multivariate cox analysis showed the three-gene signature to be an independent risk factor for the prognosis of cervical cancer. A nomogram combining the three-gene signature and clinical features was constructed, and calibration plots showed that the nomogram resulted in an accurate prognosis for patients. The three-gene signature was associated with T stage, M stage and degree of immune infiltration in patients with cervical cancer. Conclusions This research suggests that the developed three-gene signature may be applied as a biomarker to predict the prognosis of and personalized therapy for CESC.
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Affiliation(s)
- Qian Chen
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China.,Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Bingqing Qiu
- Department of Nuclear Medicine, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Xiaoyun Zeng
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Lang Hu
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Dongping Huang
- Department of Nutrition, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Kaihua Chen
- Department of Radiation Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, 530021, China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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The Multifaceted Role and Utility of MicroRNAs in Indolent B-Cell Non-Hodgkin Lymphomas. Biomedicines 2021; 9:biomedicines9040333. [PMID: 33806113 PMCID: PMC8064455 DOI: 10.3390/biomedicines9040333] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Normal B-cell development is a tightly regulated complex procedure, the deregulation of which can lead to lymphomagenesis. One common group of blood cancers is the B-cell non-Hodgkin lymphomas (NHLs), which can be categorized according to the proliferation and spread rate of cancer cells into indolent and aggressive ones. The most frequent indolent B-cell NHLs are follicular lymphoma and marginal zone lymphoma. MicroRNAs (miRNAs) are small non-coding RNAs that can greatly influence protein expression. Based on the multiple interactions among miRNAs and their targets, complex networks of gene expression regulation emerge, which normally are essential for proper B-cell development. Multiple miRNAs have been associated with B-cell lymphomas, as the deregulation of these complex networks can lead to such pathological states. The aim of the present review is to summarize the existing information regarding the multifaceted role of miRNAs in indolent B-cell NHLs, affecting the main B-cell subpopulations. We attempt to provide insight into their biological function, the complex miRNA-mRNA interactions, and their biomarker utility in these malignancies. Lastly, we address the limitations that hinder the investigation of the role of miRNAs in these lymphomas and discuss ways that these problems could be overcome in the future.
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The mutational landscape of histiocytic sarcoma associated with lymphoid malignancy. Mod Pathol 2021; 34:336-347. [PMID: 32929178 PMCID: PMC9161669 DOI: 10.1038/s41379-020-00673-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
Histiocytic sarcoma and tumors with dendritic cell differentiation (HDT) are uncommon neoplasms often with an aggressive clinical course that may occur in association with another hematologic malignancy or mediastinal germ cell tumor (secondary HDT, sHDT). Previous studies have shown mutations in the RAS/MAPK pathway in HDT and have demonstrated a clonal relationship between HDT and associated lymphoid malignancies through common translocations or identical immunoglobulin or T-cell receptor gene rearrangements. We performed whole exome sequencing on 16 cases of sHDT to further evaluate the spectrum of mutations that occur in sHDT in the context of an associated lymphoid malignancy, including cases associated with follicular lymphoma (FL), chronic lymphocytic leukemia/small lymphocytic lymphoma, B- and T-cell acute lymphoblastic leukemia/lymphoma and peripheral T-cell lymphoma, NOS. In addition, we assessed the clonal relationship between the HDT and the associated lymphoid malignancy in three cases for which matched samples were available. We found mutations in RAS/MAPK pathway genes in 14/16 cases of sHDT associated with diverse mature and precursor B-cell and T-cell neoplasms, involving KRAS (8/16), BRAF (2/16), NRAS (2/16), MAP2K1 (1/16), and NF1 (1/16). In addition, we note that FL-associated sHDT frequently shares a similar mutational profile to the associated malignancy, identifying mutations in CREBBP or KMT2D in all cases and "aberrant" somatic hypermutation in 5/6 cases. Our study confirms the role of the RAS/MAPK pathway in the pathogenesis of sHDT, provides further evidence of a common neoplastic precursor and, in the case of FL, gives additional insight into the stage in lymphomagenesis at which transdifferentiation may occur.
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Kaiser LM, Hunter ZR, Treon SP, Buske C. CXCR4 in Waldenström's Macroglobulinema: chances and challenges. Leukemia 2021; 35:333-345. [PMID: 33273682 PMCID: PMC7862063 DOI: 10.1038/s41375-020-01102-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/09/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
It is one of the major aims in cancer research to improve our understanding of the underlying mechanisms which initiate and maintain tumor growth and to translate these findings into novel clinical diagnostic and therapeutic concepts with the ultimate goal to improve patient care. One of the greater success stories in this respect has been Waldenström's Macroglobulinemia (WM), which is an incurable B-cell neoplasm characterized by serum monoclonal immunoglobulin M (IgM) and clonal lymphoplasmacytic cells infiltrating the bone marrow. Recent years have succeeded to describe the molecular landscape of WM in detail, highlighting two recurrently mutated genes, the MYD88 and the CXCR4 genes: MYD88 with an almost constant and recurrent point mutation present in over 90% of patients and CXCR4 with over 40 different mutations in the coding region affecting up to 40% of patients. Intriguingly, both mutations are activating mutations leading in the case of CXCR4 to an indelible activation and perpetual signaling of the chemokine receptor. These data have shed light on the essential role of CXCR4 in this disease and have paved the way to use these findings for predicting treatment response to the Bruton tyrosine kinase (BTK) inhibitor ibrutinib and novel therapeutic approaches in WM, which might be transferable to other related CXCR4 positive diseases. Well known for its central role in cancer progression and distribution, CXCR4 is highlighted in this review with regard to its biology, prognostic and predictive relevance and therapeutic implications in WM.
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Affiliation(s)
- Lisa Marie Kaiser
- Institute of Experimental Cancer Research, CCC and University Hospital Ulm, Germany, 89081, Ulm, Germany
| | - Zachary R Hunter
- Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Steven P Treon
- Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Christian Buske
- Institute of Experimental Cancer Research, CCC and University Hospital Ulm, Germany, 89081, Ulm, Germany.
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Munguía-Fuentes R, Maqueda-Alfaro RA, Chacón-Salinas R, Flores-Romo L, Yam-Puc JC. Germinal Center Cells Turning to the Dark Side: Neoplasms of B Cells, Follicular Helper T Cells, and Follicular Dendritic Cells. Front Oncol 2021; 10:587809. [PMID: 33520702 PMCID: PMC7843373 DOI: 10.3389/fonc.2020.587809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Gaining knowledge of the neoplastic side of the three main cells—B cells, Follicular Helper T (Tfh) cells, and follicular dendritic cells (FDCs) —involved in the germinal center (GC) reaction can shed light toward further understanding the microuniverse that is the GC, opening the possibility of better treatments. This paper gives a review of the more complex underlying mechanisms involved in the malignant transformations that take place in the GC. Whilst our understanding of the biology of the GC-related B cell lymphomas has increased—this is not reviewed in detail here—the dark side involving neoplasms of Tfh cells and FDCs are poorly studied, in great part, due to their low incidence. The aggressive behavior of Tfh lymphomas and the metastatic potential of FDCs sarcomas make them clinically relevant, merit further attention and are the main focus of this review. Tfh cells and FDCs malignancies can often be misdiagnosed. The better understanding of these entities linked to their molecular and genetic characterization will lead to prediction of high-risk patients, better diagnosis, prognosis, and treatments based on molecular profiles.
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Affiliation(s)
- Rosario Munguía-Fuentes
- Departmento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, UPIITA-IPN, Mexico City, Mexico
| | - Raúl Antonio Maqueda-Alfaro
- Department of Cell Biology, Center for Advanced Research, National Polytechnic Institute, Cinvestav-IPN, Mexico City, Mexico
| | - Rommel Chacón-Salinas
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, ENCB-IPN, Mexico City, Mexico
| | - Leopoldo Flores-Romo
- Department of Cell Biology, Center for Advanced Research, National Polytechnic Institute, Cinvestav-IPN, Mexico City, Mexico
| | - Juan Carlos Yam-Puc
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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Genetic complexity impacts the clinical outcome of follicular lymphoma patients. Blood Cancer J 2021; 11:11. [PMID: 33431798 PMCID: PMC7801414 DOI: 10.1038/s41408-020-00395-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/19/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
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Huang YH, Cai K, Xu PP, Wang L, Huang CX, Fang Y, Cheng S, Sun XJ, Liu F, Huang JY, Ji MM, Zhao WL. CREBBP/EP300 mutations promoted tumor progression in diffuse large B-cell lymphoma through altering tumor-associated macrophage polarization via FBXW7-NOTCH-CCL2/CSF1 axis. Signal Transduct Target Ther 2021; 6:10. [PMID: 33431788 PMCID: PMC7801454 DOI: 10.1038/s41392-020-00437-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/13/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic alterations play an important role in tumor progression of diffuse large B-cell lymphoma (DLBCL). However, the biological relevance of epigenetic gene mutations on tumor microenvironment remains to be determined. The core set of genes relating to histone methylation (KMT2D, KMT2C, EZH2), histone acetylation (CREBBP, EP300), DNA methylation (TET2), and chromatin remodeling (ARID1A) were detected in the training cohort of 316 patients by whole-genome/exome sequencing (WGS/WES) and in the validation cohort of 303 patients with newly diagnosed DLBCL by targeted sequencing. Their correlation with peripheral blood immune cells and clinical outcomes were assessed. Underlying mechanisms on tumor microenvironment were investigated both in vitro and in vivo. Among all 619 DLBCL patients, somatic mutations in KMT2D (19.5%) were most frequently observed, followed by mutations in ARID1A (8.7%), CREBBP (8.4%), KMT2C (8.2%), TET2 (7.8%), EP300 (6.8%), and EZH2 (2.9%). Among them, CREBBP/EP300 mutations were significantly associated with decreased peripheral blood absolute lymphocyte-to-monocyte ratios, as well as inferior progression-free and overall survival. In B-lymphoma cells, the mutation or knockdown of CREBBP or EP300 inhibited H3K27 acetylation, downregulated FBXW7 expression, activated the NOTCH pathway, and downstream CCL2/CSF1 expression, resulting in tumor-associated macrophage polarization to M2 phenotype and tumor cell proliferation. In B-lymphoma murine models, xenografted tumors bearing CREBBP/EP300 mutation presented lower H3K27 acetylation, higher M2 macrophage recruitment, and more rapid tumor growth than those with CREBBP/EP300 wild-type control via FBXW7-NOTCH-CCL2/CSF1 axis. Our work thus contributed to the understanding of aberrant histone acetylation regulation on tumor microenvironment as an alternative mechanism of tumor progression in DLBCL.
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Affiliation(s)
- Yao-Hui Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kun Cai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peng-Peng Xu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuan-Xin Huang
- Department of Immunobiology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shu Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin-Yan Huang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng-Meng Ji
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Wei-Li Zhao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.
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63
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Berditchevski F, Fennell E, Murray PG. Calcium-dependent signalling in B-cell lymphomas. Oncogene 2021; 40:6321-6328. [PMID: 34625709 PMCID: PMC8585665 DOI: 10.1038/s41388-021-02025-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022]
Abstract
Induced waves of calcium fluxes initiate multiple signalling pathways that play an important role in the differentiation and maturation of B-cells. Finely tuned transient Ca+2 fluxes from the endoplasmic reticulum in response to B-cell receptor (BCR) or chemokine receptor activation are followed by more sustained calcium influxes from the extracellular environment and contribute to the mechanisms responsible for the proliferation of B-cells, their migration within lymphoid organs and their differentiation. Dysregulation of these well-balanced mechanisms in B-cell lymphomas results in uncontrolled cell proliferation and resistance to apoptosis. Consequently, several cytotoxic drugs (and anti-proliferative compounds) used in standard chemotherapy regimens for the treatment of people with lymphoma target calcium-dependent pathways. Furthermore, ~10% of lymphoma associated mutations are found in genes with functions in calcium-dependent signalling, including those affecting B-cell receptor signalling pathways. In this review, we provide an overview of the Ca2+-dependent signalling network and outline the contribution of its key components to B cell lymphomagenesis. We also consider how the oncogenic Epstein-Barr virus, which is causally linked to the pathogenesis of a number of B-cell lymphomas, can modify Ca2+-dependent signalling.
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Affiliation(s)
- Fedor Berditchevski
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT UK
| | - Eanna Fennell
- grid.10049.3c0000 0004 1936 9692Health Research Institute, University of Limerick, Castletroy, Limerick, V94 T9PX Ireland
| | - Paul G. Murray
- grid.10049.3c0000 0004 1936 9692Health Research Institute, University of Limerick, Castletroy, Limerick, V94 T9PX Ireland ,grid.6572.60000 0004 1936 7486Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT UK
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64
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Foukas PG, Bisig B, de Leval L. Recent advances upper gastrointestinal lymphomas: molecular updates and diagnostic implications. Histopathology 2020; 78:187-214. [PMID: 33382495 DOI: 10.1111/his.14289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Approximately one-third of extranodal non-Hodgkin lymphomas involve the gastrointestinal (GI) tract, with the vast majority being diagnosed in the stomach, duodenum, or proximal small intestine. A few entities, especially diffuse large B-cell lymphoma and extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue, represent the majority of cases. In addition, there are diseases specific to or characteristic of the GI tract, and any type of systemic lymphoma can present in or disseminate to these organs. The recent advances in the genetic and molecular characterisation of lymphoid neoplasms have translated into notable changes in the classification of primary GI T-cell neoplasms and the recommended diagnostic approach to aggressive B-cell tumours. In many instances, diagnoses rely on morphology and immunophenotype, but there is an increasing need to incorporate molecular genetic markers. Moreover, it is also important to take into consideration the endoscopic and clinical presentations. This review gives an update on the most recent developments in the pathology and molecular pathology of upper GI lymphoproliferative diseases.
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Affiliation(s)
- Periklis G Foukas
- Second Department of Pathology, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Bettina Bisig
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Laurence de Leval
- Second Department of Pathology, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
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65
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Tsutsué S, Tobinai K, Yi J, Crawford B. Comparative effectiveness study of chemotherapy in follicular lymphoma patients in the rituximab era: a Japanese claims database study. Future Oncol 2020; 17:455-469. [PMID: 33021099 DOI: 10.2217/fon-2020-0832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: To evaluate comparative effectiveness of rituximub (R)-based versus non-R-based therapies for follicular lymphoma patients in Japan, where limited studies have been reported. Materials & methods: Patients who received R-based index regimens were propensity score matched to those who did not receive R, based on patient baseline attributes and clinical characteristics using Japanese retrospective claims database to assess clinical and economic outcomes. Results & conclusion: A total of 1947 patients remained in the overall follicular lymphoma cohorts: 1294 receiving an R-based and 653 a non-R-based regimen. Patients on R-based therapy underwent fewer hospitalizations and had a shorter length of stay, but had higher costs during the first year of intensive R-based therapy. Improved clinical outcomes were associated with patients who were younger, female and chose R-based regimens in first index line.
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Affiliation(s)
- Saaya Tsutsué
- Celgene K.K., a Bristol Myers Squibb Company, JP Tower, 2-7-2 Marunouchi Chiyoda-ku, Tokyo 100-7010, Japan
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66
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Pethő Z, Najder K, Carvalho T, McMorrow R, Todesca LM, Rugi M, Bulk E, Chan A, Löwik CWGM, Reshkin SJ, Schwab A. pH-Channeling in Cancer: How pH-Dependence of Cation Channels Shapes Cancer Pathophysiology. Cancers (Basel) 2020; 12:E2484. [PMID: 32887220 PMCID: PMC7565548 DOI: 10.3390/cancers12092484] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
Tissue acidosis plays a pivotal role in tumor progression: in particular, interstitial acidosis promotes tumor cell invasion, and is a major contributor to the dysregulation of tumor immunity and tumor stromal cells. The cell membrane and integral membrane proteins commonly act as important sensors and transducers of altered pH. Cell adhesion molecules and cation channels are prominent membrane proteins, the majority of which is regulated by protons. The pathophysiological consequences of proton-sensitive ion channel function in cancer, however, are scarcely considered in the literature. Thus, the main focus of this review is to highlight possible events in tumor progression and tumor immunity where the pH sensitivity of cation channels could be of great importance.
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Affiliation(s)
- Zoltán Pethő
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
| | - Karolina Najder
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
| | - Tiago Carvalho
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 90126 Bari, Italy; (T.C.); (S.J.R.)
| | - Roisin McMorrow
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, 3035 GD Rotterdam, The Netherlands; (R.M.); (C.W.G.M.L.)
| | - Luca Matteo Todesca
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
| | - Micol Rugi
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
| | - Etmar Bulk
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
| | - Alan Chan
- Percuros B.V., 2333 CL Leiden, The Netherlands;
| | - Clemens W. G. M. Löwik
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, 3035 GD Rotterdam, The Netherlands; (R.M.); (C.W.G.M.L.)
- Department of Oncology CHUV, UNIL and Ludwig Cancer Center, 1011 Lausanne, Switzerland
| | - Stephan J. Reshkin
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 90126 Bari, Italy; (T.C.); (S.J.R.)
| | - Albrecht Schwab
- Institute of Physiology II, University Münster, 48147 Münster, Germany; (K.N.); (L.M.T.); (M.R.); (E.B.); (A.S.)
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67
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Spasevska I, Matera EL, Chettab K, Ville J, Potier-Cartereau M, Jordheim LP, Thieblemont C, Sahin D, Klein C, Dumontet C. Calcium Channel Blockers Impair the Antitumor Activity of Anti-CD20 Monoclonal Antibodies by Blocking EGR-1 Induction. Mol Cancer Ther 2020; 19:2371-2381. [PMID: 32847969 DOI: 10.1158/1535-7163.mct-19-0839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/12/2020] [Accepted: 08/13/2020] [Indexed: 11/16/2022]
Abstract
Direct cell death induction, in addition to immune-effector cell-mediated mechanisms, is one of the key mechanisms of action of anti-CD20 antibodies, and yet the signaling pathways implicated remain poorly investigated. Here we show that the transcription factor EGR-1 is rapidly induced by anti-CD20 antibodies and is a key mediator for CD20-induced cell death. EGR-1 induction results from an increased calcium influx induced by anti-CD20 antibodies. We show that both rituximab and obinutuzumab induce calcium influx, albeit through different mechanisms, and this influx is crucial for cell death induction. Inhibition of the calcium flux with calcium channel blockers (CCB) abolished EGR-1 induction and impaired the efficacy of anti-CD20 antibodies in preclinical in vitro and in vivo models. Finally, we investigated the impact of CCBs in patients treated with anti-CD20 antibodies included in the clinical trials GOYA and REMARC, and found that patients simultaneously receiving CCBs and anti-CD20 therapy have a shorter progression-free survival and overall survival. These results reveal EGR-1 as a key mediator of the direct cytotoxic activity of anti-CD20 antibodies and provide a rationale to evaluate EGR-1 expression as a new biomarker to predict response to anti-CD20 treatment. In addition, our findings show that calcium influx is required for anti-CD20-mediated tumor cell death and suggest that simultaneous administration of calcium channel blocking agents could be deleterious in patients receiving anti-CD20-based immunotherapy.
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Affiliation(s)
- Ivana Spasevska
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Eva Laure Matera
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Kamel Chettab
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Jade Ville
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - Lars Petter Jordheim
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - Denis Sahin
- Pharma Development Oncology, F. Hoffmann-La Roche, Basel, Switzerland
| | - Christian Klein
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center, Zurich, Switzerland
| | - Charles Dumontet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France. .,Hospices Civils de Lyon, Lyon, France
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68
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Aberrant CXCR4 Signaling at Crossroad of WHIM Syndrome and Waldenstrom's Macroglobulinemia. Int J Mol Sci 2020; 21:ijms21165696. [PMID: 32784523 PMCID: PMC7460815 DOI: 10.3390/ijms21165696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Given its pleiotropic functions, including its prominent role in inflammation, immune responses and cancer, the C-X-C chemokine receptor type 4 (CXCR4) has gained significant attention in recent years and has become a relevant target in drug development. Although the signaling properties of CXCR4 have been extensively studied, several aspects deserve deeper investigations. Mutations in the C-term tail of the CXCR4 gene cause WHIM syndrome, a rare congenital immunodeficiency associated by chronic leukopenia. Similar mutations have also been recently identified in 30% of patients affected by Waldenstrom’s macroglobulinaemia, a B-cell neoplasia with bone marrow accumulation of malignant cells. An ample body of work has been generated to define the impact of WHIM mutations on CXCR4 signaling properties and evaluate their role on pathogenesis, diagnosis, and response to therapy, although the identity of disease-causing signaling pathways and their relevance for disease development in different genetic variants are still open questions. This review discusses the current knowledge on biochemical properties of CXCR4 mutations to identify their prototypic signaling profile potentially useful to highlighting novel opportunities for therapeutic intervention.
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69
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Zhang W, Yang L, Guan YQ, Shen KF, Zhang ML, Cai HD, Wang JC, Wang Y, Huang L, Cao Y, Wang N, Tan XH, Young KH, Xiao M, Zhou JF. Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma. BMC Cancer 2020; 20:714. [PMID: 32736575 PMCID: PMC7393908 DOI: 10.1186/s12885-020-07198-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is a spectrum of disease comprising more than 30% of non-Hodgkin lymphomas. Although studies have identified several molecular subgroups, the heterogeneous genetic background of DLBCL remains ambiguous. In this study we aimed to develop a novel approach and to provide a distinctive classification system to unravel its molecular features. Method A cohort of 342 patient samples diagnosed with DLBCL in our hospital were retrospectively enrolled in this study. A total of 46 genes were included in next-generation sequencing panel. Non-mutually exclusive genetic signatures for the factorization of complex genomic patterns were generated by random forest algorithm. Results A total of four non-mutually exclusive signatures were generated, including those with MYC-translocation (MYC-trans) (n = 62), with BCL2-translocation (BCL2-trans) (n = 69), with BCL6-translocation (BCL6-trans) (n = 108), and those with MYD88 and/or CD79B mutations (MC) signatures (n = 115). Comparison analysis between our model and traditional mutually exclusive Schmitz’s model demonstrated consistent classification pattern. And prognostic heterogeneity existed within EZB subgroup of de novo DLBCL patients. As for prognostic impact, MYC-trans signature was an independent unfavorable prognostic factor. Furthermore, tumors carrying three different signature markers exhibited significantly inferior prognoses compared with their counterparts with no genetic signature. Conclusion Compared with traditional mutually exclusive molecular sub-classification, non-mutually exclusive genetic fingerprint model generated from our study provided novel insight into not only the complex genetic features, but also the prognostic heterogeneity of DLBCL patients.
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Affiliation(s)
- Wei Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Li Yang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Yu' Qi Guan
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Ke' Feng Shen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Mei' Lan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Hao' Dong Cai
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Jia' Chen Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Ying Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Yang Cao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
| | - Xiao' Hong Tan
- Department of Hematology/Oncology, Guangxi Medical University Cancer Hospital, No. 71 Hedi Road, Nanning, Guangxi, 530021, P.R. China
| | - Ken He Young
- Department of Pathology, The University of Duke, Durham, North Carolina, USA
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China.
| | - Jian' Feng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, P.R. China
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Abstract
PURPOSE OF REVIEW Emerging evidence has shown that epigenetic derangements might drive and promote tumorigenesis in various types of malignancies and is prevalent in both B cell and T cell lymphomas. The purpose of this review is to explain how the epigenetic derangements result in a chromatin-remodeled state in lymphoma and contribute to the biology and clinical features of these tumors. RECENT FINDINGS Studies have explored on the functional role of epigenetic derangements in chromatin remodeling and lymphomagenesis. For example, the haploinsufficiency of CREBBP facilitates malignant transformation in mice and directly implicates the importance to re-establish the physiologic acetylation level. New findings identified 4 prominent DLBCL subtypes, including EZB-GC-DLBCL subtype that enriched in mutations of CREBBP, EP300, KMT2D, and SWI/SNF complex genes. EZB subtype has a worse prognosis than other GCB-tumors. Moreover, the action of the histone modifiers as well as chromatin-remodeling factors (e.g., SWI/SNF complex) cooperates to influence the chromatin state resulting in transcription repression. Drugs that alter the epigenetic landscape have been approved in T cell lymphoma. In line with this finding, epigenetic lesions in histone modifiers have recently been uncovered in this disease, further confirming the vulnerability to the therapies targeting epigenetic derangements. Modulating the chromatin state by epigenetic-modifying agents provides precision-medicine opportunities to patients with lymphomas that depend on this biology.
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Affiliation(s)
- Yuxuan Liu
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA
| | - Yulissa Gonzalez
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA
| | - Jennifer E Amengual
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA.
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Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell 2020; 182:297-316.e27. [PMID: 32619424 DOI: 10.1016/j.cell.2020.05.049] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
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Affiliation(s)
- Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Andrew Zhai
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leena Babiker
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Daleum Kim
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Tak C Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Youngjun Kim
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael D Nissen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, and Princess Margaret Cancer Centre, Toronto, ON M5S 1A8, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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72
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Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia 2020; 34:2722-2735. [PMID: 32576963 DOI: 10.1038/s41375-020-0919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/20/2022]
Abstract
Mutations in genes encoding subunits of the SWI/SNF chromatin remodeling complex are frequently found in different human cancers. While the tumor suppressor function of this complex is widely established in solid tumors, its role in hematologic malignancies is largely unknown. Recurrent point mutations in BCL7A gene, encoding a subunit of the SWI/SNF complex, have been reported in diffuse large B-cell lymphoma (DLBCL), but their functional impact remains to be elucidated. Here we show that BCL7A often undergoes biallelic inactivation, including a previously unnoticed mutational hotspot in the splice donor site of intron one. The splice site mutations render a truncated BCL7A protein, lacking a portion of the amino-terminal domain. Moreover, restoration of wild-type BCL7A expression elicits a tumor suppressor-like phenotype in vitro and in vivo. In contrast, splice site mutations block the tumor suppressor function of BCL7A by preventing its binding to the SWI/SNF complex. We also show that BCL7A restoration induces transcriptomic changes in genes involved in B-cell activation. In addition, we report that SWI/SNF complex subunits harbor mutations in more than half of patients with germinal center B-cell (GCB)-DLBCL. Overall, this work demonstrates the tumor suppressor function of BCL7A in DLBCL, and highlights that the SWI/SNF complex plays a relevant role in DLBCL pathogenesis.
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73
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Mechanisms of B Cell Receptor Activation and Responses to B Cell Receptor Inhibitors in B Cell Malignancies. Cancers (Basel) 2020; 12:cancers12061396. [PMID: 32481736 PMCID: PMC7352865 DOI: 10.3390/cancers12061396] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/27/2022] Open
Abstract
The B cell receptor (BCR) pathway has been identified as a potential therapeutic target in a number of common B cell malignancies, including chronic lymphocytic leukemia, diffuse large B cell lymphoma, Burkitt lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone B cell lymphoma, and Waldenstrom's macroglobulinemia. This finding has resulted in the development of numerous drugs that target this pathway, including various inhibitors of the kinases BTK, PI3K, and SYK. Several of these drugs have been approved in recent years for clinical use, resulting in a profound change in the way these diseases are currently being treated. However, the response rates and durability of responses vary largely across the different disease entities, suggesting a different proportion of patients with an activated BCR pathway and different mechanisms of BCR pathway activation. Indeed, several antigen-dependent and antigen-independent mechanisms have recently been described and shown to result in the activation of distinct downstream signaling pathways. The purpose of this review is to provide an overview of the mechanisms responsible for the activation of the BCR pathway in different B cell malignancies and to correlate these mechanisms with clinical responses to treatment with BCR inhibitors.
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74
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Abstract
Although outcomes for follicular lymphoma (FL) continue to improve, it remains incurable for the majority of patients. Through next generation sequencing (NGS) studies, we now recognize that the genomic landscape of FL is skewed toward highly recurrent mutations in genes that encode epigenetic regulators co-occurring with the pathognomonic t(14;18) translocation. Adopting these technologies to study longitudinal and spatially-derived lymphomas has provided unique insights into the tumoral heterogeneity, clonal evolution of the disease and supports the existence of a tumor-repopulating population, considered the Achilles' heel of this lymphoma. An in-depth understanding of the genomics and its contribution to the disease pathogenesis is identifying new biomarkers and therapeutic targets that can be translated into clinical practice and, in the not too distant future, enable us to start considering precision-based approaches to the management of FL.
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Affiliation(s)
- Lucy Pickard
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giuseppe Palladino
- 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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75
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Huet S, Salles G. Potential of Circulating Tumor DNA for the Management of Patients With Lymphoma. JCO Oncol Pract 2020; 16:561-568. [PMID: 32421389 DOI: 10.1200/jop.19.00691] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The characterization of circulating tumor-derived DNA (ctDNA) has recently emerged in the field of oncology as a powerful method to identify tumor-specific genetic aberrations using peripheral blood testing. Several technical precautions are needed at the pre-analytic stage (given the short half-life of free nucleic acids in plasma), and numerous techniques-with different sensitivities-are available to identify these molecular aberrations, ranging from the detection of single point mutations to extended genetic screening panels. Although a "liquid biopsy" cannot be substituted for the pathological examination of tissue specimens for diagnostic purposes, it can sometimes complement pathology results or serve as a proxy approach for particular lymphoma presentations where biopsies are sometimes difficult to perform. Moreover, ctDNA testing can characterize, at diagnosis or during treatment, mutations that may contribute to the choice of an optimal targeted therapy (such as Bruton tyrosine kinase or EZH2 inhibitors) or detect the emergence of resistance to those therapies. High levels of ctDNA before treatment appear to be correlated with advanced disease stages and prognosis in diffuse large B-cell and follicular lymphomas. Real-time follow-up of ctDNA levels during therapy in several lymphoma subtypes (diffuse large B-cell and Hodgkin lymphomas) has been explored: preliminary studies have demonstrated that this monitoring technique can predict clinical outcomes (end of treatment response and risk of progression after treatment completion) and that this approach may complement the information provided by metabolic imaging assessments. Technical standardization and careful prospective evaluation of the role of ctDNA monitoring in clinical studies represent current important challenges to allowing its application in routine practice.
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Affiliation(s)
- Sarah Huet
- Hospices Civils de Lyon, Service d'Hématologie Biologique, Hôpital Lyon-Sud, Pierre Bénite, France.,Université Claude Bernard Lyon-1, Université de Lyon, Lyon, France.,Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052 CNRS 5286, Equipe "Clinical and experimental models of lymphomagenesis," Lyon, France
| | - Gilles Salles
- Université Claude Bernard Lyon-1, Université de Lyon, Lyon, France.,Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052 CNRS 5286, Equipe "Clinical and experimental models of lymphomagenesis," Lyon, France.,Hospices Civils de Lyon, Service d'Hématologie Clinique, Hôpital Lyon-Sud, Pierre Bénite France
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76
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Romero-Masters JC, Ohashi M, Djavadian R, Eichelberg MR, Hayes M, Zumwalde NA, Bristol JA, Nelson SE, Ma S, Ranheim EA, Gumperz JE, Johannsen EC, Kenney SC. An EBNA3A-Mutated Epstein-Barr Virus Retains the Capacity for Lymphomagenesis in a Cord Blood-Humanized Mouse Model. J Virol 2020; 94:e02168-19. [PMID: 32132242 PMCID: PMC7199417 DOI: 10.1128/jvi.02168-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) causes B cell lymphomas and transforms B cells in vitro The EBV protein EBNA3A collaborates with EBNA3C to repress p16 expression and is required for efficient transformation in vitro An EBNA3A deletion mutant EBV strain was recently reported to establish latency in humanized mice but not cause tumors. Here, we compare the phenotypes of an EBNA3A mutant EBV (Δ3A) and wild-type (WT) EBV in a cord blood-humanized (CBH) mouse model. The hypomorphic Δ3A mutant, in which a stop codon is inserted downstream from the first ATG and the open reading frame is disrupted by a 1-bp insertion, expresses very small amounts of EBNA3A using an alternative ATG at residue 15. Δ3A caused B cell lymphomas at rates similar to their induction by WT EBV but with delayed onset. Δ3A and WT tumors expressed equivalent levels of EBNA2 and p16, but Δ3A tumors in some cases had reduced LMP1. Like the WT EBV tumors, Δ3A lymphomas were oligoclonal/monoclonal, with typically one dominant IGHV gene being expressed. Transcriptome sequencing (RNA-seq) analysis revealed small but consistent gene expression differences involving multiple cellular genes in the WT EBV- versus Δ3A-infected tumors and increased expression of genes associated with T cells, suggesting increased T cell infiltration of tumors. Consistent with an impact of EBNA3A on immune function, we found that the expression of CLEC2D, a receptor that has previously been shown to influence responses of T and NK cells, was markedly diminished in cells infected with EBNA3A mutant virus. Together, these studies suggest that EBNA3A contributes to efficient EBV-induced lymphomagenesis in CBH mice.IMPORTANCE The EBV protein EBNA3A is expressed in latently infected B cells and is important for efficient EBV-induced transformation of B cells in vitro In this study, we used a cord blood-humanized mouse model to compare the phenotypes of an EBNA3A hypomorph mutant virus (Δ3A) and wild-type EBV. The Δ3A virus caused lymphomas with delayed onset compared to the onset of those caused by WT EBV, although the tumors occurred at a similar rate. The WT EBV and EBNA3A mutant tumors expressed similar levels of the EBV protein EBNA2 and cellular protein p16, but in some cases, Δ3A tumors had less LMP1. Our analysis suggested that Δ3A-infected tumors have elevated T cell infiltrates and decreased expression of the CLEC2D receptor, which may point to potential novel roles of EBNA3A in T cell and NK cell responses to EBV-infected tumors.
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Affiliation(s)
- James C Romero-Masters
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Makoto Ohashi
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Reza Djavadian
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark R Eichelberg
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mitchell Hayes
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicholas A Zumwalde
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jillian A Bristol
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott E Nelson
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shidong Ma
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Erik A Ranheim
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jenny E Gumperz
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric C Johannsen
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shannon C Kenney
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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77
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[Progress in the research of gene mutations in follicular lymphoma]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2020; 41:172-176. [PMID: 32135639 PMCID: PMC7357952 DOI: 10.3760/cma.j.issn.0253-2727.2020.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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78
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Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell 2020; 37:551-568.e14. [PMID: 32289277 PMCID: PMC8459709 DOI: 10.1016/j.ccell.2020.03.015] [Citation(s) in RCA: 570] [Impact Index Per Article: 142.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/03/2020] [Accepted: 03/16/2020] [Indexed: 12/22/2022]
Abstract
The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.
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MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genetic Heterogeneity
- Humans
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Molecular Targeted Therapy
- Precision Medicine
- Tumor Cells, Cultured
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
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Affiliation(s)
- George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zana A Coulibaly
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandrine Roulland
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Q Wang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roland Schmitz
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jeffrey Tang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | | | | | - Calvin A Johnson
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David W Scott
- British Columbia Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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79
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New Insights on the Emerging Genomic Landscape of CXCR4 in Cancer: A Lesson from WHIM. Vaccines (Basel) 2020; 8:vaccines8020164. [PMID: 32260318 PMCID: PMC7349554 DOI: 10.3390/vaccines8020164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/16/2022] Open
Abstract
Deciphering the molecular alterations leading to disease initiation and progression is currently crucial to identify the most relevant targets for precision therapy in cancer patients. Cancers express a complex chemokine network influencing leucocyte infiltration and angiogenesis. Moreover, malignant cells also express a selective repertoire of chemokine receptors that sustain their growth and spread. At present, different cancer types have been shown to overexpress C-X-C chemokine receptor type 4 (CXCR4) and to respond to its ligand C-X-C motif chemokine 12 (CXCL12). The CXCL12/CXCR4 axis influences cancer biology, promoting survival, proliferation, and angiogenesis, and plays a pivotal role in directing migration of cancer cells to sites of metastases, making it a prognostic marker and a therapeutic target. More recently, mutations in the C-terminus of CXCR4 have been identified in the genomic landscape of patients affected by Waldenstrom's macroglobulinemia, a rare B cell neoplasm. These mutations closely resemble those occurring in Warts, Hypogammaglobulinemia, Immunodeficiency, and Myelokathexis (WHIM) syndrome, an immunodeficiency associated with CXCR4 aberrant expression and activity and with chemotherapy resistance in clinical trials. In this review, we summarize the current knowledge on the relevance of CXCR4 mutations in cancer biology, focusing on its importance as predictors of clinical presentation and response to therapy.
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80
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Wang L, Qin W, Huo YJ, Li X, Shi Q, Rasko JEJ, Janin A, Zhao WL. Advances in targeted therapy for malignant lymphoma. Signal Transduct Target Ther 2020; 5:15. [PMID: 32296035 PMCID: PMC7058622 DOI: 10.1038/s41392-020-0113-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/10/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
The incidence of lymphoma has gradually increased over previous decades, and it ranks among the ten most prevalent cancers worldwide. With the development of targeted therapeutic strategies, though a subset of lymphoma patients has become curable, the treatment of refractory and relapsed diseases remains challenging. Many efforts have been made to explore new targets and to develop corresponding therapies. In addition to novel antibodies targeting surface antigens and small molecular inhibitors targeting oncogenic signaling pathways and tumor suppressors, immune checkpoint inhibitors and chimeric antigen receptor T-cells have been rapidly developed to target the tumor microenvironment. Although these targeted agents have shown great success in treating lymphoma patients, adverse events should be noted. The selection of the most suitable candidates, optimal dosage, and effective combinations warrant further investigation. In this review, we systematically outlined the advances in targeted therapy for malignant lymphoma, providing a clinical rationale for mechanism-based lymphoma treatment in the era of precision medicine.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
| | - Wei Qin
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China
| | - Yu-Jia Huo
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China
| | - Xiao Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China
| | - Qing Shi
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, Sydney Medical School, University of Sydney, Camperdown, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Anne Janin
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China
- U1165 Inserm/Université Paris 7, Hôpital Saint Louis, Paris, France
| | - Wei-Li Zhao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China.
- Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Shanghai, China.
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81
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Taylor J, Yeomans AM, Packham G. Targeted inhibition of mRNA translation initiation factors as a novel therapeutic strategy for mature B-cell neoplasms. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:3-25. [PMID: 32924027 PMCID: PMC7116065 DOI: 10.37349/etat.2020.00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cancer development is frequently associated with dysregulation of mRNA translation to enhance both increased global protein synthesis and translation of specific mRNAs encoding oncoproteins. Thus, targeted inhibition of mRNA translation is viewed as a promising new approach for cancer therapy. In this article we review current progress in investigating dysregulation of mRNA translation initiation in mature B-cell neoplasms, focusing on chronic lymphocytic leukemia, follicular lymphoma and diffuse large B-cell lymphoma. We discuss mechanisms and regulation of mRNA translation, potential pathways by which genetic alterations and the tumor microenvironment alters mRNA translation in malignant B cells, preclinical evaluation of drugs targeted against specific eukaryotic initiation factors and current progress towards clinical development. Overall, inhibition of mRNA translation initiation factors is an exciting and promising area for development of novel targeted anti-tumor drugs.
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Affiliation(s)
- Joe Taylor
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, United Kingdom
| | - Alison M Yeomans
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, United Kingdom
| | - Graham Packham
- Cancer Research UK Centre, Cancer Sciences, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, United Kingdom
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82
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Pasqualucci L. Molecular pathogenesis of germinal center-derived B cell lymphomas. Immunol Rev 2019; 288:240-261. [PMID: 30874347 DOI: 10.1111/imr.12745] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
B cell lymphomas comprise a heterogeneous group of genetically, biologically, and clinically distinct neoplasms that, in most cases, originate from the clonal expansion of B cells in the germinal center (GC). In recent years, the advent of novel genomics technologies has revolutionized our understanding of the molecular pathogenesis of lymphoid malignancies as a multistep process that requires the progressive accumulation of multiple genetic and epigenetic alterations. A common theme that emerged from these studies is the ability of lymphoma cells to co-opt the same biological programs and signal transduction networks that operate during the normal GC reaction, and misuse them for their own survival advantage. This review summarizes recent progress in the understanding of the genetic and epigenetic mechanisms that drive the malignant transformation of GC B cells. These insights provide a conceptual framework for the identification of cellular pathways that may be explored for precision medicine approaches.
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Affiliation(s)
- Laura Pasqualucci
- Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York City, New York
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83
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Matasar MJ, Luminari S, Barr PM, Barta SK, Danilov AV, Hill BT, Phillips TJ, Jerkeman M, Magagnoli M, Nastoupil LJ, Persky DO, Okosun J. Follicular Lymphoma: Recent and Emerging Therapies, Treatment Strategies, and Remaining Unmet Needs. Oncologist 2019; 24:e1236-e1250. [PMID: 31346132 PMCID: PMC6853118 DOI: 10.1634/theoncologist.2019-0138] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
Follicular lymphoma (FL) is a heterogeneous disease with varying prognosis owing to differences in clinical, laboratory, and disease parameters. Although generally considered incurable, prognosis for early- and advanced-stage disease has improved because of therapeutic advances, several of which have resulted from elucidation of the biologic and molecular basis of the disease. The choice of treatment for FL is highly dependent on patient and disease characteristics. Several tools are available for risk stratification, although limitations in their routine clinical use exist. For limited disease, treatment options include radiotherapy, rituximab monotherapy or combination regimens, and surveillance. Treatment of advanced disease is often determined by tumor burden, with surveillance or rituximab considered for low tumor burden and chemoimmunotherapy for high tumor burden disease. Treatment for relapsed or refractory disease is influenced by initial first-line therapy and the duration and quality of the response. Presently, there is no consensus for treatment of patients with early or multiply relapsed disease; however, numerous agents, combination regimens, and transplant options have demonstrated efficacy. Although the number of therapies available to treat FL has increased together with an improved understanding of the underlying biologic basis of disease, the best approach to select the most appropriate treatment strategy for an individual patient at a particular time continues to be elucidated. This review considers prognostication and the evolving treatment landscape of FL, including recent and emergent therapies as well as remaining unmet needs. IMPLICATIONS FOR PRACTICE: In follicular lymphoma, a personalized approach to management based on disease biology, patient characteristics, and other factors continues to emerge. However, application of current management requires an understanding of the available therapeutic options for first-line treatment and knowledge of current development in therapies for previously untreated and for relapsed or refractory disease. Thus, this work reviews for clinicians the contemporary data in follicular lymphoma, from advances in characterizing disease biology to current treatments and emerging novel therapies.
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Affiliation(s)
- Matthew J Matasar
- Memorial Sloan Kettering Cancer Center and New York Presbyterian, New York New York, USA
| | - Stefano Luminari
- Hematology Unit, Azienda Unità Sanitaria Locale-IRCCS, Reggio Emilia, Italy
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Paul M Barr
- University of Rochester Medical Center, Rochester, New York, USA
| | - Stefan K Barta
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Brian T Hill
- Cleveland Clinic Taussig Cancer Institute, Cleveland, Ohio, USA
| | | | | | - Massimo Magagnoli
- Humanitas Cancer Center, Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | | | - Jessica Okosun
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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84
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Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R, Abascal F, Rodriguez-Martin B, Samur MK, Glodzik D, Roncador M, Fulciniti M, Tai YT, Minvielle S, Magrangeas F, Moreau P, Corradini P, Anderson KC, Tubio JMC, Wedge DC, Gerstung M, Avet-Loiseau H, Munshi N, Campbell PJ. Genomic landscape and chronological reconstruction of driver events in multiple myeloma. Nat Commun 2019; 10:3835. [PMID: 31444325 PMCID: PMC6707220 DOI: 10.1038/s41467-019-11680-1] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/23/2019] [Indexed: 01/11/2023] Open
Abstract
The multiple myeloma (MM) genome is heterogeneous and evolves through preclinical and post-diagnosis phases. Here we report a catalog and hierarchy of driver lesions using sequences from 67 MM genomes serially collected from 30 patients together with public exome datasets. Bayesian clustering defines at least 7 genomic subgroups with distinct sets of co-operating events. Focusing on whole genome sequencing data, complex structural events emerge as major drivers, including chromothripsis and a novel replication-based mechanism of templated insertions, which typically occur early. Hyperdiploidy also occurs early, with individual trisomies often acquired in different chronological windows during evolution, and with a preferred order of acquisition. Conversely, positively selected point mutations, whole genome duplication and chromoplexy events occur in later disease phases. Thus, initiating driver events, drawn from a limited repertoire of structural and numerical chromosomal changes, shape preferred trajectories of evolution that are biologically relevant but heterogeneous across patients.
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Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Niccoló Bolli
- Department of Medical Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nicos Angelopoulos
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, UK
| | - Kevin J Dawson
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Daniel Leongamornlert
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Inigo Martincorena
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Thomas J Mitchell
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Anthony Fullam
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Santiago Gonzalez
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK
| | - Raphael Szalat
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Federico Abascal
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Bernardo Rodriguez-Martin
- CIMUS - Molecular Medicine and Chronic Diseases Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mehmet Kemal Samur
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dominik Glodzik
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marco Roncador
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Mariateresa Fulciniti
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yu Tzu Tai
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephane Minvielle
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Florence Magrangeas
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Philippe Moreau
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Paolo Corradini
- Department of Medical Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jose M C Tubio
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- CIMUS - Molecular Medicine and Chronic Diseases Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - David C Wedge
- University of Oxford, Big Data Institute, Oxford, UK
| | - Moritz Gerstung
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK
| | | | - Nikhil Munshi
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Veterans Administration Boston Healthcare System, West Roxbury, MA, USA.
| | - Peter J Campbell
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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85
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Ortega-Molina A, Deleyto-Seldas N, Carreras J, Sanz A, Lebrero-Fernández C, Menéndez C, Vandenberg A, Fernández-Ruiz B, Marín-Arraiza L, de la Calle Arregui C, Belén Plata-Gómez A, Caleiras E, de Martino A, Martínez-Martín N, Troulé K, Piñeiro-Yáñez E, Nakamura N, Araf S, Victora GD, Okosun J, Fitzgibbon J, Efeyan A. Oncogenic Rag GTPase signaling enhances B cell activation and drives follicular lymphoma sensitive to pharmacological inhibition of mTOR. Nat Metab 2019; 1:775-789. [PMID: 31579886 PMCID: PMC6774795 DOI: 10.1038/s42255-019-0098-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
The humoral immune response demands that B cells undergo a sudden anabolic shift and high cellular nutrient levels which are required to sustain the subsequent proliferative burst. Follicular lymphoma (FL) originates from B cells that have participated in the humoral response, and 15% of FL samples harbor point, activating mutations in RRAGC, an essential activator of mTORC1 downstream of the sensing of cellular nutrients. The impact of recurrent RRAGC mutations in B cell function and lymphoma is unexplored. RRAGC mutations, targeted to the endogenous locus in mice, confer a partial insensitivity to nutrient deprivation, but strongly exacerbate B cell responses and accelerate lymphomagenesis, while creating a selective vulnerability to pharmacological inhibition of mTORC1. This moderate increase in nutrient signaling synergizes with paracrine cues from the supportive T cell microenvironment that activates B cells via the PI3K-Akt-mTORC1 axis. Hence, Rragc mutations sustain induced germinal centers and murine and human FL in the presence of decreased T cell help. Our results support a model in which activating mutations in the nutrient signaling pathway foster lymphomagenesis by corrupting a nutrient-dependent control over paracrine signals from the T cell microenvironment.
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Affiliation(s)
- Ana Ortega-Molina
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Nerea Deleyto-Seldas
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Joaquim Carreras
- Tokai University, School of Medicine, Department of Pathology. Isehara, Kanagawa, Japan
| | - Alba Sanz
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | | | - Camino Menéndez
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Andrew Vandenberg
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Beatriz Fernández-Ruiz
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Leyre Marín-Arraiza
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Celia de la Calle Arregui
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Ana Belén Plata-Gómez
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Eduardo Caleiras
- Histopathology Unit. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Alba de Martino
- Histopathology Unit. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | | | - Kevin Troulé
- Bioinformatics Unit. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Elena Piñeiro-Yáñez
- Bioinformatics Unit. Spanish National Cancer Research Center (CNIO). Madrid, Spain
| | - Naoya Nakamura
- Tokai University, School of Medicine, Department of Pathology. Isehara, Kanagawa, Japan
| | - Shamzah Araf
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
| | - Jessica Okosun
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alejo Efeyan
- Metabolism and Cell Signaling Laboratory. Spanish National Cancer Research Center (CNIO). Madrid, Spain
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86
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Wang J, Dayem Ullah AZ, Chelala C. IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome. Nucleic Acids Res 2019; 46:e47. [PMID: 29390075 PMCID: PMC5934661 DOI: 10.1093/nar/gky057] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/24/2018] [Indexed: 12/16/2022] Open
Abstract
The vast majority of germline and somatic variations occur in the noncoding part of the genome, only a small fraction of which are believed to be functional. From the tens of thousands of noncoding variations detectable in each genome, identifying and prioritizing driver candidates with putative functional significance is challenging. To address this, we implemented IW-Scoring, a new Integrative Weighted Scoring model to annotate and prioritise functionally relevant noncoding variations. We evaluate 11 scoring methods, and apply an unsupervised spectral approach for subsequent selective integration into two linear weighted functional scoring schemas for known and novel variations. IW-Scoring produces stable high-quality performance as the best predictors for three independent data sets. We demonstrate the robustness of IW-Scoring in identifying recurrent functional mutations in the TERT promoter, as well as disease SNPs in proximity to consensus motifs and with gene regulatory effects. Using follicular lymphoma as a paradigmatic cancer model, we apply IW-Scoring to locate 11 recurrently mutated noncoding regions in 14 follicular lymphoma genomes, and validate 9 of these regions in an extension cohort, including the promoter and enhancer regions of PAX5. Overall, IW-Scoring demonstrates greater versatility in identifying trait- and disease-associated noncoding variants. Scores from IW-Scoring as well as other methods are freely available from http://www.snp-nexus.org/IW-Scoring/.
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Affiliation(s)
- Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Abu Z Dayem Ullah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.,Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, UK
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87
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Wang S, Mondal S, Zhao C, Berishaj M, Ghanakota P, Batlevi CL, Dogan A, Seshan VE, Abel R, Green MR, Younes A, Wendel HG. Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity. JCI Insight 2019; 4:127566. [PMID: 31217352 DOI: 10.1172/jci.insight.127566] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Inhibition of Bruton tyrosine kinase (BTK) is a breakthrough therapy for certain B cell lymphomas and B cell chronic lymphatic leukemia. Covalent BTK inhibitors (e.g., ibrutinib) bind to cysteine C481, and mutations of this residue confer clinical resistance. This has led to the development of noncovalent BTK inhibitors that do not require binding to cysteine C481. These new compounds are now entering clinical trials. In a systematic BTK mutagenesis screen, we identify residues that are critical for the activity of noncovalent inhibitors. These include a gatekeeper residue (T474) and mutations in the kinase domain. Strikingly, co-occurrence of gatekeeper and kinase domain lesions (L512M, E513G, F517L, L547P) in cis results in a 10- to 15-fold gain of BTK kinase activity and de novo transforming potential in vitro and in vivo. Computational BTK structure analyses reveal how these lesions disrupt an intramolecular mechanism that attenuates BTK activation. Our findings anticipate clinical resistance mechanisms to a new class of noncovalent BTK inhibitors and reveal intramolecular mechanisms that constrain BTK's transforming potential.
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Affiliation(s)
- Shenqiu Wang
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | | | - Chunying Zhao
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | - Marjan Berishaj
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
| | | | | | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, and
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | | | - Michael R Green
- Department of Lymphoma and Myeloma and Department of Genomic Medicine, University of Texas MD Anderson Cancer, Houston, Texas, USA
| | | | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York USA
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88
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Castillo J, Wu E, Lowe C, Srinivasan S, McCord R, Wagle MC, Jayakar S, Edick MG, Eastham-Anderson J, Liu B, Hutchinson KE, Jones W, Stokes MP, Tarighat SS, Holcomb T, Glibicky A, Romero FA, Magnuson S, Huang SMA, Plaks V, Giltnane JM, Lackner MR, Mounir Z. CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms. Cancer Res 2019; 79:3916-3927. [PMID: 31182547 DOI: 10.1158/0008-5472.can-18-3622] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/21/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022]
Abstract
Regulatory T cells (Treg) are immunosuppressive and negatively impact response to cancer immunotherapies. CREB-binding protein (CBP) and p300 are closely related acetyltransferases and transcriptional coactivators. Here, we evaluate the mechanisms by which CBP/p300 regulate Treg differentiation and the consequences of CBP/p300 loss-of-function mutations in follicular lymphoma. Transcriptional and epigenetic profiling identified a cascade of transcription factors essential for Treg differentiation. Mass spectrometry analysis showed that CBP/p300 acetylates prostacyclin synthase, which regulates Treg differentiation by altering proinflammatory cytokine secretion by T and B cells. Reduced Treg presence in tissues harboring CBP/p300 loss-of-function mutations was observed in follicular lymphoma. Our findings provide novel insights into the regulation of Treg differentiation by CBP/p300, with potential clinical implications on alteration of the immune landscape. SIGNIFICANCE: This study provides insights into the dynamic role of CBP/p300 in the differentiation of Tregs, with potential clinical implications in the alteration of the immune landscape in follicular lymphoma.
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Affiliation(s)
- Joseph Castillo
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Esther Wu
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Christopher Lowe
- Department of Bioanalytical Sciences, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Shrividhya Srinivasan
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Ron McCord
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Marie-Claire Wagle
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Sangeeta Jayakar
- Department of Research Pathology, Genentech, Inc., South San Francisco, California
| | | | | | - Bonnie Liu
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Katherine E Hutchinson
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Wendell Jones
- Q Solutions-EA Genomics, Morrisville, North Carolina
| | | | - Somayeh S Tarighat
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Thomas Holcomb
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Andrew Glibicky
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - F Anthony Romero
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California
| | - Steven Magnuson
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California
| | - Shih-Min A Huang
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Vicki Plaks
- Department of Bioanalytical Sciences, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Jennifer M Giltnane
- Department of Research Pathology, Genentech, Inc., South San Francisco, California
| | - Mark R Lackner
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California
| | - Zineb Mounir
- Department of Oncology Biomarker Development, Development Sciences, Genentech, Inc., South San Francisco, California.
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89
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Abstract
PURPOSE OF REVIEW In addition to the recent progresses in the description of the genetic landscape of B-cell non-Hodgkin's lymphomas, tumor microenvironment has progressively emerged as a central determinant of early lymphomagenesis, subclonal evolution, drug resistance, and late progression/transformation. The purpose of this review is to outline the most recent findings regarding malignant B-cell niche composition and organization supporting direct and indirect tumor-promoting functions of lymphoma microenvironment. RECENT FINDINGS Lymphoma supportive niche integrates a dynamic and orchestrated network of immune and stromal cell subsets producing, with a high level of spatial and kinetic heterogeneity, extracellular and membrane factors regulating tumor migration, survival, proliferation, immune escape, as well as tumor microarchitecture, and mechanical constraints. Some recent insights have improved our understanding of these various components of lymphoma microenvironment, taking into account the mechanisms underlying the coevolution of malignant and nonmalignant cells within the tumor niche. SUMMARY Deciphering tumor niche characteristics, functions, and origin could offer new therapeutic opportunities through the targeting of pivotal cellular and molecular components of the supportive microenvironment, favoring immune cell reactivation and infiltration, and/or limiting tumor retention within this protective niche.
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90
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Abstract
PURPOSE OF REVIEW The treatment of the germinal center lymphomas, diffuse large B cell (DLBCL) and follicular lymphoma, has changed little beyond the introduction of immunochemotherapies. However, there exists a substantial group of patients within both diseases for which improvements in care will involve appropriate tailoring of treatment. RECENT FINDINGS DLBCL consists of two major subtypes with striking differences in their clinical outcomes paralleling their underlying genetic heterogeneity. Recent studies have seen advances in the stratification of germinal center lymphomas, through comprehensive profiling of 1001 DLBCLs alongside refinements in the identification of high-risk follicular lymphoma patients using m7-FLIPI and 23G models. A new wave of novel therapeutic agents is now undergoing clinical trials for germinal center lymphomas, with BCR and EZH2 inhibitors demonstrating preferential benefit in subgroups of patients. The emergence of cell-free DNA has raised the possibility of dynamic disease monitoring to potentially mitigate the complexity of spatial and temporal heterogeneity, whilst predicting tumor evolution in real time. SUMMARY Altogether knowledge of the genomic landscape of germinal center lymphomas is offering welcome opportunities in patient risk stratification and therapeutics. The challenge ahead is to establish how best to combine upfront or dynamic prognostication with precision therapies, while retaining practicality in clinical trials and the real-world setting.
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91
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Wang F, Gatica D, Ying ZX, Peterson LF, Kim P, Bernard D, Saiya-Cork K, Wang S, Kaminski MS, Chang AE, Phillips T, Klionsky DJ, Malek SN. Follicular lymphoma-associated mutations in vacuolar ATPase ATP6V1B2 activate autophagic flux and mTOR. J Clin Invest 2019; 129:1626-1640. [PMID: 30720463 PMCID: PMC6436860 DOI: 10.1172/jci98288] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/29/2019] [Indexed: 12/15/2022] Open
Abstract
The discovery of recurrent mutations in subunits of the vacuolar-type H+-translocating ATPase (v-ATPase) in follicular lymphoma (FL) highlights a role for the amino acid- and energy-sensing pathway to mTOR in the pathogenesis of this disease. Here, through the use of complementary experimental approaches involving mammalian cells and Saccharomyces cerevisiae, we have demonstrated that mutations in the human v-ATPase subunit ATP6V1B2 (also known as Vma2 in yeast) activate autophagic flux and maintain mTOR/TOR in an active state. Engineered lymphoma cell lines and primary FL B cells carrying mutated ATP6V1B2 demonstrated a remarkable ability to survive low leucine concentrations. The treatment of primary FL B cells with inhibitors of autophagy uncovered an addiction for survival for FL B cells harboring ATP6V1B2 mutations. These data support the idea of mutational activation of autophagic flux by recurrent hotspot mutations in ATP6V1B2 as an adaptive mechanism in FL pathogenesis and as a possible new therapeutically targetable pathway.
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Affiliation(s)
- Fangyang Wang
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Damián Gatica
- Life Sciences Institute, and
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Zhang Xiao Ying
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Luke F. Peterson
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Peter Kim
- Department of Internal Medicine, Division of Hematology and Oncology
| | | | - Kamlai Saiya-Cork
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Shaomeng Wang
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Mark S. Kaminski
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Alfred E. Chang
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Tycel Phillips
- Department of Internal Medicine, Division of Hematology and Oncology
| | - Daniel J. Klionsky
- Life Sciences Institute, and
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sami N. Malek
- Department of Internal Medicine, Division of Hematology and Oncology
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92
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Mlynarczyk C, Fontán L, Melnick A. Germinal center-derived lymphomas: The darkest side of humoral immunity. Immunol Rev 2019; 288:214-239. [PMID: 30874354 PMCID: PMC6518944 DOI: 10.1111/imr.12755] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 02/06/2023]
Abstract
One of the unusual features of germinal center (GC) B cells is that they manifest many hallmarks of cancer cells. Accordingly, most B-cell neoplasms originate from the GC reaction, and characteristically display abundant point mutations, structural genomic lesions, and clonal diversity from the genetic and epigenetic standpoints. The dominant biological theme of GC-derived lymphomas is mutation of genes involved in epigenetic regulation and immune receptor signaling, which come into play at critical transitional stages of the GC reaction. Hence, mechanistic studies of these mutations reveal fundamental insight into the biology of the normal and malignant GC B cell. The BCL6 transcription factor plays a central role in establishing the GC phenotype in B cells, and most lymphomas are dependent on BCL6 to maintain survival, proliferation, and perhaps immune evasion. Many lymphoma mutations have the commonality of enhancing the oncogenic functions of BCL6, or overcoming some of its tumor suppressive effects. Herein, we discuss how unique features of the GC reaction create vulnerabilities that select for particular lymphoma mutations. We examine the interplay between epigenetic programming, metabolism, signaling, and immune regulatory mechanisms in lymphoma, and discuss how these are leading to novel precision therapy strategies to treat lymphoma patients.
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Affiliation(s)
- Coraline Mlynarczyk
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Lorena Fontán
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Ari Melnick
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
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93
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González-Rincón J, Méndez M, Gómez S, García JF, Martín P, Bellas C, Pedrosa L, Rodríguez-Pinilla SM, Camacho FI, Quero C, Pérez-Callejo D, Rueda A, Llanos M, Gómez-Codina J, Piris MA, Montes-Moreno S, Bárcena C, Rodríguez-Abreu D, Menárguez J, de la Cruz-Merino L, Monsalvo S, Parejo C, Royuela A, Kwee I, Cascione L, Arribas A, Bertoni F, Mollejo M, Provencio M, Sánchez-Beato M. Unraveling transformation of follicular lymphoma to diffuse large B-cell lymphoma. PLoS One 2019; 14:e0212813. [PMID: 30802265 PMCID: PMC6388933 DOI: 10.1371/journal.pone.0212813] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/08/2019] [Indexed: 02/07/2023] Open
Abstract
Follicular lymphoma (FL) is an indolent but largely incurable disease. Some patients suffer histological transformation to a more aggressive subtype with poorer prognosis. This study aimed to improve our understanding of the genetics underlying FL histological transformation, and to identify genetic drivers or promoters of the transformation by elucidating the differences between FL samples from patients who did and did not transform. We conducted targeted massive parallel sequencing of 22 pre-transformed FL/transformed diffuse large B-cell lymphoma pairs and 20 diagnostic samples from non-transformed FL patients. Additionally, 22 matched samples from 11 transformed FL patients (pre-transformed FL and diffuse large B-cell lymphoma) and 9 non-transformed FLs were studied for copy number variation using SNP arrays. We identified recurrently mutated genes that were enriched at transformation, most notably LRP1B, GNA13 and POU2AF1, which have roles in B-cell differentiation, GC architecture and migration. Mutations in POU2AF1 might be associated with lower levels of expression, were more frequent in transformed FLs, and seemed to be specific to transformed- compared with de novo-diffuse large B-cell lymphomas. Pre-transformed FLs carried more mutations per sample and had greater subclonal heterogeneity than non-transformed FLs. Finally, we identified four mutated genes in FL samples that differed between patients who did and did not transform: NOTCH2, DTX1, UBE2A and HIST1H1E. The presence of mutations in these genes was associated with shorter time to transformation when mutated in the FL biopsies. This information might be useful for identifying patients at higher risk of transformation.
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MESH Headings
- Adult
- Aged
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Biopsy
- Cell Differentiation/genetics
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Female
- Follow-Up Studies
- Humans
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/metabolism
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
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Affiliation(s)
- Julia González-Rincón
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
| | - Miriam Méndez
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Sagrario Gómez
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
| | - Juan F. García
- Pathology Department, Hospital MD Anderson Cancer Center, Madrid, Spain
| | - Paloma Martín
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
- Pathology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Carmen Bellas
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
- Pathology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Lucía Pedrosa
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
| | - Socorro M. Rodríguez-Pinilla
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
- Pathology Department, Fundación Jiménez Díaz, Madrid, Spain
| | | | - Cristina Quero
- Medical Oncology Department, Hospital Universitario Virgen de la Victoria, Malaga, Spain
| | - David Pérez-Callejo
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Antonio Rueda
- Medical Oncology Department, Hospital Costa del Sol, Malaga, Spain
| | - Marta Llanos
- Medical Oncology Department, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Spain
| | - José Gómez-Codina
- Medical Oncology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Miguel A. Piris
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
- Pathology Department, Fundación Jiménez Díaz, Madrid, Spain
| | - Santiago Montes-Moreno
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC),Madrid, Spain
- Pathology Department/Translational Hematology Group, Hospital Universitario Marqués de Valdecilla/IDIVAL, Santander, Spain
| | - Carmen Bárcena
- Pathology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Delvys Rodríguez-Abreu
- Medical Oncology Department, Hospital Universitario Insular de Gran Canaria, Las Palmas de Gran Canarias, Spain
| | - Javier Menárguez
- Pathology Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Silvia Monsalvo
- Hematology Department, Fundación Jiménez Díaz, Madrid, Spain
| | - Consuelo Parejo
- TIC Unit- Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro- Segovia de Arana, Madrid, Spain
| | - Ana Royuela
- Clinical Biostatistics Unit, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
| | - Ivo Kwee
- Institute of Oncology Research (IOR), Belinzona, Switzerland
- Universitá della Svizzera Italiana (USI), Lugano, Switzerland
- Dalle Molle Institute for Artificial Intelligence (IDSIA), Belinzona, Switzerland
- Swiss Institute of Bioinformatics (SIB), Belinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research (IOR), Belinzona, Switzerland
- Universitá della Svizzera Italiana (USI), Lugano, Switzerland
- Swiss Institute of Bioinformatics (SIB), Belinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Belinzona, Switzerland
| | - Alberto Arribas
- Institute of Oncology Research (IOR), Belinzona, Switzerland
- Universitá della Svizzera Italiana (USI), Lugano, Switzerland
- Swiss Institute of Bioinformatics (SIB), Belinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Belinzona, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research (IOR), Belinzona, Switzerland
- Universitá della Svizzera Italiana (USI), Lugano, Switzerland
- Swiss Institute of Bioinformatics (SIB), Belinzona, Switzerland
- Oncology Institute of Southern Switzerland (IOSI), Belinzona, Switzerland
| | - Manuela Mollejo
- Pathology Department, Hospital Virgen de la Salud, Toledo, Spain
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Margarita Sánchez-Beato
- Lymphoma Research Group, Medical Oncology Department, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana, Madrid, Spain
- * E-mail:
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94
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Qu X, Li H, Braziel RM, Passerini V, Rimsza LM, Hsi ED, Leonard JP, Smith SM, Kridel R, Press O, Weigert O, LeBlanc M, Friedberg JW, Fang M. Genomic alterations important for the prognosis in patients with follicular lymphoma treated in SWOG study S0016. Blood 2019; 133:81-93. [PMID: 30446494 PMCID: PMC6318431 DOI: 10.1182/blood-2018-07-865428] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/06/2018] [Indexed: 02/08/2023] Open
Abstract
Although recent advances in molecular genetics have enabled improved risk classification of follicular lymphoma (FL) using, for example, the m7-FLIPI score, the impact on treatment has been limited. We aimed to assess the prognostic significance of copy-number aberrations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) identified by chromosome genomic-array testing (CGAT) at FL diagnosis using prospectively collected clinical trial specimens from 255 patients enrolled in the SWOG study S0016. The impact of genomic aberrations was assessed for early progression (progressed or died within 2 years after registration), progression-free survival (PFS), and overall survival (OS). We showed that increased genomic complexity (ie, the total number of aberration calls) was associated with poor outcome in FL. Certain chromosome arms were critical for clinical outcome. Prognostic CNAs/cnLOH were identified: whereas early progression was correlated with 2p gain (P = .007; odds ratio [OR] = 2.55 [1.29, 5.03]) and 2p cnLOH (P = .005; OR = 10.9 [2.08, 57.2]), 2p gain specifically encompassing VRK2 and FANCL predicted PFS (P = .01; hazard ratio = 1.80 [1.14, 2.68]) as well as OS (P = .005; 2.40 [1.30, 4.40]); CDKN2A/B (9p) deletion correlated with worse PFS (P = .004, 3.50 [1.51, 8.28]); whereas CREBBP (16p) (P < .001; 6.70 [2.52, 17.58]) and TP53 (17p) (P < .001; 3.90 [1.85, 8.31]) deletion predicted worse OS. An independent cohort from the m7-FLIPI study was explored, and the prognostic significance of aberration count, and TP53 and CDKN2A/B deletion were further validated. In conclusion, assessing genomic aberrations at FL diagnosis with CGAT improves risk stratification independent of known clinical parameters, and provides a framework for development of future rational targeted therapies.
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Affiliation(s)
- Xiaoyu Qu
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Hongli Li
- SWOG Statistical Center, Seattle, WA
| | - Rita M Braziel
- Department of Pathology, Oregon Health & Science University, Portland, OR
| | - Verena Passerini
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | | | - John P Leonard
- Weill Cornell Medicine/New York Presbyterian Hospital, New York, NY
| | - Sonali M Smith
- Department of Medicine, University of Chicago, Chicago, IL
| | - Robert Kridel
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON, Canada; and
| | - Oliver Press
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Min Fang
- Fred Hutchinson Cancer Research Center, Seattle, WA
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95
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Abstract
Immunoglobulin (IG) gene remodeling by V(D)J recombination plays a central role in the generation of normal B cells, and somatic hypermutation and class switching of IG genes are key processes during antigen-driven B cell differentiation. However, errors of these processes are involved in the development of B cell lymphomas. IG locus-associated translocations of proto-oncogenes are a hallmark of many B cell malignancies. Additional transforming events include inactivating mutations in various tumor suppressor genes and also latent infection of B cells with viruses, such as Epstein-Barr virus. Many B cell lymphomas require B cell antigen receptor expression, and in several instances, chronic antigenic stimulation plays a role in lymphoma development and/or sustaining tumor growth. Often, survival and proliferation signals provided by other cells in the microenvironment are a further critical factor in lymphoma development and pathophysiology. Many B cell malignancies derive from germinal center B cells, most likely because of the high proliferation rate of these cells and the high activity of mutagenic processes.
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96
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Arruga F, Vaisitti T, Deaglio S. The NOTCH Pathway and Its Mutations in Mature B Cell Malignancies. Front Oncol 2018; 8:550. [PMID: 30534535 PMCID: PMC6275466 DOI: 10.3389/fonc.2018.00550] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/06/2018] [Indexed: 12/16/2022] Open
Abstract
The systematic application of next-generation sequencing to large cohorts of oncologic samples has opened a Pandora's box full of known and novel genetic lesions implicated in different steps of cancer development and progression. Narrowing down to B cell malignancies, many previously unrecognized genes emerged as recurrently mutated. The challenge now is to determine how the mutation in a given gene affects the biology of the disease, paving the way to functional genomics studies. Mutations in NOTCH family members are shared by several disorders of the B series, even if with variable frequencies and mutational patterns. In silico predictions, revealed that mutations occurring in NOTCH receptors, despite being qualitatively different, may have similar effects on protein processing, ultimately leading to enhanced pathway activation. The discovery of mutations occurring also in downstream players, either potentiating positive signals or compromising negative regulators, indicates that multiple mechanisms in neoplastic B cells concur to activate NOTCH pathway. These findings are supported by results obtained in chronic lymphocytic leukemia and splenic marginal zone B cell lymphoma where deregulation of NOTCH signaling has been functionally characterized. The emerging picture confirms that NOTCH signaling is finely tuned in cell- and microenvironment-dependent ways. In B cell malignancies, it contributes to the regulation of proliferation, survival and migration. However, deeper biological studies are needed to pinpoint the contribution of NOTCH in the hierarchy of events driving B cells transformation, keeping in mind its role in normal B cells development. Because of its relevance in leukemia and lymphoma biology, the NOTCH pathway might represent an appealing therapeutic target: the next few years will tell whether this potential will be fulfilled.
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Affiliation(s)
- Francesca Arruga
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Medical Sciences, University of Torino, Turin, Italy
| | - Tiziana Vaisitti
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Medical Sciences, University of Torino, Turin, Italy
| | - Silvia Deaglio
- Italian Institute for Genomic Medicine, Turin, Italy.,Department of Medical Sciences, University of Torino, Turin, Italy
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97
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A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data. Nat Genet 2018; 50:1735-1743. [PMID: 30397337 DOI: 10.1038/s41588-018-0257-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022]
Abstract
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consuming, costly, poorly standardized, and non-reproducible. Here, we systematized and standardized somatic variant refinement using a machine learning approach. The final model incorporates 41,000 variants from 440 sequencing cases. This model accurately recapitulated manual refinement labels for three independent testing sets (13,579 variants) and accurately predicted somatic variants confirmed by orthogonal validation sequencing data (212,158 variants). The model improves on manual somatic refinement by reducing bias on calls otherwise subject to high inter-reviewer variability.
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98
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Duodenal-type and nodal follicular lymphomas differ by their immune microenvironment rather than their mutation profiles. Blood 2018; 132:1695-1702. [DOI: 10.1182/blood-2018-03-837252] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/10/2018] [Indexed: 11/20/2022] Open
Abstract
Key Points
The mutational landscape of DTFL is highly related to nodal FL but harbors fewer multiple/biallelic mutations in KMT2D. The immune microenvironment of DTFL is distinct from nodal FL and characterized by a chronic inflammation gene signature.
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99
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Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples. Genet Med 2018; 21:972-981. [PMID: 30287923 PMCID: PMC6450397 DOI: 10.1038/s41436-018-0278-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. METHODS This manual review standard operating procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer's confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. RESULTS After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. CONCLUSION This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
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100
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IG- MYC + neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas. Blood 2018; 132:2280-2285. [PMID: 30282799 DOI: 10.1182/blood-2018-03-842088] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022] Open
Abstract
The WHO Classification of Tumours of Haematopoietic and Lymphoid Tissue notes instances of Burkitt lymphoma/leukemia (BL) with IG-MYC rearrangement displaying a B-cell precursor immunophenotype (termed herein "preBLL"). To characterize the molecular pathogenesis of preBLL, we investigated 13 preBLL cases (including 1 cell line), of which 12 were analyzable using genome, exome, and targeted sequencing, imbalance mapping, and DNA methylation profiling. In 5 patients with reads across the IG-MYC breakpoint junctions, we found evidence that the translocation derived from an aberrant VDJ recombination, as is typical for IG translocations arising in B-cell precursors. Genomic changes like biallelic IGH translocations or VDJ rearrangements combined with translocation into the VDJ region on the second allele, potentially preventing expression of a productive immunoglobulin, were detected in 6 of 13 cases. We did not detect mutations in genes frequently altered in BL, but instead found activating NRAS and/or KRAS mutations in 7 of 12 preBLLs. Gains on 1q, recurrent in BL and preB lymphoblastic leukemia/lymphoma (pB-ALL/LBL), were detected in 7 of 12 preBLLs. DNA methylation profiling showed preBLL to cluster with precursor B cells and pB-ALL/LBL, but apart from BL. We conclude that preBLL genetically and epigenetically resembles pB-ALL/LBL rather than BL. Therefore, we propose that preBLL be considered as a pB-ALL/LBL with recurrent genetic abnormalities.
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