1
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Calbert ML, Chandramouly G, Adams CM, Saez-Ayala M, Kent T, Tyagi M, Ayyadevara VSSA, Wang Y, Krais JJ, Gordon J, Atkins J, Toma MM, Betzi S, Boghossian AS, Rees MG, Ronan MM, Roth JA, Goldman AR, Gorman N, Mitra R, Childers WE, Graña X, Skorski T, Johnson N, Hurtz C, Morelli X, Eischen CM, Pomerantz RT. 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress. Mol Cancer Ther 2024; 23:683-699. [PMID: 38064712 DOI: 10.1158/1535-7163.mct-23-0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/18/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Anticancer nucleosides are effective against solid tumors and hematologic malignancies, but typically are prone to nucleoside metabolism resistance mechanisms. Using a nucleoside-specific multiplexed high-throughput screening approach, we discovered 4'-ethynyl-2'-deoxycytidine (EdC) as a third-generation anticancer nucleoside prodrug with preferential activity against diffuse large B-cell lymphoma (DLBCL) and acute lymphoblastic leukemia (ALL). EdC requires deoxycytidine kinase (DCK) phosphorylation for its activity and induces replication fork arrest and accumulation of cells in S-phase, indicating it acts as a chain terminator. A 2.1Å cocrystal structure of DCK bound to EdC and UDP reveals how the rigid 4'-alkyne of EdC fits within the active site of DCK. Remarkably, EdC was resistant to cytidine deamination and SAMHD1 metabolism mechanisms and exhibited higher potency against ALL compared with FDA-approved nelarabine. Finally, EdC was highly effective against DLBCL tumors and B-ALL in vivo. These data characterize EdC as a preclinical nucleoside prodrug candidate for DLBCL and ALL.
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Affiliation(s)
- Marissa L Calbert
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Gurushankar Chandramouly
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Clare M Adams
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Magali Saez-Ayala
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Tatiana Kent
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Mrityunjay Tyagi
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - V S S Abhinav Ayyadevara
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Yifan Wang
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John J Krais
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John Gordon
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Jessica Atkins
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Monika M Toma
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | | | - Matthew G Rees
- Broad Institute of MIT and Harvard, Cambridge Massachusetts
| | | | | | | | | | - Ramkrishna Mitra
- Division of Biostatistics, Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Xavier Graña
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Neil Johnson
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Christian Hurtz
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Christine M Eischen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Richard T Pomerantz
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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2
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Leopizzi M, Mundo L, Messina E, Campolo F, Lazzi S, Angeloni A, Marchese C, Leoncini L, Giordano C, Slack F, Trivedi P, Anastasiadou E. Epstein-Barr virus-encoded EBNA2 downregulates ICOSL by inducing miR-24 in B-cell lymphoma. Blood 2024; 143:429-443. [PMID: 37847858 PMCID: PMC10862363 DOI: 10.1182/blood.2023021346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/12/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
ABSTRACT Hematological malignancies such as Burkitt lymphoma (BL), Hodgkin lymphoma (HL), and diffuse large B-cell lymphoma (DLBCL) cause significant morbidity in humans. A substantial number of these lymphomas, particularly HL and DLBCLs have poorer prognosis because of their association with Epstein-Barr virus (EBV). Our earlier studies have shown that EBV-encoded nuclear antigen (EBNA2) upregulates programmed cell death ligand 1 in DLBCL and BLs by downregulating microRNA-34a. Here, we investigated whether EBNA2 affects the inducible costimulator (ICOS) ligand (ICOSL), a molecule required for efficient recognition of tumor cells by T cells through the engagement of ICOS on the latter. In virus-infected and EBNA2-transfected B-lymphoma cells, ICOSL expression was reduced. Our investigation of the molecular mechanisms revealed that this was due to an increase in microRNA-24 (miR-24) by EBNA2. By using ICOSL 3' untranslated region-luciferase reporter system, we validated that ICOSL is an authentic miR-24 target. Transfection of anti-miR-24 molecules in EBNA2-expressing lymphoma cells reconstituted ICOSL expression and increased tumor immunogenicity in mixed lymphocyte reactions. Because miR-24 is known to target c-MYC, an oncoprotein positively regulated by EBNA2, we analyzed its expression in anti-miR-24 transfected lymphoma cells. Indeed, the reduction of miR-24 in EBNA2-expressing DLBCL further elevated c-MYC and increased apoptosis. Consistent with the in vitro data, EBNA2-positive DLBCL biopsies expressed low ICOSL and high miR-24. We suggest that EBV evades host immune responses through EBNA2 by inducing miR-24 to reduce ICOSL expression, and for simultaneous rheostatic maintenance of proproliferative c-MYC levels. Overall, these data identify miR-24 as a potential therapeutically relevant target in EBV-associated lymphomas.
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Affiliation(s)
- Martina Leopizzi
- Department of Medico-surgical Sciences and Biotechnologies, Sapienza University, Latina, Italy
| | - Lucia Mundo
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Elena Messina
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Stefano Lazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Carla Giordano
- Department of Radiology, Oncology and Pathology, Sapienza University, Rome, Italy
| | - Frank Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Pankaj Trivedi
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Eleni Anastasiadou
- Department of Clinical and Molecular Medicine, Sapienza University, Rome, Italy
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3
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Chung EYL, Sartori G, Ponzoni M, Cascione L, Priebe V, Xu-Monette ZY, Fang X, Zhang M, Visco C, Tzankov A, Rinaldi A, Sgrignani J, Zucca E, Rossi D, Cavalli A, Inghirami G, Scott DW, Young KH, Bertoni F. ETS1 phosphorylation at threonine 38 is associated with the cell of origin of diffuse large B cell lymphoma and sustains the growth of tumour cells. Br J Haematol 2023; 203:244-254. [PMID: 37584198 DOI: 10.1111/bjh.19018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
The transcriptional factor ETS1 is upregulated in 25% of diffuse large B cell lymphoma (DLBCL). Here, we studied the role of ETS1 phosphorylation at threonine 38, a marker for ETS1 activation, in DLBCL cellular models and clinical specimens. p-ETS1 was detected in activated B cell-like DLBCL (ABC), not in germinal centre B-cell-like DLBCL (GCB) cell lines and, accordingly, it was more common in ABC than GCB DLBCL diagnostic biopsies. MEK inhibition decreased both baseline and IgM stimulation-induced p-ETS1 levels. Genetic inhibition of phosphorylation of ETS1 at threonine 38 affected the growth and the BCR-mediated transcriptome program in DLBCL cell lines. Our data demonstrate that ETS1 phosphorylation at threonine 38 is important for the growth of DLBCL cells and its pharmacological inhibition could benefit lymphoma patients.
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Affiliation(s)
- Elaine Y L Chung
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Maurilio Ponzoni
- IRCCS San Raffaele Hospital Scientific Institute, Vita Salute San Raffaele University, Milan, Italy
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valdemar Priebe
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | - Xiaosheng Fang
- Duke University Medical Center, Durham, North Carolina, USA
| | - Mingzhi Zhang
- Duke University Medical Center, Durham, North Carolina, USA
| | - Carlo Visco
- Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital, Basel, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, USI, Bellinzona, Switzerland
| | - Emanuele Zucca
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Andrea Cavalli
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, USI, Bellinzona, Switzerland
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York, USA
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken H Young
- Duke University Medical Center, Durham, North Carolina, USA
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
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4
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Co-Targeting of BTK and TrxR as a Therapeutic Approach to the Treatment of Lymphoma. Antioxidants (Basel) 2023; 12:antiox12020529. [PMID: 36830087 PMCID: PMC9952695 DOI: 10.3390/antiox12020529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a haematological malignancy representing the most diagnosed non-Hodgkin's lymphoma (NHL) subtype. Despite the approved chemotherapies available in clinics, some patients still suffer from side effects and relapsed disease. Recently, studies have reported the role of the Trx system and the BCR signalling pathway in cancer development and drug resistance. In this regard, we assessed a potential link between the two systems and evaluated the effects of [Au(d2pype)2]Cl (TrxR inhibitor) and ibrutinib (BTK inhibitor) alone and in combination on the cell growth of two DLBCL lymphoma cell lines, SUDHL2 and SUDHL4. In this study, we show higher expression levels of the Trx system and BCR signalling pathway in the DLBCL patient samples compared to the healthy samples. The knockdown of TrxR using siRNA reduced BTK mRNA and protein expression. A combination treatment with [Au(d2pype)2]Cl and ibrutinib had a synergistic effect on the inhibition of lymphoma cell proliferation, the activation of apoptosis, and, depending on lymphoma cell subtype, ferroptosis. Decreased BTK expression and the cytoplasmic accumulation of p65 were observed after the combination treatment in the DLBCL cells, indicating the inhibition of the NF-κB pathway. Thus, the co-targeting of BTK and TrxR may be an effective therapeutic strategy to consider for DLBCL treatment.
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5
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Tyryshkin K, Moore A, Good D, Popov J, Crocker S, Rauh MJ, Baetz T, LeBrun DP. Expression of TCF3 target genes defines a subclass of diffuse large B-cell lymphoma characterized by up-regulation of MYC target genes and poor clinical outcome following R-CHOP therapy. Leuk Lymphoma 2023; 64:119-129. [PMID: 36336953 DOI: 10.1080/10428194.2022.2136968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
TCF3 is a lymphopoietic transcription factor that acquires somatic driver mutations in diffuse large B-cell lymphoma (DLBCL). Hypothesizing that expression patterns of TCF3-regulated genes can inform clinical management, we found that unsupervised clustering analysis with 15 TCF3-regulated genes and eight additional ones resolved local DLBCL cases into two main clusters, denoted Groups A and B, of which Group A manifested inferior overall survival (OS, p = 0.0005). We trained a machine learning model to classify samples into the Groups based on expression of the 23 transcripts in an independent validation cohort of 569 R-CHOP-treated DLBCL cases. Group A overlapped with the ABC cell-of-origin subgroup but its prognostic power was superior. GSEA analysis demonstrated asymmetric expression of 30 gene sets between the Groups, pointing to biological differences. We present, validate and make available a novel method to assign DLBCL cases into biologically-distinct groups with divergent OS following R-CHOP therapy.
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Affiliation(s)
- Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.,School of Computing, Queen's University, Kingston, Ontario, Canada
| | - Alison Moore
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David Good
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Jesse Popov
- Department of Internal Medicine, Queen's University, Kingston, Ontario, Canada
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Tara Baetz
- Department of Medical Oncology, Queen's University, Kingston, Ontario, Canada
| | - David P LeBrun
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
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6
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Stanwood SR, Chong LC, Steidl C, Jefferies WA. Distinct Gene Expression Patterns of Calcium Channels and Related Signaling Pathways Discovered in Lymphomas. Front Pharmacol 2022; 13:795176. [PMID: 35685639 PMCID: PMC9172636 DOI: 10.3389/fphar.2022.795176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/24/2022] [Indexed: 01/14/2023] Open
Abstract
Cell surface calcium (Ca2+) channels permit Ca2+ ion influx, with Ca2+ taking part in cellular functions such as proliferation, survival, and activation. The expression of voltage-dependent Ca2+ (CaV) channels may modulate the growth of hematologic cancers. Profile analysis of Ca2+ channels, with a focus on the Ca2+ release-activated Ca2+ (CRAC) and L-type CaV channels, was performed on RNA sequencing data from lymphoma cell lines and samples derived from patients with diffuse large B cell lymphoma (DLBCL). CaV1.2 expression was found to be elevated in classical Hodgkin lymphoma (CHL) cell lines when compared to other B cell lymphoma cell lines. In contrast, CHL exhibited reduced expression of ORAI2 and STIM2. In our differential expression analysis comparing activated B cell-like DLBCL (ABC-DLBCL) and germinal centre B cell-like DLBCL (GCB-DLBCL) patient samples, ABC-DLBCL revealed stronger expression of CaV1.3, whereas CaV1.1, CaV1.2, and CaV1.4 showed greater expression levels in GCB-DLBCL. Interestingly, no differences in ORAI/STIM expression were noted in the patient samples. As Ca2+ is known to bind to calmodulin, leading to calcineurin activation and the passage of nuclear factor of activated T cells (NFAT) to the cell nucleus, pathways for calcineurin, calmodulin, NFAT, and Ca2+ signaling were also analyzed by gene set enrichment analysis. The NFAT and Ca2+ signaling pathways were found to be upregulated in the CHL cell lines relative to other B cell lymphoma cell lines. Furthermore, the calmodulin and Ca2+ signaling pathways were shown to be downregulated in the ABC-DLBCL patient samples. The findings of this study suggest that L-type CaV channels and Ca2+-related pathways could serve as differentiating components for biologic therapies in targeted lymphoma treatments.
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Affiliation(s)
- Shawna R. Stanwood
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Lauren C. Chong
- Centre for Lymphoid Cancer, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Christian Steidl
- Lymphoid Cancer Research, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wilfred A. Jefferies
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC, Canada
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Urological Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Wilfred A. Jefferies,
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7
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Liu QH, Dai GR, Wang XN, Wang L, Li LL, Wu ZS, Xia RX. CDK12 activates MYC to repress miR-28-5p/EZH2 and amplifies tonic BCR signaling to promote the development of diffuse large B-cell lymphoma. Cancer Gene Ther 2022; 29:1207-1216. [PMID: 35082399 DOI: 10.1038/s41417-021-00415-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 11/09/2022]
Abstract
Cyclin-dependent kinase 12 (CDK12) is a transcription-associated kinase that participates in various cellular processes. However, its regulatory role in the progression of diffuse large B-cell lymphoma (DLBCL), which is the most prevalent subtype of non-Hodgkin lymphoma (NHL), is still elusive and controversial.The expression of CDK12 was detected by immunohistochemistry (IHC), RT-qPCR was performed to detect miR-28-5p expression of OCI-LY3 and SU-DHL-4 cells. MTT and soft agarose colony formation assays were used to detect cell proliferation. The cell apoptosis was determined by flow cytometry. The protein expressions changes of MYC, EZH2 and the biomarkers of BCR signaling were also detected. A subcutaneous transplantation tumor model of OCI-LY3 cells in nude mice was established to evaluate anticarcinogenic activities of CDK12 knockdown. Elevated expression of CDK12 was observed while miR-28-5p was downregulated in DLBCL tissues. CDK12 knockdown or miR-28-5p overexpression could inhibit proliferation and promote apoptosis of DLBCL cells. miR-28-5p inhibition could reverse the effect of CDK12 knockdown on proliferation and apoptosis of DLBCL cells. In addition, CDK12 knockdown could inhibit DLBCL tumor growth in the mice model. CDK12 activated MYC to repress miR-28-5p/EZH2 and amplified tonic BCR signaling to promote the development of DLBCL, which might provide potential therapeutic targets for future therapeutic intervention in DLBCL.
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Affiliation(s)
- Qin-Hua Liu
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Guan-Rong Dai
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Xiao-Nan Wang
- Laboratory of Pathogenic Microbiology and Immunology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Lin Wang
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Li-Li Li
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Zheng-Sheng Wu
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China
| | - Rui-Xiang Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui Province, China.
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8
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Elliott EK, Hopkins LN, Hensen R, Sutherland HG, Haupt LM, Griffiths LR. Epigenetic Regulation of miR-92a and TET2 and Their Association in Non-Hodgkin Lymphoma. Front Genet 2021; 12:768913. [PMID: 34899857 PMCID: PMC8661906 DOI: 10.3389/fgene.2021.768913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are well known for their ability to regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. In various cancers, miRNAs regulate gene expression by altering the epigenetic status of candidate genes that are implicated in various difficult to treat haematological malignancies such as non-Hodgkin lymphoma by acting as either oncogenes or tumour suppressor genes. Cellular and circulating miRNA biomarkers could also be directly utilised as disease markers for diagnosis and monitoring of non-Hodgkin lymphoma (NHL); however, the role of DNA methylation in miRNA expression regulation in NHL requires further scientific inquiry. In this study, we investigated the methylation levels of CpGs in CpG islands spanning the promoter regions of the miR-17–92 cluster host gene and the TET2 gene and correlated them with the expression levels of TET2 mRNA and miR-92a-3p and miR-92a-5p mature miRNAs in NHL cell lines, tumour samples, and the whole blood gDNA of an NHL case control cohort. Increased expression of both miR-92a-3p and miR-92a-5p and aberrant expression of TET2 was observed in NHL cell lines and tumour tissues, as well as disparate levels of dysfunctional promoter CGI methylation. Both miR-92a and TET2 may play a concerted role in NHL malignancy and disease pathogenesis.
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Affiliation(s)
- Esther K Elliott
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia.,Icon Cancer Centre, Brisbane, QLD, Australia
| | - Lloyd N Hopkins
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | | | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
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9
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Fan H, Wang X, Li W, Shen M, Wei Y, Zheng H, Kang Y. ASB13 inhibits breast cancer metastasis through promoting SNAI2 degradation and relieving its transcriptional repression of YAP. Genes Dev 2020; 34:1359-1372. [PMID: 32943576 PMCID: PMC7528707 DOI: 10.1101/gad.339796.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
In this study, Fan et al. studied the post-translational regulation of transcription factor SNAI2, which plays key roles during development and promotes metastasis by inducing invasive phenotype and tumor-initiating activity of cancer cells. They performed a dual-luciferase-based, genome-wide E3 ligase siRNA library screen and identified ASB13 as an E3 ubiquitin ligase that targets SNAI2 for ubiquitination and degradation, thereby establishing ASB13 as a suppressor of breast cancer metastasis. Transcription factor SNAI2 plays key roles during development and has also been known to promote metastasis by inducing invasive phenotype and tumor-initiating activity of cancer cells. However, the post-translational regulation of SNAI2 is less well studied. We performed a dual-luciferase-based, genome-wide E3 ligase siRNA library screen and identified ASB13 as an E3 ubiquitin ligase that targets SNAI2 for ubiquitination and degradation. ASB13 knockout in breast cancer cells promoted cell migration and decreased F-actin polymerization, while overexpression of ASB13 suppressed lung metastasis. Furthermore, ASB13 knockout decreased YAP expression, and such regulation is dependent on an increased protein level of SNAI2, which in turn represses YAP transcription. YAP suppresses tumor progression in breast cancer, as YAP knockout increases tumorsphere formation, anchorage-independent colony formation, cell migration in vitro, and lung metastasis in vivo. Clinical data analysis reveals that ASB13 expression is positively correlated with improved overall survival in breast cancer patients. These findings establish ASB13 as a suppressor of breast cancer metastasis by promoting degradation of SNAI2 and relieving its transcriptional repression of YAP.
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Affiliation(s)
- Huijuan Fan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xuxiang Wang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenyang Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Minhong Shen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Yong Wei
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Hanqiu Zheng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.,Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, USA
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10
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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11
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Platform independent protein-based cell-of-origin subtyping of diffuse large B-cell lymphoma in formalin-fixed paraffin-embedded tissue. Sci Rep 2020; 10:7876. [PMID: 32398793 PMCID: PMC7217957 DOI: 10.1038/s41598-020-64212-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/09/2020] [Indexed: 01/03/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is commonly classified by gene expression profiling according to its cell of origin (COO) into activated B-cell (ABC)-like and germinal center B-cell (GCB)-like subgroups. Here we report the application of label-free nano-liquid chromatography - Sequential Window Acquisition of all THeoretical fragment-ion spectra - mass spectrometry (nanoLC-SWATH-MS) to the COO classification of DLBCL in formalin-fixed paraffin-embedded (FFPE) tissue. To generate a protein signature capable of predicting Affymetrix-based GCB scores, the summed log2-transformed fragment ion intensities of 780 proteins quantified in a training set of 42 DLBCL cases were used as independent variables in a penalized zero-sum elastic net regression model with variable selection. The eight-protein signature obtained showed an excellent correlation (r = 0.873) between predicted and true GCB scores and yielded only 9 (21.4%) minor discrepancies between the three classifications: ABC, GCB, and unclassified. The robustness of the model was validated successfully in two independent cohorts of 42 and 31 DLBCL cases, the latter cohort comprising only patients aged >75 years, with Pearson correlation coefficients of 0.846 and 0.815, respectively, between predicted and NanoString nCounter based GCB scores. We further show that the 8-protein signature is directly transferable to both a triple quadrupole and a Q Exactive quadrupole-Orbitrap mass spectrometer, thus obviating the need for proprietary instrumentation and reagents. This method may therefore be used for robust and competitive classification of DLBCLs on the protein level.
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12
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Kunz M, Jeromin J, Fuchs M, Christoph J, Veronesi G, Flentje M, Nietzer S, Dandekar G, Dandekar T. In silico signaling modeling to understand cancer pathways and treatment responses. Brief Bioinform 2019; 21:1115-1117. [DOI: 10.1093/bib/bbz033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Abstract
Precision medicine has changed thinking in cancer therapy, highlighting a better understanding of the individual clinical interventions. But what role do the drivers and pathways identified from pan-cancer genome analysis play in the tumor? In this letter, we will highlight the importance of in silico modeling in precision medicine. In the current era of big data, tumor engines and pathways derived from pan-cancer analysis should be integrated into in silico models to understand the mutational tumor status and individual molecular pathway mechanism at a deeper level. This allows to pre-evaluate the potential therapy response and develop optimal patient-tailored treatment strategies which pave the way to support precision medicine in the clinic of the future.
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Affiliation(s)
- Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Julian Jeromin
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Maximilian Fuchs
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Jan Christoph
- Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | | | - Michael Flentje
- Department of Radiation Oncology, University Hospital of Würzburg, Würzburg, Germany
| | - Sarah Nietzer
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Wuerzburg, Roentgenring, Wuerzburg
| | - Gudrun Dandekar
- Chair of Tissue Engineering and Regenerative Medicine, University Hospital Wuerzburg, Roentgenring, Wuerzburg
- Fraunhofer Institute for Silicate Research (ISC), Translational Center ‘Regenerative Therapies’ (TLC-RT), Roentgenring, Wuerzburg
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of Würzburg, Würzburg, Germany
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13
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14
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Anastasiadou E, Stroopinsky D, Alimperti S, Jiao AL, Pyzer AR, Cippitelli C, Pepe G, Severa M, Rosenblatt J, Etna MP, Rieger S, Kempkes B, Coccia EM, Sui SJH, Chen CS, Uccini S, Avigan D, Faggioni A, Trivedi P, Slack FJ. Epstein-Barr virus-encoded EBNA2 alters immune checkpoint PD-L1 expression by downregulating miR-34a in B-cell lymphomas. Leukemia 2018; 33:132-147. [PMID: 29946193 PMCID: PMC6327052 DOI: 10.1038/s41375-018-0178-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 04/27/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022]
Abstract
Cancer cells subvert host immune surveillance by altering immune checkpoint (IC) proteins. Some Epstein−Barr virus (EBV)-associated tumors have higher Programmed Cell Death Ligand, PD-L1 expression. However, it is not known how EBV alters ICs in the context of its preferred host, the B lymphocyte and in derived lymphomas. Here, we found that latency III-expressing Burkitt lymphoma (BL), diffuse large B-cell lymphomas (DLBCL) or their EBNA2-transfected derivatives express high PD-L1. In a DLBCL model, EBNA2 but not LMP1 is sufficient to induce PD-L1. Latency III-expressing DLBCL biopsies showed high levels of PD-L1. The PD-L1 targeting oncosuppressor microRNA miR-34a was downregulated in EBNA2-transfected lymphoma cells. We identified early B-cell factor 1 (EBF1) as a repressor of miR-34a transcription. Short hairpin RNA (shRNA)-mediated knockdown of EBF1 was sufficient to induce miR-34a transcription, which in turn reduced PD-L1. MiR-34a reconstitution in EBNA2-transfected DLBCL reduced PD-L1 expression and increased its immunogenicity in mixed lymphocyte reactions (MLR) and in three-dimensional biomimetic microfluidic chips. Given the importance of PD-L1 inhibition in immunotherapy and miR-34a dysregulation in cancers, our findings may have important implications for combinatorial immunotherapy, which include IC inhibiting antibodies and miR-34a, for EBV-associated cancers.
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Affiliation(s)
- Eleni Anastasiadou
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dina Stroopinsky
- Department of Hematology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Stella Alimperti
- The Wyss Institute for Biological Inspired Engineering at Harvard, Harvard University, Boston, MA, USA
| | - Alan L Jiao
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Athalia R Pyzer
- Department of Hematology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Claudia Cippitelli
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Sapienza University, Rome, Italy
| | - Giuseppina Pepe
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Sapienza University, Rome, Italy
| | - Martina Severa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Jacalyn Rosenblatt
- Department of Hematology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Marilena P Etna
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Simone Rieger
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Marchioninistraße 25, 81377, Munich, Germany
| | - Bettina Kempkes
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Marchioninistraße 25, 81377, Munich, Germany
| | - Eliana M Coccia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Shannan J Ho Sui
- Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Christopher S Chen
- The Wyss Institute for Biological Inspired Engineering at Harvard, Harvard University, Boston, MA, USA
| | - Stefania Uccini
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, Sapienza University, Rome, Italy
| | - David Avigan
- Department of Hematology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alberto Faggioni
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 0161, Rome, Italy
| | - Pankaj Trivedi
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 0161, Rome, Italy.
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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15
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Prognostic Significance of High Ki-67 Index and Histogenetic Subclassification in Primary Central Nervous System Lymphoma. Appl Immunohistochem Mol Morphol 2018; 26:254-262. [DOI: 10.1097/pai.0000000000000424] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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16
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Kaymaz Y, Oduor CI, Yu H, Otieno JA, Ong'echa JM, Moormann AM, Bailey JA. Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences. Mol Cancer Res 2018; 15:563-576. [PMID: 28465297 PMCID: PMC5471630 DOI: 10.1158/1541-7786.mcr-16-0305] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 12/17/2022]
Abstract
Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes. The outstanding difference detected using surrogate variable analysis was the significantly decreased expression of key genes in the immunoproteasome complex (PSMB9/β1i, PSMB10/β2i, PSMB8/β5i, and PSME2/PA28β) in eBL tumors carrying type 2 EBV compared with type 1 EBV. Second, in comparison with previously published pediatric sBL specimens, the majority of the expression and pathway differences was related to the PTEN/PI3K/mTOR signaling pathway and was correlated most strongly with EBV status rather than geographic designation. Third, common mutations were observed significantly less frequently in eBL tumors harboring EBV type 1, with mutation frequencies similar between tumors with EBV type 2 and without EBV. In addition to the previously reported genes, a set of new genes mutated in BL, including TFAP4, MSH6, PRRC2C, BCL7A, FOXO1, PLCG2, PRKDC, RAD50, and RPRD2, were identified. Overall, these data establish that EBV, particularly EBV type 1, supports BL oncogenesis, alleviating the need for certain driver mutations in the human genome. IMPLICATIONS Genomic and mutational analyses of Burkitt lymphoma tumors identify key differences based on viral content and clinical outcomes suggesting new avenues for the development of prognostic molecular biomarkers and therapeutic interventions.
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Affiliation(s)
- Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Hongbo Yu
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Juliana A Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Health, Kisumu, Kenya
| | | | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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17
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Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma. Blood Cancer J 2017; 7:e596. [PMID: 28841210 PMCID: PMC5596382 DOI: 10.1038/bcj.2017.71] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/13/2017] [Accepted: 06/16/2017] [Indexed: 02/08/2023] Open
Abstract
Effect of alternative splicing (AS) on diffuse large B-cell lymphoma (DLBCL) pathogenesis and survival has not been systematically addressed. Here, we compared differentially expressed genes and exons in association with survival after chemoimmunotherapy, and between germinal center B-cell like (GCB) and activated B-cell like (ABC) DLBCLs. Genome-wide exon array-based screen was performed from samples of 38 clinically high-risk patients who were treated in a Nordic phase II study with dose-dense chemoimmunotherapy and central nervous system prophylaxis. The exon expression profile separated the patients according to molecular subgroups and survival better than the gene expression profile. Pathway analyses revealed enrichment of AS genes in inflammation and adhesion-related processes, and in signal transduction, such as phosphatidylinositol signaling system and adenosine triphosphate binding cassette transporters. Altogether, 49% of AS-related exons were protein coding, and domain prediction showed 28% of such exons to include a functional domain, such as transmembrane helix domain or phosphorylation sites. Validation in an independent cohort of 92 DLBCL samples subjected to RNA-sequencing confirmed differential exon usage of selected genes and association of AS with molecular subtypes and survival. The results indicate that AS events are able to discriminate GCB and ABC DLBCLs and have prognostic impact in DLBCL.
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18
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Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of mature B-cell lymphoma. While the majority of patients are cured with immunochemotherapy incorporating the anti-CD20 monoclonal antibody rituximab (R-CHOP), relapsed and refractory patients still have a dismal prognosis. DLBCL subtypes including an aggressive activated B-cell-like (ABC) and a more favorable prognosis germinal center-like (GCB) DLBCL have been identified by gene expression profiling and are characterized by distinct genetic abnormalities and oncogenic pathways. This identification of novel molecular targets is now enabling clinical trials to evaluate more effective personalized approaches to DLBCL therapy. The forkhead transcription factor FOXP1 is highly expressed in the ABC-DLBCL gene signature and has been extensively studied within the context of DLBCL for more than a decade. Here, we review the significance of FOXP1 in the pathogenesis of DLBCL, summarizing data supporting its utility as a prognostic and subtyping marker, its targeting by genetic aberrations, the importance of specific isoforms, and emerging data demonstrating a functional role in lymphoma biology. FOXP1 is one of the critical transcription factors whose deregulated expression makes important contributions to DLBCL pathogenesis. Thus, FOXP1 warrants further study as a potential theranostic in ABC-DLBCL.
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Affiliation(s)
- Duncan M Gascoyne
- a Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine , University of Oxford , Oxford , UK
| | - Alison H Banham
- a Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine , University of Oxford , Oxford , UK
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19
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McKenna MK, Gachuki BW, Alhakeem SS, Oben KN, Rangnekar VM, Gupta RC, Bondada S. Anti-cancer activity of withaferin A in B-cell lymphoma. Cancer Biol Ther 2016; 16:1088-98. [PMID: 26020511 DOI: 10.1080/15384047.2015.1046651] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Withaferin A (WA), a withanolide from the plant, Ashwagandha (Withania somnifera) used in Ayurvedic medicine, has been found to be valuable in the treatment of several medical ailments. WA has been found to have anticancer activity against various solid tumors, but its effects on hematological malignancies have not been studied in detail. WA strongly inhibited the survival of several human and murine B cell lymphoma cell lines. Additionally, in vivo studies with syngeneic-graft lymphoma cells suggest that WA inhibits the growth of tumor but does not affect other proliferative tissues. We demonstrate that WA inhibits the efficiency of NF-κB nuclear translocation in diffuse large B cell lymphomas and found that WA treatment resulted in a significant decrease in protein levels involved in B cell receptor signaling and cell cycle regulation. WA inhibited the activity of heat shock protein (Hsp) 90 as reflected by a sharp increase in Hsp70 expression levels. Hence, we propose that the anti-cancer effects of WA in lymphomas are likely due to its ability to inhibit Hsp90 function and subsequent reduction of critical kinases and cell cycle regulators that are clients of Hsp90.
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Affiliation(s)
- M K McKenna
- a Department of Microbiology, Immunology and Molecular Genetics; Markey Cancer Center; University of Kentucky ; Lexington , KY , USA
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20
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Burotto M, Berkovits A, Dunleavy K. Double hit lymphoma: from biology to therapeutic implications. Expert Rev Hematol 2016; 9:669-78. [PMID: 27166590 DOI: 10.1080/17474086.2016.1182858] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Diffuse large B-cell lymphoma (DLBCL) is a molecularly heterogeneous disease defined by different cellular origins and mechanisms of oncogenic activation. Approximately 10% of DLBCL cases harbor a MYC rearrangement and this has been associated with a more aggressive clinical course following standard therapy. AREAS COVERED So-called 'double-hit lymphomas' (DHL) or 'triple hit lymphomas' (THL) occur when MYC is concurrently rearranged with BCL2 and/or BCL6. These tumors are characterized by high proliferation rate and a very poor outcome following standard R-CHOP (rituximab, cyclophosphamide, doxorubicin vincristine and prednisone) therapy, in most (though not all) studies that have looked at this. Though there is a paucity of published experience with other chemotherapy regimens, there is emerging evidence that more intensive approaches may improve outcome. Recently, there has been a lot of focus in the literature on 'double-expresser lymphomas' (DEL) with high MYC, BCL2 and/or BCL6 expression but typically without rearrangements of these genes. These DEL cases, have a poor outcome with R-CHOP and there is little consensus on how they should be approached. Expert commentary: This review will focus on the biology and treatment of DHL and DEL, discuss the outcome of these diseases with current standard as well as promising new approaches and conclude with a section on novel agents that are in development for these diseases.
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Affiliation(s)
- Mauricio Burotto
- a Hemato-Oncology Service, Clinica Alemana de Santiago , School of Medicine Universidad del Desarrollo , Santiago , Chile
| | - Alejandro Berkovits
- a Hemato-Oncology Service, Clinica Alemana de Santiago , School of Medicine Universidad del Desarrollo , Santiago , Chile
| | - Kieron Dunleavy
- b Lymphoid Malignancies Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
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Kobayashi K, Yamaguchi M, Miyazaki K, Imai H, Yokoe K, Ono R, Nosaka T, Katayama N. Expressions of SH3BP5, LMO3, and SNAP25 in diffuse large B-cell lymphoma cells and their association with clinical features. Cancer Med 2016; 5:1802-9. [PMID: 27184832 PMCID: PMC4873606 DOI: 10.1002/cam4.753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/01/2016] [Accepted: 04/05/2016] [Indexed: 12/25/2022] Open
Abstract
Diffuse large B‐cell lymphoma (DLBCL) is clinicopathologically and genetically heterogeneous with variable clinical outcomes. We previously identified signature genes overexpressed in CD5‐positive (CD5+) DLBCL, which is a poor prognostic subgroup of DLBCL. To elucidate the clinical significance of the protein expression of the signature genes overexpressed in CD5+DLBCL with regard to all DLBCL, not otherwise specified (NOS), 10 genes (SH3BP5,LMO3,SNAP25,SYT5,SV2C,CABP1,FGF1,FGFR2,NEUROD1, and SYN2) were selected and examined immunohistochemically with samples from 28 patients with DLBCL, NOS. Only three protein expressions, SH3BP5, LMO3, and SNAP25, were detected in DLBCL cells and then analyzed further with samples from 187 patients with DLBCL, NOS. The SH3BP5, LMO3, and SNAP25 proteins were expressed in 60% (103/173), 34% (59/175), and 46% (77/168) of DLBCL patients, respectively. These protein expressions were associated with CD5 expression, and only SH3BP5 was frequently expressed in activated B‐cell‐like DLBCL (P = 0.046). Compared to the SH3BP5‐negative group, the SH3BP5+ group was correlated with elderly onset (>60 years, P = 0.0096) and advanced‐stage disease (stage III/IV, P = 0.037). The LMO3+ group showed a worse performance status (>1, P = 0.0004). The SH3BP5+ group and the LMO3+ group had significantly worse overall survival than the negative groups (P = 0.030, 0.034; respectively) for the entire group. In a subgroup analysis of patients treated with rituximab‐containing chemotherapy, there was no significant difference between groups. To the best of our knowledge, this is the first report showing the protein expressions of SH3BP5, LMO3, and SNAP25 in DLBCL cells and their clinical significance in patients with DLBCL. The SH3BP5 and LMO3 protein expressions are associated with the baseline clinical characteristics of DLBCL.
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Affiliation(s)
- Kyoko Kobayashi
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Motoko Yamaguchi
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Kana Miyazaki
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Hiroshi Imai
- Pathology Division, Mie University Hospital, Tsu, Japan
| | - Kaori Yokoe
- Mie University School of Medicine, Tsu, Japan
| | - Ryoichi Ono
- Department of Microbiology and Molecular Genetics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Tetsuya Nosaka
- Department of Microbiology and Molecular Genetics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Naoyuki Katayama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu, Japan
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22
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Brown PJ, Wong KK, Felce SL, Lyne L, Spearman H, Soilleux EJ, Pedersen LM, Møller MB, Green TM, Gascoyne DM, Banham AH. FOXP1 suppresses immune response signatures and MHC class II expression in activated B-cell-like diffuse large B-cell lymphomas. Leukemia 2015; 30:605-16. [PMID: 26500140 PMCID: PMC4777777 DOI: 10.1038/leu.2015.299] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 12/25/2022]
Abstract
The FOXP1 (forkhead box P1) transcription factor is a marker of poor prognosis in diffuse large B-cell lymphoma (DLBCL). Here microarray analysis of FOXP1-silenced DLBCL cell lines identified differential regulation of immune response signatures and major histocompatibility complex class II (MHC II) genes as some of the most significant differences between germinal center B-cell (GCB)-like DLBCL with full-length FOXP1 protein expression versus activated B-cell (ABC)-like DLBCL expressing predominantly short FOXP1 isoforms. In an independent primary DLBCL microarray data set, multiple MHC II genes, including human leukocyte antigen DR alpha chain (HLA-DRA), were inversely correlated with FOXP1 transcript expression (P<0.05). FOXP1 knockdown in ABC-DLBCL cells led to increased cell-surface expression of HLA-DRA and CD74. In R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone)-treated DLBCL patients (n=150), reduced HLA-DRA (<90% frequency) expression correlated with inferior overall survival (P=0.0003) and progression-free survival (P=0.0012) and with non-GCB subtype stratified by the Hans, Choi or Visco-Young algorithms (all P<0.01). In non-GCB DLBCL cases with <90% HLA-DRA, there was an inverse correlation with the frequency (P=0.0456) and intensity (P=0.0349) of FOXP1 expression. We propose that FOXP1 represents a novel regulator of genes targeted by the class II MHC transactivator CIITA (MHC II and CD74) and therapeutically targeting the FOXP1 pathway may improve antigen presentation and immune surveillance in high-risk DLBCL patients.
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Affiliation(s)
- P J Brown
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - K K Wong
- Department of Immunology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - S L Felce
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - L Lyne
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - H Spearman
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - E J Soilleux
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - L M Pedersen
- Department of Haematology, Roskilde Hospital, Roskilde, Denmark
| | - M B Møller
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - T M Green
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - D M Gascoyne
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - A H Banham
- NDCLS, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Bonadies N, Göttgens B, Calero-Nieto FJ. The LMO2 -25 Region Harbours GATA2-Dependent Myeloid Enhancer and RUNX-Dependent T-Lymphoid Repressor Activity. PLoS One 2015; 10:e0131577. [PMID: 26161748 PMCID: PMC4498896 DOI: 10.1371/journal.pone.0131577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/03/2015] [Indexed: 12/02/2022] Open
Abstract
Lim domain only 2 (LMO2) is a transcriptional co-factor required for angiogenesis and the specification of haematopoietic cells during development. LMO2 is widely expressed within haematopoiesis with the exception of T-cells. Failure to downregulate LMO2 during T-cell maturation leads to leukaemia, thus underlining the critical nature of context-dependent regulation of LMO2 expression. We previously identified a distal regulatory element of LMO2 (element -25) that cooperates with the proximal promoter in directing haematopoietic expression. Here we dissected the functional activity of element -25 and showed it to consist of two modules that conferred independent and cell-type specific activities: a 3' myeloid enhancer and a 5' T-cell repressor. The myeloid enhancer was bound by GATA2 in progenitors and its activity depended on a highly conserved GATA motif, whereas the T-cell repressor moiety of element -25 was bound by the Core Binding Factor in T-cells and its repressive activity depended on a highly conserved RUNT motif. Since the myeloid enhancer and nearby downstream region is recurrently involved in oncogenic translocations, our data suggest that the -25 enhancer region provides an open chromatin environment prone to translocations, which in turn cause aberrant LMO2 expression in T-cells due to the removal of the adjacent T-cell repressor.
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Affiliation(s)
- Nicolas Bonadies
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Fernando J. Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
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24
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Navari M, Etebari M, De Falco G, Ambrosio MR, Gibellini D, Leoncini L, Piccaluga PP. The presence of Epstein-Barr virus significantly impacts the transcriptional profile in immunodeficiency-associated Burkitt lymphoma. Front Microbiol 2015; 6:556. [PMID: 26113842 PMCID: PMC4462103 DOI: 10.3389/fmicb.2015.00556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/20/2015] [Indexed: 11/20/2022] Open
Abstract
Burkitt lymphoma (BL) is an aggressive neoplasm derived from mature, antigen-experienced B-lymphocytes. Three clinical/epidemiological variants have been recognized, named sporadic, endemic and immunodeficiency-associated BL (ID-BL). Although they are listed within a unique entity in the current WHO Classification, recent evidence indicated genetic and transcriptional differences among the three sub-groups. Further, the presence of latently persisting Epstein-Barr virus (EBV) has been associated with specific features in endemic and sporadic cases. In this study, we explored for the first time whether EBV infection could be related with a specific molecular profile in immunodeficiency-associated cases. We studied 30 BL cases, including nine occurring in HIV-positive patients (5 EBV-positive and 4 EBV-negative) by gene and microRNA (miRNA) expression profiling. We found that ID-BL presented with different profiles based on EBV presence. Specifically, 252 genes were differentially expressed, some of them being involved in intracellular signaling and apoptosis regulation. Furthermore, 28 miRNAs including both EBV-encoded (N = 18) and cellular (N = 10) ones were differentially regulated. Of note, genes previously demonstrated to be targeted by such miRNA were consistently found among differentially expressed genes, indicating the relevant contribution of miRNA to the molecular profile of the examined cases. Grippingly, 17 out of the 252 differentially expressed genes turned out to be potentially targeted by both cellular and EBV-encoded miRNA, suggesting a complex interaction and not excluding a potential synergism. In conclusion, we documented transcriptional differences based on the presence of EBV in ID-BL, and suggested a complex interaction between cellular and viral molecules in the determination of the global molecular profile of the tumor.
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Affiliation(s)
- Mohsen Navari
- Hematopathology Section, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine Bologna, Italy ; Department of Basic Sciences, Torbat Heydariyeh University of Medical Sciences Torbat Heydariyeh, Iran
| | - Maryam Etebari
- Hematopathology Section, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine Bologna, Italy
| | - Giulia De Falco
- School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Maria R Ambrosio
- Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Davide Gibellini
- Microbiology and Virology Unit, Department of Pathology and Diagnostic, University of Verona Verona, Italy
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena Siena, Italy
| | - Pier Paolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Specialty Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine Bologna, Italy
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25
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Wells JE, Howlett M, Cheung LC, Kees UR. The role of CCN family genes in haematological malignancies. J Cell Commun Signal 2015; 9:267-78. [PMID: 26026820 DOI: 10.1007/s12079-015-0296-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/19/2015] [Indexed: 12/12/2022] Open
Abstract
Haematological malignancies, although a broad range of specific disease types, continue to show considerable overlap in classification, and patients are treated using similar chemotherapy regimes. In this review we look at the role of the CCN family of matricellular proteins and indicate their role in nine haematological malignancies including both myeloid and lymphoid neoplasms. The potential for further haematological neoplasms with CCN family associations is argued by summarising the demonstrated role of CCN family genes in the differentiation of haematopoietic stem cells (HSC) and mesenchymal stem cells. The expanding field of knowledge encompassing CCN family genes and cancers of the HSC-lineage highlights the importance of extracellular matrix-interactions in both normal physiology and tumorigenesis of the blood, bone marrow and lymph nodes.
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Affiliation(s)
- J E Wells
- Telethon Kids Institute, The University of Western Australia, PO Box 855 West Perth, Perth, Western Australia, 6872, Australia
| | - M Howlett
- Telethon Kids Institute, The University of Western Australia, PO Box 855 West Perth, Perth, Western Australia, 6872, Australia
| | - L C Cheung
- Telethon Kids Institute, The University of Western Australia, PO Box 855 West Perth, Perth, Western Australia, 6872, Australia
| | - Ursula R Kees
- Telethon Kids Institute, The University of Western Australia, PO Box 855 West Perth, Perth, Western Australia, 6872, Australia.
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26
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Miyazaki K, Yamaguchi M, Imai H, Kobayashi K, Tamaru S, Kobayashi T, Shiku H, Katayama N. Gene expression profiling of diffuse large B-Cell lymphomas supervised by CD5 expression. Int J Hematol 2015; 102:188-94. [DOI: 10.1007/s12185-015-1812-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/14/2015] [Accepted: 05/14/2015] [Indexed: 10/23/2022]
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Abstract
Human diffuse large B-cell lymphomas (DLBCLs) often aberrantly express oncogenes that generally contain complex secondary structures in their 5' untranslated region (UTR). Oncogenes with complex 5'UTRs require enhanced eIF4A RNA helicase activity for translation. PDCD4 inhibits eIF4A, and PDCD4 knockout mice have a high penetrance for B-cell lymphomas. Here, we show that on B-cell receptor (BCR)-mediated p70s6K activation, PDCD4 is degraded, and eIF4A activity is greatly enhanced. We identified a subset of genes involved in BCR signaling, including CARD11, BCL10, and MALT1, that have complex 5'UTRs and encode proteins with short half-lives. Expression of these known oncogenic proteins is enhanced on BCR activation and is attenuated by the eIF4A inhibitor Silvestrol. Antigen-experienced immunoglobulin (Ig)G(+) splenic B cells, from which most DLBCLs are derived, have higher levels of eIF4A cap-binding activity and protein translation than IgM(+) B cells. Our results suggest that eIF4A-mediated enhancement of oncogene translation may be a critical component for lymphoma progression, and specific targeting of eIF4A may be an attractive therapeutic approach in the management of human B-cell lymphomas.
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Veldman-Jones MH, Lai Z, Wappett M, Harbron CG, Barrett JC, Harrington EA, Thress KS. Reproducible, Quantitative, and Flexible Molecular Subtyping of Clinical DLBCL Samples Using the NanoString nCounter System. Clin Cancer Res 2014; 21:2367-78. [PMID: 25301847 DOI: 10.1158/1078-0432.ccr-14-0357] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 10/03/2014] [Indexed: 11/16/2022]
Abstract
PURPOSE Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with distinct molecular subtypes. The most established subtyping approach, the "Cell of Origin" (COO) algorithm, categorizes DLBCL into activated B-cell (ABC) and germinal center B-cell (GCB)-like subgroups through gene expression profiling. Recently developed immunohistochemical (IHC) techniques and other established methodologies can deliver discordant results and have various technical limitations. We evaluated the NanoString nCounter gene expression system to address issues with current platforms. EXPERIMENTAL DESIGN We devised a scoring system using 145 genes from published datasets to categorize DLBCL samples. After cell line validation, clinical tissue segmentation was tested using commercially available diagnostic DLBCL samples. Finally, we profiled biopsies from patients with relapsed/refractory DLBCL enrolled in the fostamatinib phase IIb clinical trial using three independent RNA expression platforms: NanoString, Affymetrix, and qNPA. RESULTS Diagnostic samples showed a typical spread of subtypes with consistent gene expression profiles across matched fresh, frozen, and formalin-fixed paraffin-embedded tissues. Results from biopsy samples across platforms were remarkably consistent, in contrast to published IHC data. Interestingly, COO segmentation of longitudinal fostamatinib biopsies taken at initial diagnosis and then again at primary relapse showed 88% concordance (15/17), suggesting that COO designation remains stable over the course of disease progression. CONCLUSIONS DLBCL segmentation of patient tumor samples is possible using a number of expression platforms. However, we found that NanoString offers the most flexibility and fewest limitations in regards to robust clinical tissue subtype characterization. These subtype distinctions should help guide disease prognosis and treatment options within DLBCL clinical practice.
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Affiliation(s)
| | - Zhongwu Lai
- AstraZeneca Oncology Innovative Medicines, Waltham, Massachusetts
| | - Mark Wappett
- AstraZeneca Oncology Innovative Medicines, Macclesfield, United Kingdom
| | - Chris G Harbron
- AstraZeneca Discovery Sciences, Macclesfield, United Kingdom
| | - J Carl Barrett
- AstraZeneca Oncology Innovative Medicines, Waltham, Massachusetts
| | | | - Kenneth S Thress
- AstraZeneca Oncology Innovative Medicines, Waltham, Massachusetts.
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29
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Dai F, Zhang Y, Chen Y. Involvement of miR-29b signaling in the sensitivity to chemotherapy in patients with ovarian carcinoma. Hum Pathol 2014; 45:1285-93. [PMID: 24767251 DOI: 10.1016/j.humpath.2014.02.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 02/05/2014] [Accepted: 02/12/2014] [Indexed: 01/26/2023]
Abstract
Although the molecular mechanisms driving chemoresistance and relapse of ovarian cancer have been widely studied, the key molecules have not been identified. In this study, the expression of miR-29b messenger RNA (mRNA) and its targeted genes, myeloid cell leukemia sequence 1, mitogen-activated protein kinase 10 (MAPK10), and autophagy-related protein 9A (ATG9A), were investigated in ovarian carcinomas, and their associations with clinicopathological characteristics and survival of patients with ovarian cancer were analyzed. The protein expression of MCL1, MAPK10, and ATG9A was measured using immunohistochemistry. miR-29b mRNA and ATG9A gene mRNA levels were measured by real-time polymerase chain reaction. Results demonstrated that the percentage of MCL1, MAPK10, and ATG9A protein-positive cases were significantly higher, whereas miR-29b was significantly lower in ovarian serous, mucinous, and clear cell carcinomas than that in normal tissues. MAPK10 was significantly associated with higher histopathologic grading. The percentage of positive myeloid cell leukemia sequence 1, ATG9A, and MAPK10 protein expression and low miR-29b mRNA expression were significantly higher in cases with clinical stage III and IV ovarian cancer than in cases with clinical stage II ovarian cancer. High ATG9A protein and low miR-29b mRNA expression were significantly associated with relapse. Univariate Kaplan-Meier analysis showed a negative correlation between MAPK10 or ATG9A protein expression and overall as well as progression-free survival, whereas a positive correlation was observed between miR-29b mRNA expression and overall as well as progression-free survival. Multivariate Cox regression analysis showed that elevated MAPK10 or ATG9A protein and lowered miR-29b mRNA expression in ovarian carcinoma was an independent poor prognostic predictor. Our study suggested that miR-29b mRNA, MAPK10 protein expression, and ATG9A protein expression are closely related to chemosensitivity of ovarian carcinoma.
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Affiliation(s)
- Furong Dai
- Department of Obstetrics and Gynaecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Zhang
- Department of Obstetrics and Gynaecology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuxiang Chen
- Hepatobiliary & Enteric Surgery Research Center, Xiangya Hospital, Central South University, Changsha 410008, China.
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30
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Wells JE, Howlett M, Cole CH, Kees UR. Deregulated expression of connective tissue growth factor (CTGF/CCN2) is linked to poor outcome in human cancer. Int J Cancer 2014; 137:504-11. [PMID: 24832082 DOI: 10.1002/ijc.28972] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/13/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
Connective tissue growth factor (CTGF/CCN2) has long been associated with human cancers. The role it plays in these neoplasms is diverse and tumour specific. Recurring patterns in clinical outcome, histological desmoplasia and mechanisms of action have been found. When CTGF is overexpressed compared to low-expressing normal tissue or is underexpressed compared to high-expressing normal tissue, the functional outcome favours tumour survival and disease progression. CTGF acts by altering proliferation, drug resistance, angiogenesis, adhesion and migration contributing to metastasis. The pattern of CTGF expression and tumour response helps to clarify the role of this matricellular protein across a multitude of human cancers.
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Affiliation(s)
- Julia E Wells
- Leukaemia and Cancer Division, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - Meegan Howlett
- Leukaemia and Cancer Division, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Catherine H Cole
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - Ursula R Kees
- Leukaemia and Cancer Division, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
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31
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Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder M. STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma. G3 (BETHESDA, MD.) 2013; 3:2173-85. [PMID: 24142927 PMCID: PMC3852380 DOI: 10.1534/g3.113.007674] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/05/2013] [Indexed: 01/02/2023]
Abstract
The signal transducer and activator of transcription 3 (STAT3) is a transcription factor that, when dysregulated, becomes a powerful oncogene found in many human cancers, including diffuse large B-cell lymphoma. Diffuse large B-cell lymphoma is the most common form of non-Hodgkin's lymphoma and has two major subtypes: germinal center B-cell-like and activated B-cell-like. Compared with the germinal center B-cell-like form, activated B-cell-like lymphomas respond much more poorly to current therapies and often exhibit overexpression or overactivation of STAT3. To investigate how STAT3 might contribute to this aggressive phenotype, we have integrated genome-wide studies of STAT3 DNA binding using chromatin immunoprecipitation-sequencing with whole-transcriptome profiling using RNA-sequencing. STAT3 binding sites are present near almost a third of all genes that differ in expression between the two subtypes, and examination of the affected genes identified previously undetected and clinically significant pathways downstream of STAT3 that drive oncogenesis. Novel treatments aimed at these pathways may increase the survivability of activated B-cell-like diffuse large B-cell lymphoma.
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Affiliation(s)
- Jennifer Hardee
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Zhengqing Ouyang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Yuping Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
- Department of Computer Science, Stanford University School of Engineering, Stanford, California 94305
| | - Philippe Lacroute
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
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32
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Ning Y, Foss A, Kimball AS, Neill N, Matz T, Schultz R. Characterization of a case of follicular lymphoma transformed into B-lymphoblastic leukemia. Mol Cytogenet 2013; 6:34. [PMID: 23985173 PMCID: PMC3846067 DOI: 10.1186/1755-8166-6-34] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/01/2013] [Indexed: 02/02/2023] Open
Abstract
Follicular lymphoma (FL) is a common form of non-Hodgkin lymphoma with an ability to transform into a more aggressive disease, albeit infrequently to B-lymphoblastic leukemia/lymphoma. While t(14;18)(q32;q21) has been associated with approximately 90% cases of FL, that alteration alone is insufficient to cause FL and associated mutations are still being elucidated. The transformation of FL to B-lymphoblastic leukemia generally includes the dysregulation of MYC gene expression, typically through IGH rearrangement. Such cases of “double-hit” leukemia/lymphoma with both BCL2 and MYC translocations warrant further study as they are often not identified early, are associated with a poor prognosis, and are incompletely understood in molecular terms. Here we describe a patient with a diagnosis of FL that transformed to B-lymphoblastic leukemia. Detailed cytogenetic characterization of the transformed specimen using karyotype, fluorescence in situ hybridization, microarray and gene rearrangement analyses revealed a complex karyotype comprised principally of whole chromosome or whole arm copy number gains or losses. Smaller, single-gene copy number alterations identified by microarray were limited in number, but included amplification of a truncated EP300 gene and alterations in NEIL1 and GPHN. Analyses defined the presence of an IGH/BCL2 fusion due to a translocation as well as a MYC/IGH fusion due to an insertion, with both rearrangements involving the same IGH allele. The data illustrate the value in characterizing double-hit lymphoma cases with both traditional and novel technologies in the detailed cytogenetic workup.
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Affiliation(s)
- Yi Ning
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Aubry Foss
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Amy S Kimball
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholas Neill
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Tricia Matz
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
| | - Roger Schultz
- Signature Genomic Laboratories/Perkin Elmer, 2820 N Astor, Spokane, WA, 99207, USA
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Nalepa G, Barnholtz-Sloan J, Enzor R, Dey D, He Y, Gehlhausen JR, Lehmann AS, Park SJ, Yang Y, Yang X, Chen S, Guan X, Chen Y, Renbarger J, Yang FC, Parada LF, Clapp W. The tumor suppressor CDKN3 controls mitosis. ACTA ACUST UNITED AC 2013; 201:997-1012. [PMID: 23775190 PMCID: PMC3691455 DOI: 10.1083/jcb.201205125] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitosis is controlled by a network of kinases and phosphatases. We screened a library of small interfering RNAs against a genome-wide set of phosphatases to comprehensively evaluate the role of human phosphatases in mitosis. We found four candidate spindle checkpoint phosphatases, including the tumor suppressor CDKN3. We show that CDKN3 is essential for normal mitosis and G1/S transition. We demonstrate that subcellular localization of CDKN3 changes throughout the cell cycle. We show that CDKN3 dephosphorylates threonine-161 of CDC2 during mitotic exit and we visualize CDC2(pThr-161) at kinetochores and centrosomes in early mitosis. We performed a phosphokinome-wide mass spectrometry screen to find effectors of the CDKN3-CDC2 signaling axis. We found that one of the identified downstream phosphotargets, CKβ phosphorylated at serine 209, localizes to mitotic centrosomes and controls the spindle checkpoint. Finally, we show that CDKN3 protein is down-regulated in brain tumors. Our findings indicate that CDKN3 controls mitosis through the CDC2 signaling axis. These results have implications for targeted anticancer therapeutics.
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Affiliation(s)
- Grzegorz Nalepa
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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34
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Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. Hum Genomics 2013; 7:2. [PMID: 23289441 PMCID: PMC3618031 DOI: 10.1186/1479-7364-7-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/14/2012] [Indexed: 11/23/2022] Open
Abstract
A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differentially expressed genes in microarray experiments. The model utility was illustrated using a dog and human lymphoma data set prepared by a group of scientists in the College of Veterinary Medicine at North Carolina State University. A small number of genes were identified as being differentially expressed in both species and the human genes in this cluster serve as a good predictor for classifying diffuse large-B-cell lymphoma (DLBCL) patients into two subgroups, the germinal center B-cell-like diffuse large B-cell lymphoma and the activated B-cell-like diffuse large B-cell lymphoma. The number of human genes that were observed to be significantly differentially expressed (21) from the two-species analysis was very small compared to the number of human genes (190) identified with only one-species analysis (human data). The genes may be clinically relevant/important, as this small set achieved low misclassification rates of DLBCL subtypes. Additionally, the two subgroups defined by this cluster of human genes had significantly different survival functions, indicating that the stratification based on gene-expression profiling using the proposed mixture model provided improved insight into the clinical differences between the two cancer subtypes.
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35
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Ramos-Medina R, Montes-Moreno S, Maestre L, Cañamero M, Rodríguez-Pinilla M, Martínez-Torrecuadrada J, Piris MÁ, Majid A, Dyer MJS, Pulford K, Roncador G. BCL7A protein expression in normal and malignant lymphoid tissues. Br J Haematol 2012; 160:106-9. [PMID: 23043359 DOI: 10.1111/bjh.12080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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36
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Loi TH, Campain A, Bryant A, Molloy TJ, Lutherborrow M, Turner J, Yang YHJ, Ma DDF. Discriminating lymphomas and reactive lymphadenopathy in lymph node biopsies by gene expression profiling. BMC Med Genomics 2011; 4:27. [PMID: 21453471 PMCID: PMC3080274 DOI: 10.1186/1755-8794-4-27] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 03/31/2011] [Indexed: 12/11/2022] Open
Abstract
Background Diagnostic accuracy of lymphoma, a heterogeneous cancer, is essential for patient management. Several ancillary tests including immunophenotyping, and sometimes cytogenetics and PCR are required to aid histological diagnosis. In this proof of principle study, gene expression microarray was evaluated as a single platform test in the differential diagnosis of common lymphoma subtypes and reactive lymphadenopathy (RL) in lymph node biopsies. Methods 116 lymph node biopsies diagnosed as RL, classical Hodgkin lymphoma (cHL), diffuse large B cell lymphoma (DLBCL) or follicular lymphoma (FL) were assayed by mRNA microarray. Three supervised classification strategies (global multi-class, local binary-class and global binary-class classifications) using diagonal linear discriminant analysis was performed on training sets of array data and the classification error rates calculated by leave one out cross-validation. The independent error rate was then evaluated by testing the identified gene classifiers on an independent (test) set of array data. Results The binary classifications provided prediction accuracies, between a subtype of interest and the remaining samples, of 88.5%, 82.8%, 82.8% and 80.0% for FL, cHL, DLBCL, and RL respectively. Identified gene classifiers include LIM domain only-2 (LMO2), Chemokine (C-C motif) ligand 22 (CCL22) and Cyclin-dependent kinase inhibitor-3 (CDK3) specifically for FL, cHL and DLBCL subtypes respectively. Conclusions This study highlights the ability of gene expression profiling to distinguish lymphoma from reactive conditions and classify the major subtypes of lymphoma in a diagnostic setting. A cost-effective single platform "mini-chip" assay could, in principle, be developed to aid the quick diagnosis of lymph node biopsies with the potential to incorporate other pathological entities into such an assay.
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Affiliation(s)
- To Ha Loi
- Blood Stem Cell and Cancer Research Unit, Department of Haematology, St Vincent's Hospital, Victoria Street, Darlinghurst, Australia
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37
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Rütgen BC, Hammer SE, Gerner W, Christian M, de Arespacochaga AG, Willmann M, Kleiter M, Schwendenwein I, Saalmüller A. Establishment and characterization of a novel canine B-cell line derived from a spontaneously occurring diffuse large cell lymphoma. Leuk Res 2010; 34:932-8. [DOI: 10.1016/j.leukres.2010.01.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 01/20/2010] [Accepted: 01/22/2010] [Indexed: 11/28/2022]
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