1
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Jeong H, Grimes K, Rauwolf KK, Bruch PM, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann JC, Marschall T, Nowak D, Bourquin JP, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO. Functional analysis of structural variants in single cells using Strand-seq. Nat Biotechnol 2022:10.1038/s41587-022-01551-4. [PMID: 36424487 DOI: 10.1038/s41587-022-01551-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
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Affiliation(s)
- Hyobin Jeong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
| | - Karen Grimes
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Kerstin K Rauwolf
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Peter-Martin Bruch
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Tobias Rausch
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Eva Benito
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Tobias Roider
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | | | - David Porubsky
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarbrücken, Germany.,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sophie A Herbst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany
| | - Büşra Erarslan-Uysal
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Johann-Christoph Jann
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Nowak
- Department of Hematology and Oncology, Medical Faculty Mannheim of the Heidelberg University, Heidelberg, Germany
| | - Jean-Pierre Bourquin
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Andreas E Kulozik
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg and Hopp Children's Cancer Center, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany.,Department of Hematology and Oncology, University Hospital Düsseldorf, Düsseldorf, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beat Bornhauser
- Division of Pediatric Oncology, University Children's Hospital, Zürich, Switzerland
| | - Ashley D Sanders
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany. .,Charité-Universitätsmedizin, Berlin, Germany.
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, University of Heidelberg, Heidelberg, Germany. .,Bridging Research Division on Mechanisms of Genomic Variation and Data Science, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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2
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Takata K, Steidl C. Genetic mechanism for the loss of PRAME in B cell lymphomas. Reply. J Clin Invest 2022; 132:161979. [PMID: 35838054 PMCID: PMC9282923 DOI: 10.1172/jci161979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Mraz M. Genetic mechanism for the loss of PRAME in B cell lymphomas. J Clin Invest 2022; 132:160983. [PMID: 35838053 PMCID: PMC9282919 DOI: 10.1172/jci160983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Marek Mraz
- Molecular Medicine, CEITEC Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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4
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Tang Z, Kanagal-Shamanna R, Tang G, Patel K, Medeiros LJ, Toruner GA. Analytical and clinical performance of chromosomal microarrays compared with FISH panel and conventional karyotyping in patients with chronic lymphocytic leukemia. Leuk Res 2021; 108:106616. [PMID: 34022744 DOI: 10.1016/j.leukres.2021.106616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
In this single center retrospective analysis on 102 CLL patients, we assessed analytical and clinical performance of CMA against a targeted FISH panel (ATM, TP53, CEP12, D13S319 and LAMP1 loci) and karyotyping. CMA yielded additional information compared to karyotype in 39 cases (38 %). On the other hand, while CMA detected aberrations were also detected by FISH in all 31 cases (30 %), aberrations with low clonal size (<30 %) detected by FISH were missed by CMA. When evaluated with National Cancer Center Network (NCCN) guidelines, the capture rate of prognostic relevant cytogenetic information for FISH only, FISH + Chromosomes and FISH + CMA analyses were 95, 96 and 100 % respectively. With Cancer Cytogenomics Consortium (CGC) Criteria, these figures for FISH only, FISH + Chromosomes and FISH + CMA were 88 %, 92 and 100 % respectively. In conclusion, CMA provides additional analytical information to FISH and karyotyping, but this information has a clinical utility only in a small number of patients. Limit of detection (LOD) issues preclude replacement of FISH by CMA, but CMA may be a viable alternative to karyotyping. Further research is warranted.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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5
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Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
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Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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6
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Li J, Zou J, Wan X, Sun C, Peng F, Chu Z, Hu Y. The Role of Noncoding RNAs in B-Cell Lymphoma. Front Oncol 2020; 10:577890. [PMID: 33194698 PMCID: PMC7645065 DOI: 10.3389/fonc.2020.577890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, emerging evidence has suggested that noncoding RNAs (ncRNAs) participate in nearly every aspect of biological processes and play a crucial role in the genesis and progression of numerous tumors, including B-cell lymphoma. The exploration of ncRNA dysregulations and their functions in B-cell lymphoma provides new insights into lymphoma pathogenesis and is essential for indicating future clinical trials and optimizing the diagnostic and therapeutic strategies. In this review, we summarize the role of ncRNAs in B-cell lymphoma and discuss their potential in clinical applications.
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Affiliation(s)
- Jingwen Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyue Wan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyan Sun
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangbo Chu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, Wuhan, China
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7
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Identification of recurrent noncoding mutations in B-cell lymphoma using capture Hi-C. Blood Adv 2020; 3:21-32. [PMID: 30606723 DOI: 10.1182/bloodadvances.2018026419] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/24/2018] [Indexed: 12/22/2022] Open
Abstract
The identification of driver mutations is fundamental to understanding oncogenesis. Although genes frequently mutated in B-cell lymphoma have been identified, the search for driver mutations has largely focused on the coding genome. Here we report an analysis of the noncoding genome using whole-genome sequencing data from 117 patients with B-cell lymphoma. Using promoter capture Hi-C data in naive B cells, we define cis-regulatory elements, which represent an enriched subset of the noncoding genome in which to search for driver mutations. Regulatory regions were identified whose mutation significantly alters gene expression, including copy number variation at cis-regulatory elements targeting CD69, IGLL5, and MMP14, and single nucleotide variants in a cis-regulatory element for TPRG1 We also show the commonality of pathways targeted by coding and noncoding mutations, exemplified by MMP14, which regulates Notch signaling, a pathway important in lymphomagenesis and whose expression is associated with patient survival. This study provides an enhanced understanding of lymphomagenesis and describes the advantages of using chromosome conformation capture to decipher noncoding mutations relevant to cancer biology.
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8
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Accumulation of Cytoplasmic DNA Due to ATM Deficiency Activates the Microglial Viral Response System with Neurotoxic Consequences. J Neurosci 2019; 39:6378-6394. [PMID: 31189575 DOI: 10.1523/jneurosci.0774-19.2019] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/07/2023] Open
Abstract
ATM (ataxia-telangiectasia mutated) is a PI3K-like kinase best known for its role in the DNA damage response (DDR), especially after double-strand breaks. Mutations in the ATM gene result in a condition known as ataxia-telangiectasia (A-T) that is characterized by cancer predisposition, radiosensitivity, neurodegeneration, sterility, and acquired immune deficiency. We show here that the innate immune system is not spared in A-T. ATM-deficient microglia adopt an active phenotype that includes the overproduction of proinflammatory cytokines that are toxic to cultured neurons and likely contribute to A-T neurodegeneration. Causatively, ATM dysfunction results in the accumulation of DNA in the cytoplasm of microglia as well as a variety of other cell types. In microglia, cytoplasmic DNA primes an antiviral response via the DNA sensor, STING (stimulator of interferon genes). The importance of this response pathway is supported by our finding that inhibition of STING blocks the overproduction of neurotoxic cytokines. Cytosolic DNA also activates the AIM2 (absent in melanoma 2) containing inflammasome and induces proteolytic processing of cytokine precursors such as pro-IL-1β. Our study furthers our understanding of neurodegeneration in A-T and highlights the role of cytosolic DNA in the innate immune response.SIGNIFICANCE STATEMENT Conventionally, the immune deficiencies found in ataxia-telangiectasia (A-T) patients are viewed as defects of the B and T cells of the acquired immune system. In this study, we demonstrate the microglia of the innate immune system are also affected and uncover the mechanism by which this occurs. Loss of ATM (ataxia-telangiectasia mutated) activity leads to a slowing of DNA repair and an accumulation of cytoplasmic fragments of genomic DNA. This ectopic DNA induces the antivirus response, which triggers the production of neurotoxic cytokines. This expands our understanding of the neurodegeneration found in A-T and offers potentially new therapeutic options.
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9
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Spunarova M, Tom N, Pavlova S, Mraz M, Brychtova Y, Doubek M, Panovska A, Skuhrova Francova H, Brzobohata A, Pospisilova S, Mayer J, Trbusek M. Impact of gene mutations and chromosomal aberrations on progression-free survival in chronic lymphocytic leukemia patients treated with front-line chemoimmunotherapy: Clinical practice experience. Leuk Res 2019; 81:75-81. [DOI: 10.1016/j.leukres.2019.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023]
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10
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Mraz M, Pospisilova S. Detection of a deletion at 22q11 locus involving ZNF280A/ZNF280B/PRAME/GGTLC2 in B-cell malignancies: simply a consequence of an immunoglobulin lambda light chain rearrangement. Br J Haematol 2019; 186:e91-e94. [PMID: 30989644 DOI: 10.1111/bjh.15922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Marek Mraz
- Molecular Medicine, CEITEC Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine MU, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine MU, Brno, Czech Republic
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11
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Mestichelli F, Dalsass A, Ferretti S, Camaioni E, Angelini M, Mei S, Pezzoni V, Travaglini F, Troiani E, Angelini S, Galieni P. Array CGH analysis reveals deletion of chromosome 22q11 in CLL with normal karyotype and no fish alterations. Br J Haematol 2017; 183:152-155. [DOI: 10.1111/bjh.14949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Alessia Dalsass
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | - Silvia Ferretti
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | - Elisa Camaioni
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | - Mario Angelini
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | - Sabrina Mei
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | - Valerio Pezzoni
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
| | | | | | | | - Piero Galieni
- U.O.C Ematologia, Ospedale C.G. Mazzoni; Ascoli Piceno Italy
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12
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Yang L, Wang YZ, Zhu HH, Chang Y, Li LD, Chen WM, Long LY, Zhang YH, Liu YR, Lu J, Qin YZ. PRAME Gene Copy Number Variation Is Related to Its Expression in Multiple Myeloma. DNA Cell Biol 2017; 36:1099-1107. [PMID: 28953414 DOI: 10.1089/dna.2017.3951] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multiple myeloma (MM) patients commonly present abnormal expression of cancer-testis antigens, which may serve as immunotherapeutic targets and prognostic factors. We previously reported that preferentially expressed antigen of melanoma (PRAME) overexpression in bone marrow mononuclear cells is related to progression in MM patients treated with non-bortezomib-containing regimens. The mechanism underlying variations in PRAME expression remains unknown. To investigate the impact of gene copy number variation (CNV) on PRAME expression, plasma cells were sorted from 50 newly diagnosed patients and 8 healthy volunteers to measure PRAME transcript levels and gene copy numbers by real-time quantitative polymerase chain reaction. A total of 14 (28.0%), 7 (14.0%), and 29 (58.0%) patients exhibited overexpression, expression within the normal range, and low expression, respectively. PRAME overexpression was significantly related to a lower 1-year progression-free survival rate compared with PRAME low expression (20.0% vs. 88.9%, p = 0.043). The mean PRAME gene copy number relative to albumin (ALB) in normal samples was ∼1.0, whereas 4.0%, 24.0%, 70.0%, and 2.0% of patients had PRAME gene relative copy numbers of approximately 0, 0.5, 1.0, and 2.0, respectively. Patients with PRAME gene deletion (relative copy number of 0 or 0.5) had significantly higher frequency of PRAME nonoverexpression and lambda light chain expression than those with no deletion (p = 0.011 and 0.003). Thus, PRAME gene CNV occurs in MM. Gene deletion may be one mechanism leading to PRAME nonoverexpression and related to immunoglobulin lambda light chain locus rearrangement. PRAME overexpression in plasma cells might be an adverse prognostic factor for progression in MM.
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Affiliation(s)
- Lu Yang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ya-Zhe Wang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Hong-Hu Zhu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan Chang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ling-Di Li
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Wen-Min Chen
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ling-Yu Long
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan-Huan Zhang
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Yan-Rong Liu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Jin Lu
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
| | - Ya-Zhen Qin
- Peking University People's Hospital, Peking University Institute of Hematology , Beijing, China
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13
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Adult high-grade B-cell lymphoma with Burkitt lymphoma signature: genomic features and potential therapeutic targets. Blood 2017; 130:1819-1831. [PMID: 28801451 DOI: 10.1182/blood-2017-02-767335] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/22/2017] [Indexed: 12/15/2022] Open
Abstract
The adult high-grade B-cell lymphomas sharing molecular features with Burkitt lymphoma (BL) are highly aggressive lymphomas with poor clinical outcome. High-resolution structural and functional genomic analysis of adult Burkitt lymphoma (BL) and high-grade B-cell lymphoma with BL gene signature (adult-molecularly defined BL [mBL]) revealed the MYC-ARF-p53 axis as the primary deregulated pathway. Adult-mBL had either unique or more frequent genomic aberrations (del13q14, del17p, gain8q24, and gain18q21) compared with pediatric-mBL, but shared commonly mutated genes. Mutations in genes promoting the tonic B-cell receptor (BCR)→PI3K pathway (TCF3 and ID3) did not differ by age, whereas effectors of chronic BCR→NF-κB signaling were associated with adult-mBL. A subset of adult-mBL had BCL2 translocation and mutation and elevated BCL2 mRNA and protein expression, but had a mutation profile similar to mBL. These double-hit lymphomas may have arisen from a tumor precursor that acquired both BCL2 and MYC translocations and/or KMT2D (MLL2) mutation. Gain/amplification of MIR17HG and its paralogue loci was observed in 50% of adult-mBL. In vitro studies suggested miR-17∼92's role in constitutive activation of BCR signaling and sensitivity to ibrutinib. Overall integrative analysis identified an interrelated gene network affected by copy number and mutation, leading to disruption of the p53 pathway and the BCR→PI3K or NF-κB activation, which can be further exploited in vivo by small-molecule inhibitors for effective therapy in adult-mBL.
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14
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Copy number variation analysis on a non-Hodgkin lymphoma case-control study identifies an 11q25 duplication associated with diffuse large B-cell lymphoma. PLoS One 2014; 9:e105382. [PMID: 25133503 PMCID: PMC4136881 DOI: 10.1371/journal.pone.0105382] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/23/2014] [Indexed: 11/19/2022] Open
Abstract
Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the LOC283177 long non-coding RNA that was further confirmed by quantitative PCR. For chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), known somatic deletions were identified on chromosomes 13q14, 11q22-23, 14q32 and 22q11.22. Our study shows that GWAS data can be used to identify germline CNVs associated with disease risk for DLBCL and somatic CNVs for CLL/SLL.
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15
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Stevens-Kroef MJ, van den Berg E, Olde Weghuis D, Geurts van Kessel A, Pfundt R, Linssen-Wiersma M, Benjamins M, Dijkhuizen T, Groenen PJ, Simons A. Identification of prognostic relevant chromosomal abnormalities in chronic lymphocytic leukemia using microarray-based genomic profiling. Mol Cytogenet 2014; 7:3. [PMID: 24401281 PMCID: PMC3905918 DOI: 10.1186/1755-8166-7-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characteristic genomic abnormalities in patients with B cell chronic lymphocytic leukemia (CLL) have been shown to provide important prognostic information. Fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA), currently used in clinical diagnostics of CLL, are targeted tests aimed at specific genomic loci. Microarray-based genomic profiling is a new high-resolution tool that enables genome-wide analyses. The aim of this study was to compare two recently launched genomic microarray platforms, i.e., the CytoScan HD Array (Affymetrix) and the HumanOmniExpress Array (Illumina), with FISH and MLPA to ascertain whether these latter tests can be replaced by either one of the microarray platforms in a clinical diagnostic setting. RESULT Microarray-based genomic profiling and FISH were performed in all 28 CLL patients. For an unbiased comparison of the performance of both microarray platforms 9 patients were evaluated on both platforms, resulting in the identification of exactly identical genomic aberrations. To evaluate the detection limit of the microarray platforms we included 7 patients in which the genomic abnormalities were present in a relatively low percentage of the cells (range 5-28%) as previously determined by FISH. We found that both microarray platforms allowed the detection of copy number abnormalities present in as few as 16% of the cells. In addition, we found that microarray-based genomic profiling allowed the identification of genomic abnormalities that could not be detected by FISH and/or MLPA, including a focal TP53 loss and copy neutral losses of heterozygosity of chromosome 17p. CONCLUSION From our results we conclude that although the microarray platforms exhibit a somewhat lower limit of detection compared to FISH, they still allow the detection of copy number abnormalities present in as few as 16% of the cells. By applying similar interpretation criteria, the results obtained from both platforms were comparable. In addition, we conclude that both microarray platforms allow the identification of additional potential prognostic relevant abnormalities such as focal TP53 deletions and copy neutral losses of heterozygosity of chromosome 17p, which would have remained undetected by FISH or MLPA. The prognostic relevance of these novel genomic alterations requires further evaluation in prospective clinical trials.
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Affiliation(s)
- Marian Jpl Stevens-Kroef
- Department of Human Genetics, Radboud university medical center, P,O, Box 9101, Nijmegen 6500 HB, The Netherlands.
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