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Vlasevska S, Garcia-Ibanez L, Duval R, Holmes A, Jahan R, Cai B, Kim A, Mo T, Basso K, Soni R, Bhagat G, Dalla-Favera R, Pasqualucci L. KMT2D acetylation by CREBBP reveals a cooperative functional interaction at enhancers in normal and malignant germinal center B cells. Proc Natl Acad Sci U S A 2023; 120:e2218330120. [PMID: 36893259 PMCID: PMC10089214 DOI: 10.1073/pnas.2218330120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 03/11/2023] Open
Abstract
Heterozygous inactivating mutations of the KMT2D methyltransferase and the CREBBP acetyltransferase are among the most common genetic alterations in B cell lymphoma and co-occur in 40 to 60% of follicular lymphoma (FL) and 30% of EZB/C3 diffuse large B cell lymphoma (DLBCL) cases, suggesting they may be coselected. Here, we show that combined germinal center (GC)-specific haploinsufficiency of Crebbp and Kmt2d synergizes in vivo to promote the expansion of abnormally polarized GCs, a common preneoplastic event. These enzymes form a biochemical complex on select enhancers/superenhancers that are critical for the delivery of immune signals in the GC light zone and are only corrupted upon dual Crebbp/Kmt2d loss, both in mouse GC B cells and in human DLBCL. Moreover, CREBBP directly acetylates KMT2D in GC-derived B cells, and, consistently, its inactivation by FL/DLBCL-associated mutations abrogates its ability to catalyze KMT2D acetylation. Genetic and pharmacologic loss of CREBBP and the consequent decrease in KMT2D acetylation lead to reduced levels of H3K4me1, supporting a role for this posttranslational modification in modulating KMT2D activity. Our data identify a direct biochemical and functional interaction between CREBBP and KMT2D in the GC, with implications for their role as tumor suppressors in FL/DLBCL and for the development of precision medicine approaches targeting enhancer defects induced by their combined loss.
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Affiliation(s)
- Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | | | - Romain Duval
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Antony B. Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Rahat Jahan
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Bowen Cai
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Andrew Kim
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Tongwei Mo
- Institute for Cancer Genetics, Columbia University, New York, NY10032
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY10032
| | - Rajesh K. Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
- Department of Genetics and Development, Columbia University, New York, NY10032
- Department of Microbiology and Immunology, Columbia University, New York, NY10032
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY10032
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Author Correction: Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 2022; 611:E2. [PMID: 36253470 DOI: 10.1038/s41586-022-05285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Mohammad Hadigol
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C H Wong
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,Genome Sciences Center, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.,Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. .,Department of Genetics & Development, Columbia University, New York, NY, USA. .,Department of Microbiology & Immunology, Columbia University, New York, NY, USA.
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong J, Vlasevska S, Corinaldesi C, Soni RKS, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Abstract A12: Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Coding-genome sequencing efforts have identified several genes/pathways altered in Diffuse Large B-cell Lymphoma (DLBCL), including new potential therapeutic targets. However, the mutational contribution of the non-coding genome of DLBCL remains largely unexplored. To identify functionally relevant non-coding mutations targeting regulatory domains, we integrated enhancer (E)/super-enhancer (SE) identification, by ChIP-seq analysis of the hallmark H3K27 histone mark, with whole genome sequencing (WGS) and RNA-seq analysis in 29 DLBCL cell lines representative of the major DLBCL subtypes, along with germinal center (GC) B cells representing the normal counterpart of DLBCL. Following validation in 93 normal/tumor DLBCL biopsies, we found that active SEs are specifically hypermutated (≥3 somatic mutations/Kb) in 99% of DLBCLs, as compared to the same loci when not active as SE (in total, 159 hypermutated SEs, with at least 2/case). As evidence of oncogenic relevance, we have shown that the hypermutated SEs linked to the BCL6 and BCL2 proto-oncogenes prevent the binding and transcriptional downregulation by transcriptional repressors. Genetic correction of selected mutations using the CRISPR/Cas9 technology restored repressor DNA-binding, downregulated target gene expression, and led to the counter-selection of cells harboring corrected alleles, indicating oncogenic dependency from the SE mutations. A third recurrently hypermutated SE was the CXCR4-SE, affected in 19% of cases. CXCR4 encodes for a G-protein coupled chemokine receptor involved in cell migration within the GC, and is mutationally activated in 40% of Waldenström macrobulinemia (WM), a post-GC lymphoproliferative disease. We identified a mutational hotspot preventing the binding of the NR3C1 glucocorticoid receptor in 7.5% of DLBCL cases. Correction of the mutations in cell lines led to counter selection and reduced expression of CXCR4. Conversely, the introduction of a mutation disrupting NR3C1 binding in WT DLBCL cells increased CXCR4 expression. Together, these results are consistent with dependency of the mutant cells on the CXCR4-SE mutation, and confirm a direct link between SE mutations in this region and deregulated gene expression through escape from NR3C1-mediated suppression. In primary cases, mutations in the NR3C1 binding site of the CXCR4-SE were observed in the absence of NR3C1 coding mutations and correlated with increased CXCR4 transcript levels, as documented by RNA-seq. Together with the oncogenic role of CXCR4 in WM, these findings reveal this chemokine receptor as a potential oncogenic target in DLBCL. Collectively, these findings reveal a new layer of genetic alterations, which identifies novel mechanisms of dysregulation for known oncogenes, as well as new dysregulated genes and pathways, with implications for precision classification and therapeutic targeting of DLBCL. * Co-senior authors.
Citation Format: Elodie Bal, Rahul Kumar, Mohammad Hadigol, Antony B. Holmes, Laura K. Hilton, Jui Wan Loh, Kostiantyn Dreval, Jasper Wong, Sofija Vlasevska, Clarissa Corinaldesi, Rajesh Kumar Soni Soni, Katia Basso, Ryan D. Morin, Hossein Khiabanian, Laura Pasqualucci, Riccardo Dalla-Favera. Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A12.
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Affiliation(s)
- Elodie Bal
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Rahul Kumar
- 2Institute for Cancer Genetics, Columbia University, New York, NB,
| | - Mohammad Hadigol
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
| | - Antony B. Holmes
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Laura K. Hilton
- 4Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Jui Wan Loh
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
| | - Kostiantyn Dreval
- 5Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,
| | - Jasper Wong
- 4Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Sofija Vlasevska
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | | | - Rajesh Kumar Soni Soni
- 6Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY
| | - Katia Basso
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Ryan D. Morin
- 5Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,
| | - Hossein Khiabanian
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 2022; 607:808-815. [PMID: 35794478 PMCID: PMC9583699 DOI: 10.1038/s41586-022-04906-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 05/25/2022] [Indexed: 12/16/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.
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Affiliation(s)
- Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Mohammad Hadigol
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C H Wong
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Genome Sciences Center, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
- Department of Genetics & Development, Columbia University, New York, NY, USA.
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA.
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5
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Corinaldesi C, Holmes AB, Shen Q, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K. Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis. Front Immunol 2022; 12:818758. [PMID: 35095922 PMCID: PMC8789751 DOI: 10.3389/fimmu.2021.818758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
In response to T-cell-dependent antigens, mature B cells in the secondary lymphoid organs are stimulated to form germinal centers (GCs), which are histological structures deputed to antibody affinity maturation, a process associated with immunoglobulin gene editing by somatic hypermutation (SHM) and class switch recombination (CSR). GC B cells are heterogeneous and transition across multiple stages before being eliminated by apoptosis or committing to post-GC differentiation as memory B cells or plasma cells. In order to explore the dynamics of SHM and CSR during the GC reaction, we identified GC subpopulations by single-cell (sc) transcriptomics and analyzed the load of immunoglobulin variable (V) region mutations as well as the isotype class distribution in each subpopulation. The results showed that the large majority of GC B cells display a quantitatively similar mutational load in the V regions and analogous IGH isotype class distribution, except for the precursors of memory B cells (PreM) and plasma cells (PBL). PreM showed a bimodal pattern with about half of the cells displaying high V region germline identity and enrichment for unswitched IGH, while the rest of the cells carried a mutational load similar to the bulk of GC B cells and showed a switched isotype. PBL displayed a bias toward expression of IGHG and higher V region germline identity compared to the bulk of GC B cells. Genes implicated in SHM and CSR were significantly induced in specific GC subpopulations, consistent with the occurrence of SHM in dark zone cells and suggesting that CSR can occur within the GC.
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Affiliation(s)
| | - Antony B. Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
| | - Eli Grunstein
- Department of Otolaringology Head and Neck Surgery, Columbia University, New York, NY, United States
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
- Department of Microbiology and Immunology, Columbia University, New York, NY, United States
- Department of Genetics and Development, Columbia University, New York, NY, United States
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
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DeLomba W, Bernstein M, Basso K, Suárez E, McLean S, Beaudoin F. 231 The Tolerability and Effectiveness of Duloxetine for the Prevention of Persistent Musculoskeletal Pain After Trauma and Injury: A Pilot Three-Group Randomized Controlled Trial. Ann Emerg Med 2021. [DOI: 10.1016/j.annemergmed.2021.09.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bal E, Kumar R, Hadigol M, Holmes A, Basso K, Khiabanian H, Pasqualucci L, Dalla‐Favera R. PERVASIVE HYPERMUTATION OF SUPER‐ENHANCER REGIONS DYSREGULATES ONCOGENE EXPRESSION IN DIFFUSE LARGE B‐CELL LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.4_2879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- E Bal
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
| | - R Kumar
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
| | - M Hadigol
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
- Rutgers University Center for Systems and Computational Biology Rutgers Cancer Institute New Brunswick New Jersey USA
| | - A Holmes
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
| | - K Basso
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
| | - H Khiabanian
- Rutgers University Center for Systems and Computational Biology Rutgers Cancer Institute New Brunswick New Jersey USA
| | - L Pasqualucci
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
| | - R Dalla‐Favera
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology the Herbert Irving Comprehensive Cancer Center, New York New York SA
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Fangazio M, Ladewig E, Gomez K, Garcia-Ibanez L, Kumar R, Teruya-Feldstein J, Rossi D, Filip I, Pan-Hammarström Q, Inghirami G, Boldorini R, Ott G, Staiger AM, Chapuy B, Gaidano G, Bhagat G, Basso K, Rabadan R, Pasqualucci L, Dalla-Favera R. Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2021; 118:e2104504118. [PMID: 34050029 PMCID: PMC8179151 DOI: 10.1073/pnas.2104504118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fifty percent of diffuse large B cell lymphoma (DLBCL) cases lack cell-surface expression of the class I major histocompatibility complex (MHC-I), thus escaping recognition by cytotoxic T cells. Here we show that, across B cell lymphomas, loss of MHC-I, but not MHC-II, is preferentially restricted to DLBCL. To identify the involved mechanisms, we performed whole exome and targeted HLA deep-sequencing in 74 DLBCL samples, and found somatic inactivation of B2M and the HLA-I loci in 80% (34 of 42) of MHC-INEG tumors. Furthermore, 70% (22 of 32) of MHC-IPOS DLBCLs harbored monoallelic HLA-I genetic alterations (MHC-IPOS/mono), indicating allele-specific inactivation. MHC-INEG and MHC-IPOS/mono cases harbored significantly higher mutational burden and inferred neoantigen load, suggesting potential coselection of HLA-I loss and sustained neoantigen production. Notably, the analysis of >500,000 individuals across different cancer types revealed common germline HLA-I homozygosity, preferentially in DLBCL. In mice, germinal-center B cells lacking HLA-I expression did not progress to lymphoma and were counterselected in the context of oncogene-driven lymphomagenesis, suggesting that additional events are needed to license immune evasion. These results suggest a multistep process of HLA-I loss in DLBCL development including both germline and somatic events, and have direct implications for the pathogenesis and immunotherapeutic targeting of this disease.
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Affiliation(s)
- Marco Fangazio
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | - Erik Ladewig
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | - Karen Gomez
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | | | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | | | - Davide Rossi
- Laboratory of Experimental Hematology, Institute of Oncology Research, 6500 Bellinzona, Switzerland
- Clinic of Hematology, Oncology Institute of Southern Switzerland, 6500 Bellinzona, Switzerland
- Faculty of Biomedical Science, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Ioan Filip
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Renzo Boldorini
- Department of Health Sciences, Division of Pathology, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - German Ott
- Department of Clinical Pathology, Robert Bosch Krankenhaus, 70376 Stuttgart, Germany
| | - Annette M Staiger
- Department of Clinical Pathology, Robert Bosch Krankenhaus, 70376 Stuttgart, Germany
- Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, 72074 Tuebingen, Germany
| | - Björn Chapuy
- Department of Hematology and Oncology, University of Göttingen, 37073 Göttingen, Germany
| | - Gianluca Gaidano
- Department of Translational Medicine, Division of Hematology, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy
| | - Govind Bhagat
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY 10032
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
- Program for Mathematical Genomics, Columbia University, New York, NY 10032
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032
- Department of Genetics and Development, Columbia University, New York, NY 10032
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Vlasevska S, Garcia‐Ibanez L, Duval R, Holmes A, Jahan R, Basso K, Dalla‐Favera R, Pasqualucci L. CREBBP MEDIATED ACETYLATION OF KMT2D IN NORMAL AND TRANSFORMED GC B CELLS. Hematol Oncol 2021. [DOI: 10.1002/hon.42_2879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- S. Vlasevska
- Columbia University Institute for Cancer Genetics New York, New York USA
| | - L. Garcia‐Ibanez
- Columbia University Institute for Cancer Genetics New York, New York USA
| | - R. Duval
- Columbia University Institute for Cancer Genetics New York, New York USA
| | - A.B. Holmes
- Columbia University Institute for Cancer Genetics New York, New York USA
| | - R. Jahan
- Columbia University Institute for Cancer Genetics New York, New York USA
| | - K. Basso
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology and the Herbert Irving Comprehensive Cancer Center New York, New York USA
| | - R. Dalla‐Favera
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology and the Herbert Irving Comprehensive Cancer Center New York, New York USA
| | - L. Pasqualucci
- Columbia University Institute for Cancer Genetics the Department of Pathology and Cell Biology and the Herbert Irving Comprehensive Cancer Center New York, New York USA
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10
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Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, Nitzan M, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K. Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome. J Exp Med 2021; 217:151908. [PMID: 32603407 PMCID: PMC7537389 DOI: 10.1084/jem.20200483] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
In response to T cell-dependent antigens, mature B cells are stimulated to form germinal centers (GCs), the sites of B cell affinity maturation and the cell of origin (COO) of most B cell lymphomas. To explore the dynamics of GC B cell development beyond the known dark zone and light zone compartments, we performed single-cell (sc) transcriptomic analysis on human GC B cells and identified multiple functionally linked subpopulations, including the distinct precursors of memory B cells and plasma cells. The gene expression signatures associated with these GC subpopulations were effective in providing a sc-COO for ∼80% of diffuse large B cell lymphomas (DLBCLs) and identified novel prognostic subgroups of DLBCL.
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Affiliation(s)
- Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Nicolo Compagno
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Zhong Wang
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | | | - Eli Grunstein
- Department of Otolaryngology Head and Neck Surgery, Columbia University, New York, NY
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY.,Department of Pathology and Cell Biology, Columbia University, New York, NY.,The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY.,Department of Pathology and Cell Biology, Columbia University, New York, NY.,Department of Microbiology and Immunology, Columbia University, New York, NY.,Department of Genetics and Development, Columbia University, New York, NY.,The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY.,Department of Pathology and Cell Biology, Columbia University, New York, NY
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11
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Garbin A, Lovisa F, Holmes AB, Damanti CC, Gallingani I, Carraro E, Accordi B, Veltri G, Pizzi M, d'Amore ESG, Pillon M, Biffi A, Basso K, Mussolin L. miR-939 acts as tumor suppressor by modulating JUNB transcriptional activity in pediatric anaplastic large cell lymphoma. Haematologica 2021; 106:610-613. [PMID: 32299901 PMCID: PMC7849582 DOI: 10.3324/haematol.2019.241307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Anna Garbin
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Federica Lovisa
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Carlotta C Damanti
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Ilaria Gallingani
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Elisa Carraro
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Benedetta Accordi
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Giulia Veltri
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Marco Pizzi
- Surgical Pathology and Cytopathology Unit, Department of Medicine, University of Padova, Italy
| | | | - Marta Pillon
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Alessandra Biffi
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
| | - Katia Basso
- Institute for Cancer Genetics and Dept of Pathology and Cell Biology, Columbia University, New York, USA
| | - Lara Mussolin
- Dept Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padua, Italy
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12
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Nizami T, Aluisio A, Jay G, Bhatt R, Feroze T, Suarez E, Basso K, Berenson R, Beaudoin F. 112 Evaluation of MicroMend Wound Closure Device in Repairing Skin Lacerations. Ann Emerg Med 2020. [DOI: 10.1016/j.annemergmed.2020.09.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Meyer SN, Scuoppo C, Vlasevska S, Bal E, Holmes AB, Holloman M, Garcia-Ibanez L, Nataraj S, Duval R, Vantrimpont T, Basso K, Brooks N, Dalla-Favera R, Pasqualucci L. Unique and Shared Epigenetic Programs of the CREBBP and EP300 Acetyltransferases in Germinal Center B Cells Reveal Targetable Dependencies in Lymphoma. Immunity 2019; 51:535-547.e9. [PMID: 31519498 DOI: 10.1016/j.immuni.2019.08.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/03/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022]
Abstract
Inactivating mutations of the CREBBP and EP300 acetyltransferases are among the most common genetic alterations in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). Here, we examined the relationship between these two enzymes in germinal center (GC) B cells, the normal counterpart of FL and DLBCL, and in lymphomagenesis by using conditional GC-directed deletion mouse models targeting Crebbp or Ep300. We found that CREBBP and EP300 modulate common as well as distinct transcriptional programs implicated in separate anatomic and functional GC compartments. Consistently, deletion of Ep300 but not Crebbp impaired the fitness of GC B cells in vivo. Combined loss of Crebbp and Ep300 completely abrogated GC formation, suggesting that these proteins partially compensate for each other through common transcriptional targets. This synthetic lethal interaction was retained in CREBBP-mutant DLBCL cells and could be pharmacologically targeted with selective small molecule inhibitors of CREBBP and EP300 function. These data provide proof-of-principle for the clinical development of EP300-specific inhibitors in FL and DLBCL.
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Affiliation(s)
- Stefanie N Meyer
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Mara Holloman
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | | | - Sarah Nataraj
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Romain Duval
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Thomas Vantrimpont
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Nigel Brooks
- Cell Centric, Chesterford Research Park, Little Chesterford, Cambridge, CB10 1XL, UK
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Department of Genetics & Development, Columbia University, New York, NY 10032, USA; Department of Microbiology & Immunology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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14
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Scuoppo C, Wang J, Persaud M, Mittan SK, Basso K, Pasqualucci L, Rabadan R, Inghirami G, Grandori C, Bosch F, Dalla-Favera R. Repurposing dasatinib for diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2019; 116:16981-16986. [PMID: 31383760 PMCID: PMC6708382 DOI: 10.1073/pnas.1905239116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To repurpose compounds for diffuse large B cell lymphoma (DLBCL), we screened a library of drugs and other targeted compounds approved by the US Food and Drug Administration on 9 cell lines and validated the results on a panel of 32 genetically characterized DLBCL cell lines. Dasatinib, a multikinase inhibitor, was effective against 50% of DLBCL cell lines, as well as against in vivo xenografts. Dasatinib was more broadly active than the Bruton kinase inhibitor ibrutinib and overcame ibrutinib resistance. Tumors exhibiting dasatinib resistance were commonly characterized by activation of the PI3K pathway and loss of PTEN expression as a specific biomarker. PI3K suppression by mTORC2 inhibition synergized with dasatinib and abolished resistance in vitro and in vivo. These results provide a proof of concept for the repurposing approach in DLBCL, and point to dasatinib as an attractive strategy for further clinical development in lymphomas.
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Affiliation(s)
- Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Jiguang Wang
- Department of Systems Biology, Columbia University, New York, NY 10032
| | - Mirjana Persaud
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | - Sandeep K Mittan
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY 10032
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065
| | - Carla Grandori
- Cure First and SEngine Precision Medicine, Seattle, WA 98109
| | - Francesc Bosch
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
- Department of Hematology and Vall d'Hebron Institute of Oncology, University Hospital Vall d'Hebron, 08035 Barcelona, Spain
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY 10032;
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
- Department of Genetics and Development, Columbia University, New York, NY 10032
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032
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15
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Brescia P, Schneider C, Holmes AB, Shen Q, Hussein S, Pasqualucci L, Basso K, Dalla-Favera R. MEF2B Instructs Germinal Center Development and Acts as an Oncogene in B Cell Lymphomagenesis. Cancer Cell 2018; 34:453-465.e9. [PMID: 30205047 PMCID: PMC6223119 DOI: 10.1016/j.ccell.2018.08.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/15/2018] [Accepted: 08/08/2018] [Indexed: 12/30/2022]
Abstract
The gene encoding the MEF2B transcription factor is mutated in germinal center (GC)-derived B cell lymphomas, but its role in GC development and lymphomagenesis is unknown. We demonstrate that Mef2b deletion reduces GC formation in mice and identify MEF2B transcriptional targets in GC, with roles in cell proliferation, apoptosis, GC confinement, and differentiation. The most common lymphoma-associated MEF2B mutant (MEF2BD83V) is hypomorphic, yet escapes binding and negative regulation by components of the HUCA complex and class IIa HDACs. Mef2bD83V expression in mice leads to GC enlargement and lymphoma development, a phenotype that becomes fully penetrant in combination with BCL2 de-regulation, an event associated with human MEF2B mutations. These results identify MEF2B as a critical GC regulator and a driver oncogene in lymphomagenesis.
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Affiliation(s)
- Paola Brescia
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Christof Schneider
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Shafinaz Hussein
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA; The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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16
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Pomari E, Lovisa F, Carraro E, Primerano S, D'Amore ESG, Bonvini P, Nigro LL, Vito RD, Vinti L, Farruggia P, Pillon M, Basso G, Basso K, Mussolin L. Clinical impact of miR-223 expression in pediatric T-Cell lymphoblastic lymphoma. Oncotarget 2017; 8:107886-107898. [PMID: 29296210 PMCID: PMC5746112 DOI: 10.18632/oncotarget.22386] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/28/2017] [Indexed: 01/24/2023] Open
Abstract
Although probability of event-free survival in pediatric lymphoblastic T-cell lymphoma (T-LBL) is about 75%, survival in relapsed patients is very poor, so the identification of new molecular markers is crucial for treatment optimization. Here, we demonstrated that the over-expression of miR-223 promotes tumor T-LBL cell growth, migration and invasion in vitro. We found out that SIK1, an anti-metastatic protein, is a direct target of miR-223 and consequently is significantly reduced in miR-223-overexpressing tumor cells. We measured miR-223 expression levels at diagnosis in tumor biopsies from 67 T-LBL pediatric patients for whom complete clinical and follow up data were available, and we found that high miR-223 expression (above the median value) is associated with worse prognosis (PFS 66% vs 94%, P=0.0036). In addition, the multivariate analysis, conducted taking into account miR-223 expression level and other molecular and clinical characteristics, showed that only high level of miR-223 is an independent factor for worse prognosis. MiR-223 represents a promising marker for treatment stratification in pediatric patients with T-LBL and we provide the first evidence of miR-223 potential role as oncomir by SIK1 repression.
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Affiliation(s)
- Elena Pomari
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy.,Centre for Tropical Diseases, Ospedale Sacro Cuore-Don Calabria, 37024 Negrar, Italy
| | - Federica Lovisa
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy.,Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Elisa Carraro
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy
| | - Simona Primerano
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy.,Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, 35127 Padova, Italy
| | | | - Paolo Bonvini
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy.,Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Luca Lo Nigro
- Center of Paediatric Haematology, Azienda Policlinico-OVE, 95123 Catania, Italy
| | - Rita De Vito
- Department of Paediatric Haemato-Oncology, IRCCS Ospedale Bambino Gesù, 00165 Roma, Italy
| | - Luciana Vinti
- Department of Paediatric Haemato-Oncology, IRCCS Ospedale Bambino Gesù, 00165 Roma, Italy
| | - Piero Farruggia
- Department of Paediatric Haemato-Oncology, ARNAS Ospedali Civico, G Di Cristina, 90127 Palermo, Italy
| | - Marta Pillon
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy
| | - Giuseppe Basso
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy
| | - Katia Basso
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, NY 10027, New York, USA
| | - Lara Mussolin
- Department of Women's and Children's Health, Clinic of Pediatric Hemato-Oncology, University of Padova, 35128 Padova, Italy.,Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, 35127 Padova, Italy
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17
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Zhang J, Vlasevska S, Wells VA, Nataraj S, Holmes AB, Duval R, Meyer SN, Mo T, Basso K, Brindle PK, Hussein S, Dalla-Favera R, Pasqualucci L. The CREBBP Acetyltransferase Is a Haploinsufficient Tumor Suppressor in B-cell Lymphoma. Cancer Discov 2017; 7:322-337. [PMID: 28069569 DOI: 10.1158/2159-8290.cd-16-1417] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 01/12/2023]
Abstract
Inactivating mutations of the CREBBP acetyltransferase are highly frequent in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most common germinal center (GC)-derived cancers. However, the role of CREBBP inactivation in lymphomagenesis remains unclear. Here, we show that CREBBP regulates enhancer/super-enhancer networks with central roles in GC/post-GC cell fate decisions, including genes involved in signal transduction by the B-cell receptor and CD40 receptor, transcriptional control of GC and plasma cell development, and antigen presentation. Consistently, Crebbp-deficient B cells exhibit enhanced response to mitogenic stimuli and perturbed plasma cell differentiation. Although GC-specific loss of Crebbp was insufficient to initiate malignant transformation, compound Crebbp-haploinsufficient/BCL2-transgenic mice, mimicking the genetics of FL and DLBCL, develop clonal lymphomas recapitulating the features of the human diseases. These findings establish CREBBP as a haploinsufficient tumor-suppressor gene in GC B cells and provide insights into the mechanisms by which its loss contributes to lymphomagenesis.Significance: Loss-of-function mutations of CREBBP are common and early lesions in FL and DLBCL, suggesting a prominent role in lymphoma initiation. Our studies identify the cellular program by which reduced CREBBP dosage facilitates malignant transformation, and have direct implications for targeted lymphoma therapy based on drugs affecting CREBBP-mediated chromatin acetylation. Cancer Discov; 7(3); 322-37. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 235.
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Affiliation(s)
- Jiyuan Zhang
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Victoria A Wells
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Sarah Nataraj
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Romain Duval
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Stefanie N Meyer
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Tongwei Mo
- Institute for Cancer Genetics, Columbia University, New York, New York
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, New York.,Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Paul K Brindle
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shafinaz Hussein
- Department of Pathology and Laboratory Medicine, NorthWell Health, Staten Island University Hospital, Staten Island, New York
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, New York.,Department of Pathology and Cell Biology, Columbia University, New York, New York.,Department of Genetics and Development, Columbia University, New York, New York.,Department of Microbiology and Immunology, Columbia University, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, New York. .,Department of Pathology and Cell Biology, Columbia University, New York, New York.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
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18
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Schneider C, Kon N, Amadori L, Shen Q, Schwartz FH, Tischler B, Bossennec M, Dominguez-Sola D, Bhagat G, Gu W, Basso K, Dalla-Favera R. FBXO11 inactivation leads to abnormal germinal-center formation and lymphoproliferative disease. Blood 2016; 128:660-6. [PMID: 27166359 PMCID: PMC9709922 DOI: 10.1182/blood-2015-11-684357] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/22/2016] [Indexed: 12/14/2022] Open
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor that is required for the germinal center (GC) reaction and is implicated in lymphomagenesis. BCL6 protein stability is regulated by F-box protein 11 (FBXO11)-mediated ubiquitination and degradation, which is impaired in ∼6% of diffuse large B-cell lymphomas that carry inactivating genetic alterations targeting the FBXO11 gene. In order to investigate the role of FBXO11 in vivo, we analyzed GC-specific FBXO11 knockout mice. FBXO11 reduction or loss led to an increased number of GC B cells, to an altered ratio of GC dark zone to light zone cells, and to higher levels of BCL6 protein in GC B cells. B-cell receptor-mediated degradation of BCL6 was reduced in the absence of FBXO11, suggesting that FBXO11 contributes to the physiologic downregulation of BCL6 at the end of the GC reaction. Finally, FBXO11 inactivation was associated with the development of lymphoproliferative disorders in mice.
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Affiliation(s)
| | - Ning Kon
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Letizia Amadori
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Qiong Shen
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | | | - Marion Bossennec
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Govind Bhagat
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Wei Gu
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology and Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
- Department of Microbiology and Immunology, Columbia University, New York, NY
- Department of Genetics and Development, Columbia University, New York, NY
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19
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Zhang J, Dominguez-Sola D, Hussein S, Lee JE, Holmes AB, Bansal M, Vlasevska S, Mo T, Tang H, Basso K, Ge K, Dalla-Favera R, Pasqualucci L. Abstract B25: Disruption of KMT2D-dependent histone methylation perturbs GC B cell development and cooperates with BCL2 deregulation in lymphomagenesis. Cancer Res 2016. [DOI: 10.1158/1538-7445.chromepi15-b25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Modulation of chromatin accessibility through histone modification is a key step in the regulation of gene transcription and its disruption by genetic lesions has been implicated in malignant transformation. Indeed, a consistent theme in recent cancer genome studies has been the discovery of recurrent mutations in multiple histone/chromatin modifier genes, including methyltransferases, acetyltransferases and histone themselves. Among these, KMT2D (MLL2 or MLL4), encoding for a histone H3K4 methyltransferase, emerged as one of the most common targets of genetic lesion in B cell non-Hodgkin lymphoma, being found in ~30% of diffuse large B cell lymphoma (DLBCL) and ~90% of follicular lymphoma (FL), which together account for over 70% of all lymphoma diagnoses (Pasqualucci et al, Nat Genetics 2011; Morin et al, Nature 2011). KMT2D mutations are mostly represented by truncating events that are predicted to remove the protein C-terminal enzymatic domains, thus inactivating its function; however, missense mutations were also found in a subset of cases, suggesting selection for a functional role. These events are biallelically distributed in one third of mutated cases, while the remaining >60% harbor monoallelic mutations, consistent with a role as a tumor suppressor. Interestingly, analysis of the history of clonal evolution during FL transformation to DLBCL suggests that KMT2D mutations may be already present in a common precursor clone before divergent evolution to FL or DLBCL, suggesting an early role during B cell clonal expansion (Pasqualucci et al, Cell Rep, 2014; Green et al, Blood, 2013).
To elucidate the functional consequences of KMT2D mutations, we first examined the effects of 16 DLBCL/FL-derived KMT2D missense mutant alleles on its enzymatic activity in vitro. The results showed that all 8 mutants located in the C-terminal portion of the protein were associated with significantly diminished H3K4 mono-, di- and tri-methylation activity. Consistently, a significant reduction in global methylation was observed in Kmt2d deficient murine B-cells, as well as in 4 biallelically truncated cell lines, indicating that this methyltransferase can influence all three H3K4 modifications.
To gain further insights into the program regulated by KMT2D in germinal center (GC) B cells (i.e. the normal counterpart of FL/DLBCL) and the mechanism by which its loss contributes to lymphomagenesis, we crossed mice carrying a conditional Kmt2d knockout allele (Lee J et al, Elife, 2013) with either CD19Cre or Cγ1Cre deletor mice, leading to gene inactivation early during B-cell development (Kmt2dCD19KO), thus mimicking the postulated “common precursor model,” or specifically in mature, GC B-cells (Kmt2dCγ1KO). Notably, deletion of Kmt2d before, but not after initiation of the GC reaction led to a significant increase in GC B-cells and enhanced B cell proliferation. These changes were accompanied by the acquisition of distinct transcriptional signatures enriched in cell cycle regulation and apoptosis genes. A cross-species strategy combining gene expression profile analysis of murine GC B-cells and Kmt2d chromatin immunoprecipitation and sequencing of purified human GC B cells identified a core of KMT2D direct targets genes involved in biological programs with critical functions in B cells physiology, including B cell receptor signaling, lymphocyte migration, and chemokine signaling components. Finally, while loss of Kmt2d alone in Kmt2dCγ1KO was not sufficient to induce tumor development, its combination with VavP-BCL2 transgenic mice increased the incidence of GC-derived lymphomas resembling the features of the human tumors. These data support a role for KMT2D as a tumor suppressor gene whose early loss during B cell development facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cell.
Citation Format: Jiyuan Zhang, David Dominguez-Sola, Shafinaz Hussein, Ji-Eun Lee, Antony B. Holmes, Mukesh Bansal, Sofija Vlasevska, Tongwei Mo, Hongyan Tang, Katia Basso, Kai Ge, Riccardo Dalla-Favera, Laura Pasqualucci. Disruption of KMT2D-dependent histone methylation perturbs GC B cell development and cooperates with BCL2 deregulation in lymphomagenesis. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B25.
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Zhang J, Dominguez-Sola D, Hussein S, Lee JE, Holmes AB, Bansal M, Vlasevska S, Mo T, Tang H, Basso K, Ge K, Dalla-Favera R, Pasqualucci L. Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. Nat Med 2015; 21:1190-8. [PMID: 26366712 PMCID: PMC5145002 DOI: 10.1038/nm.3940] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/11/2015] [Indexed: 12/12/2022]
Abstract
Mutations in the gene encoding the KMT2D (or MLL2) methyltransferase are highly recurrent and occur early during tumorigenesis in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the functional consequences of these mutations and their role in lymphomagenesis are unknown. Here we show that FL- and DLBCL-associated KMT2D mutations impair KMT2D enzymatic activity, leading to diminished global H3K4 methylation in germinal-center (GC) B cells and DLBCL cells. Conditional deletion of Kmt2d early during B cell development, but not after initiation of the GC reaction, results in an increase in GC B cells and enhances B cell proliferation in mice. Moreover, genetic ablation of Kmt2d in mice overexpressing Bcl2 increases the incidence of GC-derived lymphomas resembling human tumors. These findings suggest that KMT2D acts as a tumor suppressor gene whose early loss facilitates lymphomagenesis by remodeling the epigenetic landscape of the cancer precursor cells. Eradication of KMT2D-deficient cells may thus represent a rational therapeutic approach for targeting early tumorigenic events.
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Affiliation(s)
- Jiyuan Zhang
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - David Dominguez-Sola
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shafinaz Hussein
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Mukesh Bansal
- Department of Systems Biology, Columbia University, New York, New York, USA
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Tongwei Mo
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Hongyan Tang
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Department of Genetics &Development, Columbia University, New York, New York, USA.,Department of Microbiology &Immunology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, New York, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
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Abstract
Germinal centres (GCs) are involved in the selection of B cells secreting high-affinity antibodies and are also the origin of most human B cell lymphomas. Recent progress has been made in identifying the functionally relevant stages of the GC and the complex trafficking mechanisms of B cells within the GC. These studies have identified transcription factors and signalling pathways that regulate distinct phases of GC development. Notably, these factors and pathways are hijacked during tumorigenesis, as revealed by analyses of the genetic lesions associated with various types of B cell lymphomas. This Review focuses on recent insights into the mechanisms that regulate GC development and that are relevant for human B cell lymphomagenesis.
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Affiliation(s)
- Katia Basso
- 1] Institute for Cancer Genetics, Columbia University. [2] Department of Pathology and Cell Biology, Columbia University
| | - Riccardo Dalla-Favera
- 1] Institute for Cancer Genetics, Columbia University. [2] Department of Pathology and Cell Biology, Columbia University. [3] Department of Genetics and Development, Columbia University. [4] Department of Microbiology and Immunology, Columbia University. [5] The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
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Mussolin L, Holmes AB, Romualdi C, Sales G, D'Amore ESG, Ghisi M, Pillon M, Rosolen A, Basso K. An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways. Leukemia 2014; 28:1909-12. [PMID: 24727675 DOI: 10.1038/leu.2014.134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- L Mussolin
- 1] Istituto di Ricerca Pediatrico Fondazione Citta' della Speranza, Padova, Italy [2] Clinica di Oncoematologia Pediatrica, Azienda Ospedaliera-Universita' di Padova, Padova, Italy
| | - A B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - C Romualdi
- Department of Biology, University of Padova, Padova, Italy
| | - G Sales
- Department of Biology, University of Padova, Padova, Italy
| | - E S G D'Amore
- Department of Pathology, San Bortolo Hospital, Vicenza, Italy
| | - M Ghisi
- Department of Oncology and Surgical Sciences, University of Padova, Padova, Italy
| | - M Pillon
- Clinica di Oncoematologia Pediatrica, Azienda Ospedaliera-Universita' di Padova, Padova, Italy
| | - A Rosolen
- 1] Istituto di Ricerca Pediatrico Fondazione Citta' della Speranza, Padova, Italy [2] Clinica di Oncoematologia Pediatrica, Azienda Ospedaliera-Universita' di Padova, Padova, Italy
| | - K Basso
- 1] Institute for Cancer Genetics, Columbia University, New York, NY, USA [2] Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Hussein S, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R. MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol 2013; 14:1084-92. [PMID: 23974956 PMCID: PMC3954820 DOI: 10.1038/ni.2688] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
MEF2B encodes a transcriptional activator and is mutated in ∼11% of diffuse large B cell lymphomas (DLBCLs) and ∼12% of follicular lymphomas (FLs). Here we found that MEF2B directly activated the transcription of the proto-oncogene BCL6 in normal germinal-center (GC) B cells and was required for DLBCL proliferation. Mutation of MEF2B resulted in enhanced transcriptional activity of MEF2B either through disruption of its interaction with the corepressor CABIN1 or by rendering it insensitive to inhibitory signaling events mediated by phosphorylation and sumoylation. Consequently, the transcriptional activity of Bcl-6 was deregulated in DLBCLs with MEF2B mutations. Thus, somatic mutations of MEF2B may contribute to lymphomagenesis by deregulating BCL6 expression, and MEF2B may represent an alternative target for blocking Bcl-6 activity in DLBCLs.
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Affiliation(s)
- Carol Y Ying
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
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24
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Maute RL, Dalla-Favera R, Basso K. RNAs with multiple personalities. WIREs RNA 2013; 5:1-13. [DOI: 10.1002/wrna.1193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/19/2013] [Accepted: 07/25/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Roy L. Maute
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
- Department of Microbiology and Immunology; Columbia University; New York NY USA
| | - Katia Basso
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
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Basso K, Klein U. Gene expression profile analysis of lymphomas. Methods Mol Biol 2013; 971:213-26. [PMID: 23296966 DOI: 10.1007/978-1-62703-269-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Through the genome-wide characterization of a cell type's transcriptome, gene expression profile analysis provides a potent tool for analyzing the pathogenesis of lymphomas and has had a major impact on the understanding of lymphoid neoplasia. The analysis of gene expression patterns of lymphomas and normal lymphocytes permits (1) the definition of molecular subtypes of lymphoma; (2) the identification of the normal cellular counterpart of a lymphoma subtype; (3) the identification of diagnostic markers and therapeutic targets; and (4) the identification of signaling pathways affected by the oncogenic transformation. This chapter presents an approach to accomplish these goals.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
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Basso K, Schneider C, Shen Q, Holmes AB, Setty M, Leslie C, Dalla-Favera R. BCL6 positively regulates AID and germinal center gene expression via repression of miR-155. ACTA ACUST UNITED AC 2012; 209:2455-65. [PMID: 23166356 PMCID: PMC3526356 DOI: 10.1084/jem.20121387] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor that is required for germinal center (GC) formation and whose de-regulation is involved in lymphomagenesis. Although substantial evidence indicates that BCL6 exerts its function by repressing the transcription of hundreds of protein-coding genes, its potential role in regulating gene expression via microRNAs (miRNAs) is not known. We have identified a core of 15 miRNAs that show binding of BCL6 in their genomic loci and are down-regulated in GC B cells. Among BCL6 validated targets, miR-155 and miR-361 directly modulate AID expression, indicating that via repression of these miRNAs, BCL6 up-regulates AID. Similarly, the expression of additional genes relevant for the GC phenotype, including SPI1, IRF8, and MYB, appears to be sustained via BCL6-mediated repression of miR-155. These findings identify a novel mechanism by which BCL6, in addition to repressing protein coding genes, promotes the expression of important GC functions by repressing specific miRNAs.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10027, USA.
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Abstract
BCL6 is a transcriptional repressor required in mature B cells during the germinal center (GC) reaction. Multiple mechanisms act coordinately to timely modulate BCL6 expression at transcriptional and post-transcriptional levels. BCL6 prevents premature activation and differentiation of GC B cells and provides an environment tolerant of the DNA breaks associated with immunoglobulin gene remodeling mechanisms involved in the production of high-affinity antibodies of different isotypes. The critical functions exerted by BCL6 during normal B-cell development can be hijacked by the malignant transformation process. Indeed, BCL6 is targeted by genetic aberrations and acts as an oncogene in GC-derived lymphomas. The aberrations affecting BCL6 interfere with the multiple levels of regulation that grant a fine tuning of BCL6 expression and activity in physiologic conditions. This review summarizes the current knowledge on BCL6 function and its role in lymphomagenesis.
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Affiliation(s)
- Katia Basso
- Department of Pathology and Cell Biology, Institute for Cancer Genetics, the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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Kitagawa Y, Brahmachary M, Tiacci E, Dalla-Favera R, Falini B, Basso K. A microRNA signature specific for hairy cell leukemia and associated with modulation of the MAPK-JNK pathways. Leukemia 2012; 26:2564-7. [PMID: 22660186 DOI: 10.1038/leu.2012.149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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D'Agostino DM, Ruggero K, Biasiolo M, Bortoluzzi S, Pise-Masison CA, Corradin A, Basso K, Guffanti A, De Bellis G, Corti G, Zanovello P, Bronte V, Ciminale V. MicroRNA expression in HTLV-1 infection and pathogenesis. Retrovirology 2011. [PMCID: PMC3112627 DOI: 10.1186/1742-4690-8-s1-a156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Basso K, Mussolin L, Lettieri A, Brahmachary M, Lim WK, Califano A, Basso G, Biondi A, Cazzaniga G, Rosolen A. T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses. Genes Chromosomes Cancer 2011; 50:1063-75. [PMID: 21987448 DOI: 10.1002/gcc.20924] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/01/2010] [Indexed: 11/09/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) share common morphological and immunophenotypic features and are treated with similar therapeutic approaches. Nonetheless, they show distinct clinical presentations, suggesting that they may represent two different biological entities. To investigate the genetic characteristics of T-LBL and T-ALL, we used genomic and transcriptional profiling approaches. Genome-wide gene expression profiling, performed on 20 T-LBL and 10 T-ALL diagnostic specimens, revealed that the two malignancies shared a large fraction of their transcriptional profile while a subset of genes appeared to be differentially expressed in T-LBL versus T-ALL. This signature included genes involved in chemotactic responses and angiogenesis, which may play a role in tumor cell localization. Genome-wide copy number alteration analysis was performed on a subset of the samples analyzed by gene expression profiling and detected 41 recurrently altered genetic loci. Although most aberrations were found in both entities, several were selectively identified in T-LBL or T-ALL. In addition, NOTCH1 mutational status was found to correlate with a subset of genetic aberrations. Taken together, these results suggest that T-LBL and T-ALL are indeed two distinct diseases with unique transcriptional and genetic characteristics.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY10032, USA.
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Novak U, Basso K, Pasqualucci L, Dalla-Favera R, Bhagat G. Genomic analysis of non-splenic marginal zone lymphomas (MZL) indicates similarities between nodal and extranodal MZL and supports their derivation from memory B-cells. Br J Haematol 2011; 155:362-5. [PMID: 21883140 DOI: 10.1111/j.1365-2141.2011.08841.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Three distinct categories of marginal zone lymphomas (MZLs) are currently recognized, principally based on their site of occurrence. They are thought to represent unique entities, but the relationship of one subtype with another is poorly understood. We investigated 17 non-splenic MZLs (seven nodal, 10 extranodal) by gene expression profiling to distinguish between subtypes and determine their cell of origin. Our findings suggest biological inter-relatedness of these entities despite occurrence at different locations and associations with possibly different aetiologies. Furthermore, the expression profiles of non-splenic MZL were similar to memory B cells.
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Affiliation(s)
- Urban Novak
- Departments of Pathology and Cell Biology Genetics and Development Herbert Irving Comprehensive Cancer Center Institute for Cancer Genetics, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
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Pasqualucci L, Bereshchenko O, Bereschenko O, Niu H, Klein U, Basso K, Guglielmino R, Cattoretti G, Dalla-Favera R. Molecular Pathogenesis of Non-Hodgkin's Lymphoma: the Role of Bcl-6. Leuk Lymphoma 2011; 44 Suppl 3:S5-12. [PMID: 15202519 DOI: 10.1080/10428190310001621588] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Non-Hodgkin's lymphomas (NHL) form a heterogeneous group of diseases, with diffuse large B-cell lymphoma (DLBCL) comprising the largest subgroup. The commonest chromosomal translocations found in DLBCL are those affecting band 3q27. In 35% of DLBCL cases, as well as in a small fraction of follicular lymphomas, the normal transcriptional regulation of Bcl-6 is disrupted by these chromosomal translocations. In addition, about three-quarters of cases of DLBCL display multiple somatic mutations in the 5' non-coding region of Bcl-6, which occur independently of chromosomal translocations and appear to be due to the IgV-associated somatic hypermutation process. Bcl-6 is a 95-kD nuclear phosphoprotein belonging to the BTB/POZ (bric-a-brac, tramtrack, broad complex/Pox virus zinc finger) zinc finger family of transcription factors. It has been suggested that Bcl-6 is important in the repression of genes involved in the control of lymphocyte activation, differentiation, and apoptosis within the germinal center, and that its down-regulation is necessary for normal B-cells to exit the germinal center. Bcl-6 remains constitutively expressed in a substantial proportion of B-cell lymphomas. Recently, acetylation has been identified as a mode for down-regulating Bcl-6 activity by inhibition of the ability of Bcl-6 to recruit complexes containing histone deacetylases (HDAC). The pharmacologic inhibition of two recently identified deacetylation pathways, HDAC- and silent information regulator (SIR)-2-dependent deacetylation, results in the accumulation of inactive acetylated Bcl-6 and thus in cell cycle arrest and apoptosis in B-cell lymphoma cells. These results reveal a new method of regulating Bcl-6, with the potential for therapeutic exploitation. These studies also indicate a novel mechanism by which acetylation promotes transcription, not only by modifying histones and activating transcriptional activators, but also by inhibiting transcriptional repressors.
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Affiliation(s)
- Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
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Abstract
BCL6 is a transcriptional repressor which has emerged as a critical regulator of germinal centers (GC), the sites where B cells are selected based on the production of antibodies with high affinity for the antigen. BCL6 is also a frequently activated oncogene in the pathogenesis of human B cell lymphomas, most of which derive from the GC B cells. A thorough understanding of the biological role of BCL6 in normal B cell development and lymphomagenesis depends upon the identification of the full set of genes that are targets of its transcriptional regulatory function. Recently, the identification of BCL6 targets has been implemented with the use of genome-wide chromatin immunoprecipitation and gene expression profiling approaches. A large set of promoters have been shown to be physically bound by BCL6, but only a fraction of them appears to be subjected to transcriptional repression in GC B cells. This set of BCL6 targets points to a number of cellular functions which are likely to be directly controlled by BCL6 during GC development, including activation, survival, DNA-damage response, cell cycle arrest, cytokine-, toll-like receptor-, TGFbeta-, WNT-signaling, and differentiation. Overall, BCL6 is revealing its dual role of "safe-keeper" in preventing centroblasts from responding to signals leading to a premature exit from the GC and of contributor to lymphomagenesis by allowing the instauration of conditions favorable to malignant transformation.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
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Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol 2009; 27:829-39. [PMID: 19741643 PMCID: PMC2753889 DOI: 10.1038/nbt.1563] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 08/11/2009] [Indexed: 01/06/2023]
Abstract
The ability of a transcription factor (TF) to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms, resulting in highly context-dependent regulatory networks. However, high-throughput methods for the identification of proteins that affect TF activity are still largely unavailable. Here we introduce an algorithm, modulator inference by network dynamics (MINDy), for the genome-wide identification of post-translational modulators of TF activity within a specific cellular context. When used to dissect the regulation of MYC activity in human B lymphocytes, the approach inferred novel modulators of MYC function, which act by distinct mechanisms, including protein turnover, transcription complex formation and selective enzyme recruitment. MINDy is generally applicable to study the post-translational modulation of mammalian TFs in any cellular context. As such it can be used to dissect context-specific signaling pathways and combinatorial transcriptional regulation.
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Affiliation(s)
- Kai Wang
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
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35
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Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen CZ, Califano A, Dalla-Favera R. Identification of the human mature B cell miRNome. Immunity 2009; 30:744-52. [PMID: 19446474 DOI: 10.1016/j.immuni.2009.03.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 02/09/2009] [Accepted: 03/05/2009] [Indexed: 12/26/2022]
Abstract
The full set of microRNAs (miRNAs) in the human genome is not known. Because presently known miRNAs have been identified by virtue of their abundant expression in a few cell types, many tissue-specific miRNAs remain unrevealed. To understand the role of miRNAs in B cell function and lymphomagenesis, we generated short-RNA libraries from normal human B cells at different stages of development (naive, germinal center, memory) and from a Burkitt lymphoma cell line. A combination of cloning and computational analysis identified 178 miRNAs (miRNome) expressed in normal and/or transformed B cell libraries. Most notably, the B cell miRNome included 75 miRNAs which to our knowledge have not been previously reported and of which 66 have been validated by RNA blot and/or RT-PCR analyses. Numerous miRNAs were expressed in a stage- or transformation-specific fashion in B cells, suggesting specific functional or pathologic roles. These results provide a resource for studying the role of miRNAs in B cell development, immune function, and lymphomagenesis.
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Affiliation(s)
- Katia Basso
- Institute of Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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Abstract
In recent years, we experienced an increasing development of new technologies that aim to comprehensively dissect the molecular genetics of cellular phenotypes. Pioneering studies have been performed on leukemia and lymphoma and then extended to many other types of malignancies. Genome-wide technologies allow taking snapshots of defined cellular context from an unbiased angle highlighting a complexity that we still struggle to fully interpret. The increasing availability of technologies to detect genetic, transcriptional and post-transcriptional characteristics of cellular systems needs to be associated with the development of computational tools to fully investigate these data in an integrated way. The evolution of different genome-wide technologies as well as data mining and integration tools will be discussed following studies performed on normal and malignant human mature B cells.
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Affiliation(s)
- K Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.
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37
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Vakiani E, Basso K, Klein U, Mansukhani MM, Narayan G, Smith PM, Murty VV, Dalla-Favera R, Pasqualucci L, Bhagat G. Genetic and phenotypic analysis of B-cell post-transplant lymphoproliferative disorders provides insights into disease biology. Hematol Oncol 2009; 26:199-211. [PMID: 18457340 DOI: 10.1002/hon.859] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
B-cell post-transplant lymphoproliferative disorders (PTLD) are classified as early lesions, polymorphic lymphomas (P-PTLD) and monomorphic lymphomas (M-PTLD). These morphologic categories are thought to reflect a biologic continuum, although supporting genetic data are lacking. To gain better insights into PTLD pathogenesis, we characterized the phenotypes, immunoglobulin (Ig) gene alterations and non-Ig gene (BCL6, RhoH/TTF, c-MYC, PAX5, CIITA, BCL7A, PIM1) mutations of 21 PTLD, including an IM-like lesion, 8 P-PTLD and 12 M-PTLD. Gene expression profile analysis was also performed in 12 cases. All PTLD with clonal Ig rearrangements showed evidence of germinal centre (GC) transit based on the analysis of Ig and BCL6 gene mutations, and 74% had a non-GC phenotype (BCL6 +/- MUM1+). Although surface Ig abnormalities were seen in 6/19 (32%) PTLD, only three showed 'crippling' Ig mutations indicating other etiologies for loss of the B-cell receptor. Aberrant somatic hypermutation (ASHM) was almost exclusively observed in M-PTLD (8/12 vs. 1/8 P-PTLD) and all three recurrent cases analysed showed additional mutations in genes targeted by ASHM. Gene expression analysis showed distinct clustering of PTLD compared to B-cell non-Hodgkin lymphomas (B-NHL) without segregation of P-PTLD from non-GC M-PTLD or EBV+ from EBV- PTLD. The gene expression pattern of PTLD appeared more related to that of memory and activated B-cells. Together, our results suggest that PTLD represent a distinct type of B-NHL deriving from an antigen experienced B-cell, whose evolution is associated with accrual of genetic lesions.
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Affiliation(s)
- Efsevia Vakiani
- Department of Pathology, Columbia University, New York, NY 10032, USA
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38
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Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Favera RD, Califano A. Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput 2009:264-275. [PMID: 19209707 PMCID: PMC2716143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A key role of signal transduction pathways is to control transcriptional programs in the nucleus as a function of signals received by the cell via complex post-translational modification cascades. This determines cell-context specific responses to environmental stimuli. Given the difficulty of quantitating protein concentration and post-translational modifications, signaling pathway studies are still for the most part conducted one interaction at the time. Thus, genome-wide, cell-context specific dissection of signaling pathways is still an open challenge in molecular systems biology. In this manuscript we extend the MINDy algorithm for the identification of posttranslational modulators of transcription factor activity, to produce a first genome-wide map of the interface between signaling and transcriptional regulatory programs in human B cells. We show that the serine-threonine kinase STK38 emerges as the most pleiotropic signaling protein in this cellular context and we biochemically validate this finding by shRNA-mediated silencing of this kinase, followed by gene expression profile analysis. We also extensively validate the inferred interactions using protein-protein interaction databases and the kinase-substrate interaction prediction algorithm NetworKIN.
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Affiliation(s)
- Kai Wang
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Joint Centers for Systems Biology, Columbia University, New York, NY, USA
| | - Mariano J. Alvarez
- Joint Centers for Systems Biology, Columbia University, New York, NY, USA
| | | | - Rune Linding
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Katia Basso
- Institute of Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Andrea Califano
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Joint Centers for Systems Biology, Columbia University, New York, NY, USA
- Institute of Cancer Genetics, Columbia University, New York, NY, USA
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39
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Montesinos-Rongen M, Brunn A, Bentink S, Basso K, Lim WK, Klapper W, Schaller C, Reifenberger G, Rubenstein J, Wiestler OD, Spang R, Dalla-Favera R, Siebert R, Deckert M. Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell. Leukemia 2007; 22:400-5. [PMID: 17989719 DOI: 10.1038/sj.leu.2405019] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSLs of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B-cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B-cell lymphomas (DLBCLs) and (iii) to be in part assigned to the activated B-cell-like (ABC) or the germinal center B-cell-like (GCB) subtype of DLBCL.
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Affiliation(s)
- M Montesinos-Rongen
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
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40
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Saito M, Gao J, Basso K, Kitagawa Y, Smith PM, Bhagat G, Pernis A, Pasqualucci L, Dalla-Favera R. A signaling pathway mediating downregulation of BCL6 in germinal center B cells is blocked by BCL6 gene alterations in B cell lymphoma. Cancer Cell 2007; 12:280-92. [PMID: 17785208 DOI: 10.1016/j.ccr.2007.08.011] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 06/15/2007] [Accepted: 08/13/2007] [Indexed: 11/16/2022]
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor necessary for the development of germinal centers (GCs) and directly implicated in lymphomagenesis. Post-GC development of B cells requires BCL6 downregulation, while its constitutive expression caused by chromosomal translocations leads to diffuse large B cell lymphoma (DLBCL). Herein we identify a signaling pathway that downregulates BCL6 expression in normal GC B cells and is blocked in a subset of DLBCL due to alterations in the BCL6 gene. Activation of the CD40 receptor leads to NF-kappaB-mediated induction of the IRF4 transcription factor, which, in turn, represses BCL6 expression by binding to its promoter region. A subset of DLBCL displays chromosomal translocations or mutations that disrupt the IRF4-responsive region in the BCL6 promoter and block its downregulation by CD40 signaling.
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Affiliation(s)
- Masumichi Saito
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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41
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Narayan G, Bourdon V, Chaganti S, Arias-Pulido H, Nandula SV, Rao PH, Gissmann L, Dürst M, Schneider A, Pothuri B, Mansukhani M, Basso K, Chaganti RSK, Murty VV. Gene dosage alterations revealed by cDNA microarray analysis in cervical cancer: identification of candidate amplified and overexpressed genes. Genes Chromosomes Cancer 2007; 46:373-84. [PMID: 17243165 DOI: 10.1002/gcc.20418] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Cervical cancer (CC) cells exhibit complex karyotypic alterations, which is consistent with deregulation of numerous critical genes in its formation and progression. To characterize this karyotypic complexity at the molecular level, we used cDNA array comparative genomic hybridization (aCGH) to analyze 29 CC cases and identified a number of over represented and deleted genes. The aCGH analysis revealed at least 17 recurrent amplicons and six common regions of deletions. These regions contain several known tumor-associated genes, such as those involved in transcription, apoptosis, cytoskeletal remodeling, ion-transport, drug metabolism, and immune response. Using the fluorescence in situ hybridization (FISH) approach we demonstrated the presence of high-level amplifications at the 8q24.3, 11q22.2, and 20q13 regions in CC cell lines. To identify amplification-associated genes that correspond to focal amplicons, we examined one or more genes in each of the 17 amplicons by Affymetrix U133A expression arrays and semiquantitative reverse-transcription PCR (RT-PCR) in 31 CC tumors. This analysis exhibited frequent and robust upregulated expression in CC relative to normal cervix for genes EPHB2 (1p36), CDCA8 (1p34.3), AIM2 (1q22-23), RFC4, MUC4, and HRASLS (3q27-29), SKP2 (5p12-13), CENTD3 (5q31.3), PTK2, RECQL4 (8q24), MMP1 and MMP13 (11q22.2), AKT1 (14q32.3), ABCC3 (17q21-22), SMARCA4 (19p13.3) LIG1 (19q13.3), UBE2C (20q13.1), SMC1L1 (Xp11), KIF4A (Xq12), TMSNB (Xq22), and CSAG2 (Xq28). Thus, the gene dosage and expression profiles generated here have enabled the identification of focal amplicons characteristic for the CC genome and facilitated the validation of relevant genes in these amplicons. These data, thus, form an important step toward the identification of biologically relevant genes in CC pathogenesis. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
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Affiliation(s)
- Gopeshwar Narayan
- Department of Pathology, Columbia University Medical Center, NY 10032, USA
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42
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Piccaluga PP, Agostinelli C, Califano A, Rossi M, Basso K, Zupo S, Went P, Klein U, Zinzani PL, Baccarani M, Dalla Favera R, Pileri SA. Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets. J Clin Invest 2007; 117:823-34. [PMID: 17304354 PMCID: PMC1794115 DOI: 10.1172/jci26833] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Accepted: 12/14/2006] [Indexed: 12/16/2022] Open
Abstract
Peripheral T cell lymphoma, unspecified (PTCL/U), the most common form of PTCL, displays heterogeneous morphology and phenotype, poor response to treatment, and poor prognosis. We demonstrate that PTCL/U shows a gene expression profile clearly distinct from that of normal T cells. Comparison with the profiles of purified T cell subpopulations (CD4+, CD8+, resting [HLA-DR-], and activated [HLA-DR+]) reveals that PTCLs/U are most closely related to activated peripheral T lymphocytes, either CD4+ or CD8+. Interestingly, the global gene expression profile cannot be surrogated by routine CD4/CD8 immunohistochemistry. When compared with normal T cells, PTCLs/U display deregulation of functional programs often involved in tumorigenesis (e.g., apoptosis, proliferation, cell adhesion, and matrix remodeling). Products of deregulated genes can be detected in PTCLs/U by immunohistochemistry with an ectopic, paraphysiologic, or stromal location. PTCLs/U aberrantly express, among others, PDGFRalpha, a tyrosine-kinase receptor, whose deregulation is often related to a malignant phenotype. Notably, both phosphorylation of PDGFRalpha and sensitivity of cultured PTCL cells to imatinib (as well as to an inhibitor of histone deacetylase) were found. These results, which might be extended to other more rare PTCL categories, provide insight into tumor pathogenesis and clinical management of PTCL/U.
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Affiliation(s)
- Pier Paolo Piccaluga
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Claudio Agostinelli
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Andrea Califano
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Maura Rossi
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Katia Basso
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Simonetta Zupo
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Philip Went
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Ulf Klein
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Pier Luigi Zinzani
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Michele Baccarani
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Riccardo Dalla Favera
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Stefano A. Pileri
- Institute of Hematology and Medical Oncology “L. and A. Seràgnoli,” Hematology and Hematopathology Units, Sant’Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
Institute for Cancer Genetics and
Center for Computational Biology and Biochemistry, Columbia University, New York, New York, USA.
S.S.D. Diagnostica Malattie Linfoproliferative, Istituto Nazionale per la Ricerca sul Cancro, Genoa University, Genoa, Italy.
Institute of Pathology, Basel University, Basel, Switzerland.
Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
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Abstract
Gene expression profiling is a powerful tool to analyze the complexity of cancer biology. Recent methods allow the generation of gene expression profiles for all known genes in the human genome. The genome-wide analysis of the gene expression patterns of neoplastic and normal cells provides insights into: (1) the identification of previously unknown tumor subtypes; (2) the normal cellular counterparts of tumor cells; (3) the identification of cellular pathways that may be affected by malignant transformation; (4) the identification of new diagnostic markers and potential therapeutic targets. This chapter summarizes experimental approaches addressing these goals using examples from studies on B-cell malignancies.
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Affiliation(s)
- Katia Basso
- Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, College of Physicians and Surgeons, New York, NY, USA
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44
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Shaknovich R, Basso K, Bhagat G, Mansukhani M, Hatzivassiliou G, Murty VV, Buettner M, Niedobitek G, Alobeid B, Cattoretti G. Identification of rare Epstein-Barr virus infected memory B cells and plasma cells in non-monomorphic post-transplant lymphoproliferative disorders and the signature of viral signaling. Haematologica 2006; 91:1313-20. [PMID: 17018379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND AND OBJECTIVES In early and polymorphic post-transplant lymphoproliferative disorders (PTLD) Epstein-Barr virus (EBV), through its latency proteins, drives the proliferation of B lymphocytes, a process which in immunocompetent individuals leads to the establishment of latently infected memory B cells. DESIGN AND METHODS We analyzed 11 cases, which included early and polymorphic PTLD, and 12 controls for latency of EBV infection and their antigenic profile. RESULTS We identified a minority of terminally differentiated EBER+ IRTA1+ memory B cells and EBER+ CD138+ PRDM1+ plasma cells in these samples. These elements were identified both in PTLD and in tumor-free tonsils from post-transplant patients but not in EBV- control tonsils. The expression of EBV latency proteins is heterogeneous, and is associated with activation of the NF-kB pathway. EBV signaling (through EBNA2, LMP1 and LMP2A) and NF-kB activation correlated with upregulation of target proteins: cMYC, JunB, CCL22, TRAF1 and IRF4. EBV-infected lymphocytes in early and polymorphic PTLDs represent a mixture of latencies II, III and, in at least 1/3 of infected cells, of latency 0. INTERPRETATION AND CONCLUSIONS EBV infection correlates with NF-kB activation, with EBV-dependent cell signaling, and lastly, with the presence of EBV-infected plasma cells and memory cells.
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Affiliation(s)
- Rita Shaknovich
- Department of Pathology, Columbia University Medical Center, Columbia University, New York, NY 10032, USA.
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45
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Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006; 7 Suppl 1:S7. [PMID: 16723010 PMCID: PMC1810318 DOI: 10.1186/1471-2105-7-s1-s7] [Citation(s) in RCA: 1542] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the majority of indirect interactions inferred by co-expression methods. Results We prove that ARACNE reconstructs the network exactly (asymptotically) if the effect of loops in the network topology is negligible, and we show that the algorithm works well in practice, even in the presence of numerous loops and complex topologies. We assess ARACNE's ability to reconstruct transcriptional regulatory networks using both a realistic synthetic dataset and a microarray dataset from human B cells. On synthetic datasets ARACNE achieves very low error rates and outperforms established methods, such as Relevance Networks and Bayesian Networks. Application to the deconvolution of genetic networks in human B cells demonstrates ARACNE's ability to infer validated transcriptional targets of the cMYC proto-oncogene. We also study the effects of misestimation of mutual information on network reconstruction, and show that algorithms based on mutual information ranking are more resilient to estimation errors. Conclusion ARACNE shows promise in identifying direct transcriptional interactions in mammalian cellular networks, a problem that has challenged existing reverse engineering algorithms. This approach should enhance our ability to use microarray data to elucidate functional mechanisms that underlie cellular processes and to identify molecular targets of pharmacological compounds in mammalian cellular networks.
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Affiliation(s)
- Adam A Margolin
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
| | - Ilya Nemenman
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY 10032
| | - Chris Wiggins
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10032
| | | | | | - Andrea Califano
- Department of Biomedical Informatics, Columbia University, New York, NY 10032
- Joint Centers for Systems Biology, Columbia University, New York, NY 10032
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46
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Phan RT, Saito M, Basso K, Niu H, Dalla-Favera R. BCL6 interacts with the transcription factor Miz-1 to suppress the cyclin-dependent kinase inhibitor p21 and cell cycle arrest in germinal center B cells. Nat Immunol 2005; 6:1054-60. [PMID: 16142238 DOI: 10.1038/ni1245] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Accepted: 08/01/2005] [Indexed: 01/04/2023]
Abstract
The BCL6 proto-oncogene encodes a transcriptional repressor that is required for germinal center formation and has been linked to lymphomagenesis. BCL6 functions by directly binding to specific DNA sequences and suppressing the transcription of target genes. Here we report an alternative mechanism by which BCL6 controls the transcription of genes lacking a BCL6 binding site and show that this mechanism was required for the prevention of tumor suppressor p53-independent cell cycle arrest in germinal center B cells. BCL6 interacted with the transcriptional activator Miz-1 and, via Miz-1, bound to the promoter and suppressed transcription of the cell cycle arrest gene CDKN1A. Through this mechanism, BCL6 may facilitate the proliferative expansion of germinal centers during the normal immune response and, when deregulated, the pathological expansion of B cell lymphomas.
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Affiliation(s)
- Ryan T Phan
- Institute for Cancer Genetics, Department of Pathology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
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47
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Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005; 37:382-90. [PMID: 15778709 DOI: 10.1038/ng1532] [Citation(s) in RCA: 911] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 02/08/2005] [Indexed: 12/16/2022]
Abstract
Cellular phenotypes are determined by the differential activity of networks linking coregulated genes. Available methods for the reverse engineering of such networks from genome-wide expression profiles have been successful only in the analysis of lower eukaryotes with simple genomes. Using a new method called ARACNe (algorithm for the reconstruction of accurate cellular networks), we report the reconstruction of regulatory networks from expression profiles of human B cells. The results are suggestive a hierarchical, scale-free network, where a few highly interconnected genes (hubs) account for most of the interactions. Validation of the network against available data led to the identification of MYC as a major hub, which controls a network comprising known target genes as well as new ones, which were biochemically validated. The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, 1300 St. Nicholas Avenue, Room 912, New York, New York 10032, USA
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Abstract
Substantial evidence indicates that signaling through the CD40 receptor (CD40) is required for germinal center (GC) and memory B-cell formation. However, it is not fully understood at which stages of B-cell development the CD40 pathway is activated in vivo. To address this question, we induced CD40 signaling in human transformed GC B cells in vitro and identified a CD40 gene expression signature by DNA microarray analysis. This signature was then investigated in the gene expression profiles of normal B cells and found in pre- and post-GC B cells (naive and memory) but, surprisingly, not in GC B cells. This finding was validated in lymphoid tissues by showing that the nuclear factor-kappaB (NF-kappaB) transcription factors, which translocate to the nucleus upon CD40 stimulation, are retained in the cytoplasm in most GC B cells, indicating the absence of CD40 signaling. Nevertheless, a subset of centrocytes and B cells in the subepithelium showed nuclear staining of multiple NF-kappaB subunits, suggesting that a fraction of naive and memory B cells may be subject to CD40 signaling or to other signals that activate NF-kappaB. Together, these results show that GC expansion occurs in the absence of CD40 signaling, which may act only in the initial and final stages of the GC reaction.
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Affiliation(s)
- Katia Basso
- Institute for Cancer Genetics, Department of Pathology and Genetics and Development, Joint Centers for Systems Biology, Columbia University, 1150 St Nicholas Ave, New York, NY 10032, USA
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Basso K, Liso A, Tiacci E, Benedetti R, Pulsoni A, Foa R, Di Raimondo F, Ambrosetti A, Califano A, Klein U, Dalla Favera R, Falini B. Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. ACTA ACUST UNITED AC 2004; 199:59-68. [PMID: 14707115 PMCID: PMC1887727 DOI: 10.1084/jem.20031175] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hairy cell leukemia (HCL) is a chronic B cell malignancy characterized by the diffuse infiltration of bone marrow and spleen by cells displaying a typical "hairy" morphology. However, the nature of the HCL phenotype and its relationship to normal B cells and to other lymphoma subtypes remains unclear. Using gene expression profiling, we show here that HCL displays a homogeneous pattern of gene expression, which is clearly distinct from that of other B cell non-Hodgkin lymphomas. Comparison with the gene expression profiles of purified normal B cell subpopulations, including germinal center (GC), pre-GC (naive), and post-GC (memory) B cells, shows that HCL cells are more related to memory cells, suggesting a derivation from this B cell population. Notably, when compared with memory cells, HCL cells displayed a remarkable conservation in proliferation, apoptosis, and DNA metabolism programs, whereas they appeared significantly altered in the expression of genes controlling cell adhesion and response to chemokines. Finally, these analyses have identified several genes that are specifically expressed in HCL and whose expression was confirmed at the protein level by immunocytochemical analysis of primary HCL cases. These results have biological implications relevant to the pathogenesis of this malignancy as well as clinical implications for its diagnosis and therapy.
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Affiliation(s)
- Katia Basso
- Institute of Hematology, Policlinico Monteluce, Perugia 06100, Italy
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Hoefnagel JJ, Dijkman R, Basso K, Jansen PM, Hallermann C, Willemze R, Tensen CP, Vermeer MH. Distinct types of primary cutaneous large B-cell lymphoma identified by gene expression profiling. Blood 2004; 105:3671-8. [PMID: 15308563 DOI: 10.1182/blood-2004-04-1594] [Citation(s) in RCA: 209] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the European Organization for Research and Treatment of Cancer (EORTC) classification 2 types of primary cutaneous large B-cell lymphoma (PCLBCL) are distinguished: primary cutaneous follicle center cell lymphomas (PCFCCL) and PCLBCL of the leg (PCLBCL-leg). Distinction between both groups is considered important because of differences in prognosis (5-year survival > 95% and 52%, respectively) and the first choice of treatment (radiotherapy or systemic chemotherapy, respectively), but is not generally accepted. To establish a molecular basis for this subdivision in the EORTC classification, we investigated the gene expression profiles of 21 PCLBCLs by oligonucleotide microarray analysis. Hierarchical clustering based on a B-cell signature (7450 genes) classified PCLBCL into 2 distinct subgroups consisting of, respectively, 8 PCFCCLs and 13 PCLBCLsleg. PCLBCLs-leg showed increased expression of genes associated with cell proliferation; the proto-oncogenes Pim-1, Pim-2, and c-Myc; and the transcription factors Mum1/IRF4 and Oct-2. In the group of PCFCCL high expression of SPINK2 was observed. Further analysis suggested that PCFCCLs and PCLBCLs-leg have expression profiles similar to that of germinal center B-cell-like and activated B-cell-like diffuse large B-cell lymphoma, respectively. The results of this study suggest that different pathogenetic mechanisms are involved in the development of PCFCCLs and PCLBCLs-leg and provide molecular support for the subdivision used in the EORTC classification.
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Affiliation(s)
- Juliette J Hoefnagel
- Department of Dermatology, B1-Q, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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