51
|
Three-dimensional genome rewiring during the development of antibody-secreting cells. Biochem Soc Trans 2021; 48:1109-1119. [PMID: 32453419 PMCID: PMC7329350 DOI: 10.1042/bst20191104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 01/08/2023]
Abstract
The development of B lymphocytes into antibody-secreting plasma cells is central to the adaptive immune system in that it confers protective and specific antibody response against invading pathogen. This developmental process involves extensive morphological and functional alterations that begin early after antigenic stimulation. These include chromatin restructuring that is critical in regulating gene expression, DNA rearrangement and other cellular processes. Here we outline the recent understanding of the three-dimensional architecture of the genome, specifically focused on its contribution to the process of B cell activation and terminal differentiation into antibody-secreting cells.
Collapse
|
52
|
Rivas MA, Meydan C, Chin CR, Challman MF, Kim D, Bhinder B, Kloetgen A, Viny AD, Teater MR, McNally DR, Doane AS, Béguelin W, Fernández MTC, Shen H, Wang X, Levine RL, Chen Z, Tsirigos A, Elemento O, Mason CE, Melnick AM. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol 2021; 22:240-253. [PMID: 33432228 PMCID: PMC7855695 DOI: 10.1038/s41590-020-00827-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/25/2020] [Indexed: 01/28/2023]
Abstract
During the germinal center (GC) reaction, B cells undergo extensive redistribution of cohesin complex and three-dimensional reorganization of their genomes. Yet, the significance of cohesin and architectural programming in the humoral immune response is unknown. Herein we report that homozygous deletion of Smc3, encoding the cohesin ATPase subunit, abrogated GC formation, while, in marked contrast, Smc3 haploinsufficiency resulted in GC hyperplasia, skewing of GC polarity and impaired plasma cell (PC) differentiation. Genome-wide chromosomal conformation and transcriptional profiling revealed defects in GC B cell terminal differentiation programs controlled by the lymphoma epigenetic tumor suppressors Tet2 and Kmt2d and failure of Smc3-haploinsufficient GC B cells to switch from B cell- to PC-defining transcription factors. Smc3 haploinsufficiency preferentially impaired the connectivity of enhancer elements controlling various lymphoma tumor suppressor genes, and, accordingly, Smc3 haploinsufficiency accelerated lymphomagenesis in mice with constitutive Bcl6 expression. Collectively, our data indicate a dose-dependent function for cohesin in humoral immunity to facilitate the B cell to PC phenotypic switch while restricting malignant transformation.
Collapse
MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins/deficiency
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Chondroitin Sulfate Proteoglycans/deficiency
- Chondroitin Sulfate Proteoglycans/genetics
- Chondroitin Sulfate Proteoglycans/metabolism
- Chromosomal Proteins, Non-Histone/deficiency
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dioxygenases
- Gene Deletion
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Haploinsufficiency
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Immunity, Humoral
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- Signal Transduction
- Cohesins
- Mice
Collapse
Affiliation(s)
- Martín A Rivas
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher R Chin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matt F Challman
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Aaron D Viny
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matt R Teater
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dylan R McNally
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Doane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Wendy Béguelin
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Hao Shen
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiang Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Institute for Computational Medicine, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
53
|
Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun 2021; 12:651. [PMID: 33510161 PMCID: PMC7844026 DOI: 10.1038/s41467-020-20849-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.
Collapse
|
54
|
Abstract
Although we are just beginning to understand the mechanisms that regulate the epigenome, aberrant epigenetic programming has already emerged as a hallmark of hematologic malignancies including acute myeloid leukemia (AML) and B-cell lymphomas. Although these diseases arise from the hematopoietic system, the epigenetic mechanisms that drive these malignancies are quite different. Yet, in all of these tumors, somatic mutations in transcription factors and epigenetic modifiers are the most commonly mutated set of genes and result in multilayered disruption of the epigenome. Myeloid and lymphoid neoplasms generally manifest epigenetic allele diversity, which contributes to tumor cell population fitness regardless of the underlying genetics. Epigenetic therapies are emerging as one of the most promising new approaches for these patients. However, effective targeting of the epigenome must consider the need to restore the various layers of epigenetic marks, appropriate biological end points, and specificity of therapeutic agents to truly realize the potential of this modality.
Collapse
Affiliation(s)
- Cihangir Duy
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Wendy Béguelin
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| |
Collapse
|
55
|
Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
Collapse
Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
56
|
Sangaletti S, Iannelli F, Zanardi F, Cancila V, Portararo P, Botti L, Vacca D, Chiodoni C, Di Napoli A, Valenti C, Rizzello C, Vegliante MC, Pisati F, Gulino A, Ponzoni M, Colombo MP, Tripodo C. Intra-tumour heterogeneity of diffuse large B-cell lymphoma involves the induction of diversified stroma-tumour interfaces. EBioMedicine 2020; 61:103055. [PMID: 33096480 PMCID: PMC7581880 DOI: 10.1016/j.ebiom.2020.103055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Intra-tumour heterogeneity in lymphoid malignancies encompasses selection of genetic events and epigenetic regulation of transcriptional programs. Clonal-related neoplastic cell populations are unsteadily subjected to immune editing and metabolic adaptations within different tissue microenvironments. How tissue-specific mesenchymal cells impact on the diversification of aggressive lymphoma clones is still unknown. Methods Combining in situ quantitative immunophenotypical analyses and RNA sequencing we investigated the intra-tumour heterogeneity and the specific mesenchymal modifications that are associated with A20 diffuse large B-cell lymphoma (DLBCL) cells seeding of different tissue microenvironments. Furthermore, we characterized features of lymphoma-associated stromatogenesis in human DLBCL samples using Digital Spatial Profiling, and established their relationship with prognostically relevant variables, such as MYC. Findings We found that the tissue microenvironment casts a relevant influence over A20 transcriptional landscape also impacting on Myc and DNA damage response programs. Extending the investigation to mice deficient for the matricellular protein SPARC, a stromal prognostic factor in human DLBCL, we demonstrated a different immune imprint on A20 cells according to stromal Sparc proficiency. Through Digital Spatial Profiling of 87 immune and stromal genes on human nodal DLBCL regions characterized by different mesenchymal composition, we demonstrate intra-lesional heterogeneity arising from diversified mesenchymal contextures and impacting on the stromal and immune milieu. Interpretation Our study provides experimental evidence that stromal microenvironment generates topological determinants of intra-tumour heterogeneity in DLBCL involving key transcriptional pathways such as Myc expression, damage response programs and immune checkpoints. Funding This study has been supported by the Italian Foundation for Cancer Research (AIRC) (grants 15999 and 22145 to C. Tripodo) and by the University of Palermo.
Collapse
MESH Headings
- Animals
- Biomarkers, Tumor
- Cell Line, Tumor
- Computational Biology/methods
- Disease Models, Animal
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Genetic Heterogeneity
- Humans
- Immunophenotyping
- In Situ Hybridization
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice
- Models, Biological
- Phenotype
- Prognosis
- Sequence Analysis, RNA
- Stromal Cells/metabolism
- Stromal Cells/pathology
- Transcriptome
- Tumor Microenvironment/genetics
Collapse
Affiliation(s)
- Sabina Sangaletti
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Fabio Iannelli
- Bioinformatics Core Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Federica Zanardi
- Bioinformatics Core Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, University of Palermo, Palermo, Italy
| | - Paola Portararo
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Laura Botti
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Davide Vacca
- Tumor Immunology Unit, University of Palermo, Palermo, Italy
| | - Claudia Chiodoni
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Arianna Di Napoli
- Pathology Unit, Sapienza University of Rome, Sant'Andrea Hospital, Rome, Italy
| | - Cesare Valenti
- Department of Mathematics and Informatics, University of Palermo, Palermo, Italy
| | - Celeste Rizzello
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Federica Pisati
- Tumor and Microenvironment Histopathology Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Maurilio Ponzoni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University Milan, Milan, Italy
| | - Mario Paolo Colombo
- Molecular Immunology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Palermo, Italy; Tumor and Microenvironment Histopathology Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy.
| |
Collapse
|
57
|
Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
Collapse
Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
| |
Collapse
|
58
|
Sun D, Stopka-Farooqui U, Barry S, Aksoy E, Parsonage G, Vossenkämper A, Capasso M, Wan X, Norris S, Marshall JL, Clear A, Gribben J, MacDonald TT, Buckley CD, Korbonits M, Haworth O. Aryl Hydrocarbon Receptor Interacting Protein Maintains Germinal Center B Cells through Suppression of BCL6 Degradation. Cell Rep 2020; 27:1461-1471.e4. [PMID: 31042473 PMCID: PMC6506688 DOI: 10.1016/j.celrep.2019.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/03/2018] [Accepted: 03/28/2019] [Indexed: 10/29/2022] Open
Abstract
B cell lymphoma-6 (BCL6) is highly expressed in germinal center B cells, but how its expression is maintained is still not completely clear. Aryl hydrocarbon receptor interacting protein (AIP) is a co-chaperone of heat shock protein 90. Deletion of Aip in B cells decreased BCL6 expression, reducing germinal center B cells and diminishing adaptive immune responses. AIP was required for optimal AKT signaling in response to B cell receptor stimulation, and AIP protected BCL6 from ubiquitin-mediated proteasomal degradation by the E3-ubiquitin ligase FBXO11 by binding to the deubiquitinase UCHL1, thus helping to maintain the expression of BCL6. AIP was highly expressed in primary diffuse large B cell lymphomas compared to healthy tissue and other tumors. Our findings describe AIP as a positive regulator of BCL6 expression with implications for the pathobiology of diffuse large B cell lymphoma.
Collapse
Affiliation(s)
- Dijue Sun
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Urszula Stopka-Farooqui
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sayka Barry
- Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ezra Aksoy
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Gregory Parsonage
- Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anna Vossenkämper
- Center for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Melania Capasso
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Xinyu Wan
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sherine Norris
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jennifer L Marshall
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew Clear
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - John Gribben
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Thomas T MacDonald
- Center for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Christopher D Buckley
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK
| | - Márta Korbonits
- Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Oliver Haworth
- Center of Biochemical Pharmacology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Department of Biological Sciences, Westminster University, London W1W 6UW, UK.
| |
Collapse
|
59
|
Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Nat Commun 2020; 11:3294. [PMID: 32620744 PMCID: PMC7335045 DOI: 10.1038/s41467-020-17089-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/02/2020] [Indexed: 01/14/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is mediated by autoreactive antibodies that damage multiple tissues. Genome-wide association studies (GWAS) link >60 loci with SLE risk, but the causal variants and effector genes are largely unknown. We generated high-resolution spatial maps of SLE variant accessibility and gene connectivity in human follicular helper T cells (TFH), a cell type required for anti-nuclear antibodies characteristic of SLE. Of the ~400 potential regulatory variants identified, 90% exhibit spatial proximity to genes distant in the 1D genome sequence, including variants that loop to regulate the canonical TFH genes BCL6 and CXCR5 as confirmed by genome editing. SLE ‘variant-to-gene’ maps also implicate genes with no known role in TFH/SLE disease biology, including the kinases HIPK1 and MINK1. Targeting these kinases in TFH inhibits production of IL-21, a cytokine crucial for class-switched B cell antibodies. These studies offer mechanistic insight into the SLE-associated regulatory architecture of the human genome. T cells are a major cell type involved in systemic lupus erythematosus (SLE). Here, the authors use promoter capture-C and ATAC-seq in human follicular T helper cells to identify SLE genes distant from GWAS loci (via 3D interaction) and validate the function of key regulatory elements and genes in vitro.
Collapse
|
60
|
Bortnick A, He Z, Aubrey M, Chandra V, Denholtz M, Chen K, Lin YC, Murre C. Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs. Cell Rep 2020; 31:107470. [PMID: 32268089 PMCID: PMC10871151 DOI: 10.1016/j.celrep.2020.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/31/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
The transition from the follicular B to the plasma cell stage is associated with large-scale changes in cell morphology. Here, we examine whether plasma cell development is also associated with changes in nuclear architecture. We find that the onset of plasma cell development is concomitant with a decline in remote genomic interactions; a gain in euchromatic character at loci encoding for factors that specify plasma cell fate, including Prdm1 and Atf4; and establishment of de novo inter-chromosomal hubs. We find that, in developing plasma cells and concurrent with transcriptional silencing, the Ebf1 locus repositions from an euchromatic to peri-centromeric heterochromatic environment. Finally, we find that inter-chromosomal hubs are enriched for the deposition of either H3K27Ac or H3K27me3. These data indicate that plasma cell fate is orchestrated by elaborate changes in genome topology and that epigenetic marks, linked with super-enhancers or transcriptionally repressed regions, are enriched at inter-chromosomal hubs.
Collapse
Affiliation(s)
- Alexandra Bortnick
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoren He
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Aubrey
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Denholtz
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kenian Chen
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246, USA
| | - Yin C Lin
- Baylor Institute for Immunology Research, Baylor Research Institute, Dallas, TX 75246, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
61
|
Luo H, Yu Q, Liu Y, Tang M, Liang M, Zhang D, Xiao TS, Wu L, Tan M, Ruan Y, Bungert J, Lu J. LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding. SCIENCE ADVANCES 2020; 6:eaaw4651. [PMID: 32128389 PMCID: PMC7030924 DOI: 10.1126/sciadv.aaw4651] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Chromatin topological organization is instrumental in gene transcription. Gene-enhancer interactions are accommodated in the same CTCF-mediated insulated neighborhoods. However, it remains poorly understood whether and how the 3D genome architecture is dynamically restructured by external signals. Here, we report that LATS kinases phosphorylated CTCF in the zinc finger (ZF) linkers and disabled its DNA-binding activity. Cellular stress induced LATS nuclear translocation and CTCF ZF linker phosphorylation, and altered the landscape of CTCF genomic binding partly by dissociating it selectively from a small subset of its genomic binding sites. These sites were highly enriched for the boundaries of chromatin domains containing LATS signaling target genes. The stress-induced CTCF phosphorylation and locus-specific dissociation from DNA were LATS-dependent. Loss of CTCF binding disrupted local chromatin domains and down-regulated genes located within them. The study suggests that external signals may rapidly modulate the 3D genome by affecting CTCF genomic binding through ZF linker phosphorylation.
Collapse
Affiliation(s)
- Huacheng Luo
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Qin Yu
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ming Tang
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mingwei Liang
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dingpeng Zhang
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lizi Wu
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ming Tan
- Center for Cell Death and Metabolism, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36688, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
62
|
Peters R, Stevenson M. Immunological detection of Zika virus: A summary in the context of general viral diagnostics. J Microbiol Methods 2020. [DOI: 10.1016/bs.mim.2019.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
63
|
Pasqualucci L. Molecular pathogenesis of germinal center-derived B cell lymphomas. Immunol Rev 2019; 288:240-261. [PMID: 30874347 DOI: 10.1111/imr.12745] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
B cell lymphomas comprise a heterogeneous group of genetically, biologically, and clinically distinct neoplasms that, in most cases, originate from the clonal expansion of B cells in the germinal center (GC). In recent years, the advent of novel genomics technologies has revolutionized our understanding of the molecular pathogenesis of lymphoid malignancies as a multistep process that requires the progressive accumulation of multiple genetic and epigenetic alterations. A common theme that emerged from these studies is the ability of lymphoma cells to co-opt the same biological programs and signal transduction networks that operate during the normal GC reaction, and misuse them for their own survival advantage. This review summarizes recent progress in the understanding of the genetic and epigenetic mechanisms that drive the malignant transformation of GC B cells. These insights provide a conceptual framework for the identification of cellular pathways that may be explored for precision medicine approaches.
Collapse
Affiliation(s)
- Laura Pasqualucci
- Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York City, New York
| |
Collapse
|
64
|
Azagra A, Marina-Zárate E, Ramiro AR, Javierre BM, Parra M. From Loops to Looks: Transcription Factors and Chromatin Organization Shaping Terminal B Cell Differentiation. Trends Immunol 2019; 41:46-60. [PMID: 31822368 DOI: 10.1016/j.it.2019.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
B lymphopoiesis is tightly regulated at the level of gene transcription. In recent years, investigators have shed light on the transcription factor networks and the epigenetic machinery involved at all differentiation steps of mammalian B cell development. During terminal differentiation, B cells undergo dramatic changes in gene transcriptional programs to generate germinal center B cells, plasma cells and memory B cells. Recent evidence indicates that mature B cell formation involves an essential contribution from 3D chromatin conformations through its interplay with transcription factors and epigenetic machinery. Here, we provide an up-to-date overview of the coordination between transcription factors, epigenetic changes, and chromatin architecture during terminal B cell differentiation, focusing on recent discoveries and technical advances for studying 3D chromatin structures.
Collapse
Affiliation(s)
- Alba Azagra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain
| | - Ester Marina-Zárate
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Biola M Javierre
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain.
| | - Maribel Parra
- Lymphocyte Development and Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-Germans Trias i Pujol, Badalona, Spain.
| |
Collapse
|
65
|
Choi SY, Pi JH, Park SK, Kang CJ. Crlz-1 Controls Germinal Center Reaction by Relaying a Wnt Signal to the Bcl-6 Expression in Centroblasts during Humoral Immune Responses. THE JOURNAL OF IMMUNOLOGY 2019; 203:2630-2643. [PMID: 31586036 DOI: 10.4049/jimmunol.1900326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/09/2019] [Indexed: 01/11/2023]
Abstract
Crlz-1 was expressed along with Wnt3a in the rapidly proliferating centroblasts within the dark zone of germinal center (GC) during humoral immune responses. Significantly, Crlz-1 relayed a Wnt/β-catenin signal to the expression of Bcl-6, the master regulator of centroblasts, by mobilizing the cytoplasmic CBFβ into the nucleus to allow Runx/CBFβ heterodimerization and its subsequent binding to the Bcl-6 promoter. The knockdown of Crlz-1 or β-catenin, as well as inhibition of Wnt signaling in the centroblasts, led to the decreased expression of Bcl-6 and, thereby, the altered expression of its various target genes, resulting in their diminished proliferation. Consistently, the administration of Wnt inhibitors into the immunized mice impaired or abolished GC reaction, with concomitant decreases of Crlz-1 and Bcl-6 expression and, thus, centroblastic proliferation. Our observation that Wnt/β-catenin signaling via Crlz-1 regulates GC reaction would suggest developmental strategies for vaccine adjuvants and cancer therapeutics because both immune efficacy and accidental lymphoma depend on GC reaction. Our studies of Crlz-1 were performed using human cell lines, mice, and their primary cells.
Collapse
Affiliation(s)
- Seung Young Choi
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Giheung, Yongin, Gyeonggi 17104, Republic of Korea; and
| | - Joo Hyun Pi
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Giheung, Yongin, Gyeonggi 17104, Republic of Korea; and
| | - Sung-Kyun Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Chang Joong Kang
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Giheung, Yongin, Gyeonggi 17104, Republic of Korea; and
| |
Collapse
|
66
|
Suppression of BCL6 function by HDAC inhibitor mediated acetylation and chromatin modification enhances BET inhibitor effects in B-cell lymphoma cells. Sci Rep 2019; 9:16495. [PMID: 31712669 PMCID: PMC6848194 DOI: 10.1038/s41598-019-52714-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Multiple genetic aberrations in the regulation of BCL6, including in acetyltransferase genes, occur in clinically aggressive B-cell lymphomas and lead to higher expression levels and activity of this transcriptional repressor. BCL6 is, therefore, an attractive target for therapy in aggressive lymphomas. In this study romidepsin, a potent histone deacetylase inhibitor (HDACi), induced apoptosis and cell cycle arrest in Burkitt and diffuse large B-cell lymphoma cell lines, which are model cells for studying the mechanism of action of BCL6. Romidepsin caused BCL6 acetylation at early timepoints inhibiting its function, while at later timepoints BCL6 expression was reduced and target gene expression increased due to chromatin modification. MYC contributes to poor prognosis in aggressive lymphoma. MYC function is reduced by inhibition of chromatin readers of the bromodomain and extra-terminal repeat (BET) family, which includes BRD4. The novel combination of romidepsin and JQ1, a BRD4 inhibitor was investigated and showed synergy. Collectively we suggest that the combination of HDACi and BRD4i should be pursued in further pre-clinical testing.
Collapse
|
67
|
Zhang H, Kuchroo V. Epigenetic and transcriptional mechanisms for the regulation of IL-10. Semin Immunol 2019; 44:101324. [PMID: 31676122 DOI: 10.1016/j.smim.2019.101324] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023]
Abstract
IL-10 is a critical immunoregulatory cytokine expressed in virtually all immune cell types. Maintaining a delicate balance between effective immune response and tolerance requires meticulous and dynamic control of IL-10 expression both epigenetically and transcriptionally. In this Review, we describe the epigenetic mechanisms controlling IL-10 expression, including chromatin remodeling, 3D chromatin loops, histone modification and DNA methylation. We discuss the role of transcription factors in directing chromatin modifications, with a special highlight on the emerging concept of pioneer transcription factors in setting up the chromatin landscape in T helper cells for IL-10 induction. Besides summarizing the recent progress on transcriptional regulation in specialized IL-10 producers such as type 1 regulatory T cells, regulatory B cells and regulatory innate lymphoid cells, we also discuss common transcriptional mechanisms for IL-10 regulation that are shared with other IL-10 producing cells.
Collapse
Affiliation(s)
- Huiyuan Zhang
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, United States
| | - Vijay Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, United States; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, United States; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States.
| |
Collapse
|
68
|
Cildir G, Toubia J, Yip KH, Zhou M, Pant H, Hissaria P, Zhang J, Hong W, Robinson N, Grimbaldeston MA, Lopez AF, Tergaonkar V. Genome-wide Analyses of Chromatin State in Human Mast Cells Reveal Molecular Drivers and Mediators of Allergic and Inflammatory Diseases. Immunity 2019; 51:949-965.e6. [PMID: 31653482 DOI: 10.1016/j.immuni.2019.09.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 02/18/2019] [Accepted: 09/25/2019] [Indexed: 12/21/2022]
Abstract
Mast cells (MCs) are versatile immune cells capable of rapidly responding to a diverse range of extracellular cues. Here, we mapped the genomic and transcriptomic changes in human MCs upon diverse stimuli. Our analyses revealed broad H3K4me3 domains and enhancers associated with activation. Notably, the rise of intracellular calcium concentration upon immunoglobulin E (IgE)-mediated crosslinking of the high-affinity IgE receptor (FcεRI) resulted in genome-wide reorganization of the chromatin landscape and was associated with a specific chromatin signature, which we term Ca2+-dependent open chromatin (COC) domains. Examination of differentially expressed genes revealed potential effectors of MC function, and we provide evidence for fibrinogen-like protein 2 (FGL2) as an MC mediator with potential relevance in chronic spontaneous urticaria. Disease-associated single-nucleotide polymorphisms mapped onto cis-regulatory regions of human MCs suggest that MC function may impact a broad range of pathologies. The datasets presented here constitute a resource for the further study of MC function.
Collapse
Affiliation(s)
- Gökhan Cildir
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Kwok Ho Yip
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Mingyan Zhou
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Harshita Pant
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | | | - Jingxian Zhang
- Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Nirmal Robinson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | | | - Angel F Lopez
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia
| | - Vinay Tergaonkar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5000, Australia; Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore.
| |
Collapse
|
69
|
High-resolution architecture and partner genes of MYC rearrangements in lymphoma with DLBCL morphology. Blood Adv 2019; 2:2755-2765. [PMID: 30348671 DOI: 10.1182/bloodadvances.2018023572] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Genomic rearrangements in the MYC locus occur in ∼12% of lymphomas with diffuse large B-cell lymphoma (DLBCL) morphology and are associated with inferior outcome. Previous studies exploring MYC rearrangements have primarily used fluorescence in situ hybridization (FISH) assays to characterize break-apart status but have rarely examined breakpoint location, and in some cases have not examined partner identity. We performed targeted sequencing of MYC, BCL2, BCL6, and the immunoglobulin (IG) loci in 112 tumors with DLBCL morphology harboring MYC rearrangement. We characterized the location of the MYC rearrangement at base pair resolution and identified the partner in 88 cases. We observed a cluster of breakpoints upstream of the MYC coding region and in intron 1 (the "genic cluster"). Genic cluster rearrangements were enriched for translocations involving IGH (80%), whereas nongenic rearrangements occurred mostly downstream of the MYC gene with a variety of partners, including IGL and IGK Other recurrent partners included BCL6, ZCCHC7, and RFTN1, which has not previously been described as a MYC partner. We compared 2 commercially available FISH break-apart assays for the MYC locus and observed discordant results in 32% of cases examined, including some with MYC-IGL and MYC-IGK rearrangements. In cases of high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangement (HGBL-DH), so-called "double-hit" lymphomas, the majority of MYC rearrangements had non-IG partners (65%), with breakpoints outside the genic cluster (72%). In patients with de novo HGBL-DH of DLBCL morphology, MYC-IG rearrangements showed a trend toward inferior time to progression and overall survival compared with MYC-non-IG rearrangements. Our data reveal clinically relevant architecture of MYC rearrangements in lymphomas with DLBCL morphology.
Collapse
|
70
|
3D Chromosomal Landscapes in Hematopoiesis and Immunity. Trends Immunol 2019; 40:809-824. [PMID: 31422902 DOI: 10.1016/j.it.2019.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/25/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
Abstract
Epigenetic dysregulation plays a profound role in the pathogenesis of hematological malignancies, which is often the result of somatic mutations of chromatin regulators. Previously, these mutations were largely considered to alter gene expression in two dimensions, by activating or repressing chromatin states; however, research in the last decade has highlighted the increasing impact of the 3D organization of the genome in gene regulation and disease pathogenesis. Here, we summarize the current principles of 3D chromatin organization, how the integrity of the 3D genome governs immune cell development and malignant transformation, as well as how underlying (epi-)genetic drivers of 3D chromatin alterations might act as potential novel therapeutic targets for hematological malignancies.
Collapse
|
71
|
Hurtz C, Chan LN, Geng H, Ballabio E, Xiao G, Deb G, Khoury H, Chen CW, Armstrong SA, Chen J, Ernst P, Melnick A, Milne T, Müschen M. Rationale for targeting BCL6 in MLL-rearranged acute lymphoblastic leukemia. Genes Dev 2019; 33:1265-1279. [PMID: 31395741 PMCID: PMC6719625 DOI: 10.1101/gad.327593.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/02/2019] [Indexed: 12/27/2022]
Abstract
Chromosomal rearrangements of the mixed lineage leukemia (MLL) gene occur in ∼10% of B-cell acute lymphoblastic leukemia (B-ALL) and define a group of patients with dismal outcomes. Immunohistochemical staining of bone marrow biopsies from most of these patients revealed aberrant expression of BCL6, a transcription factor that promotes oncogenic B-cell transformation and drug resistance in B-ALL. Our genetic and ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) analyses showed that MLL-AF4 and MLL-ENL fusions directly bound to the BCL6 promoter and up-regulated BCL6 expression. While oncogenic MLL fusions strongly induced aberrant BCL6 expression in B-ALL cells, germline MLL was required to up-regulate Bcl6 in response to physiological stimuli during normal B-cell development. Inducible expression of Bcl6 increased MLL mRNA levels, which was reversed by genetic deletion and pharmacological inhibition of Bcl6, suggesting a positive feedback loop between MLL and BCL6. Highlighting the central role of BCL6 in MLL-rearranged B-ALL, conditional deletion and pharmacological inhibition of BCL6 compromised leukemogenesis in transplant recipient mice and restored sensitivity to vincristine chemotherapy in MLL-rearranged B-ALL patient samples. Oncogenic MLL fusions strongly induced transcriptional activation of the proapoptotic BH3-only molecule BIM, while BCL6 was required to curb MLL-induced expression of BIM. Notably, peptide (RI-BPI) and small molecule (FX1) BCL6 inhibitors derepressed BIM and synergized with the BH3-mimetic ABT-199 in eradicating MLL-rearranged B-ALL cells. These findings uncover MLL-dependent transcriptional activation of BCL6 as a previously unrecognized requirement of malignant transformation by oncogenic MLL fusions and identified BCL6 as a novel target for the treatment of MLL-rearranged B-ALL.
Collapse
Affiliation(s)
- Christian Hurtz
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Lai N Chan
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Huimin Geng
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Erica Ballabio
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Gang Xiao
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Gauri Deb
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA
| | - Haytham Khoury
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA
| | - Chun-Wei Chen
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jianjun Chen
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA
| | - Patricia Ernst
- Department of Pediatrics, University of Colorado, Denver, Colorado 80045, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, USA.,Department of Pharmacology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Thomas Milne
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Markus Müschen
- Department of Systems Biology, City of Hope Comprehensive Cancer Center, Monrovia, California 91016, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| |
Collapse
|
72
|
Placek K, Schultze JL, Aschenbrenner AC. Epigenetic reprogramming of immune cells in injury, repair, and resolution. J Clin Invest 2019; 129:2994-3005. [PMID: 31329166 DOI: 10.1172/jci124619] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Immune cells are pivotal in the reaction to injury, whereupon, under ideal conditions, repair and resolution phases restore homeostasis following initial acute inflammation. Immune cell activation and reprogramming require transcriptional changes that can only be initiated if epigenetic alterations occur. Recently, accelerated deciphering of epigenetic mechanisms has extended knowledge of epigenetic regulation, including long-distance chromatin remodeling, DNA methylation, posttranslational histone modifications, and involvement of small and long noncoding RNAs. Epigenetic changes have been linked to aspects of immune cell development, activation, and differentiation. Furthermore, genome-wide epigenetic landscapes have been established for some immune cells, including tissue-resident macrophages, and blood-derived cells including T cells. The epigenetic mechanisms underlying developmental steps from hematopoietic stem cells to fully differentiated immune cells led to development of epigenetic technologies and insights into general rules of epigenetic regulation. Compared with more advanced research areas, epigenetic reprogramming of immune cells in injury remains in its infancy. While the early epigenetic mechanisms supporting activation of the immune response to injury have been studied, less is known about resolution and repair phases and cell type-specific changes. We review prominent recent findings concerning injury-mediated epigenetic reprogramming, particularly in stroke and myocardial infarction. Lastly, we illustrate how single-cell technologies will be crucial to understanding epigenetic reprogramming in the complex sequential processes following injury.
Collapse
Affiliation(s)
- Katarzyna Placek
- Immunology and Metabolism, LIMES Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| |
Collapse
|
73
|
Abstract
PURPOSE OF REVIEW Chromatin organization during interphase is nonrandom, and dictated by a delicate equilibrium between biophysics, transcription factor expression, and topological regulators of the chromatin. Emerging evidence demonstrate a role for chromosomal conformation at different stages of B-cell development. In the present review, we provide an updated picture of the current knowledge regarding how chromosomal conformation regulates the B-cell phenotype and how disruption of this architecture could lead to B-cell lymphoma. RECENT FINDINGS B-cell development requires proper assembly of a rearranged VDJ locus, which will determine antigen receptor specificity. Recently, evidence pointed to a role for topological regulators during VDJ recombination. Research studies also demonstrated a link between shifts in nuclear chromosomal architecture during B-cell activation and in formation of germinal centers, which is required for immunoglobulin affinity maturation. Class-switch recombination was shown to be dependent on the presence of topology regulators. Loss of topological insulation of enhancers may lead to oncogene activation, suggesting that misfolding of chromatin may constitute a new epigenetic mechanism of malignant transformation. Finally, CCCTC-binding factor and cohesin binding sites have shown a higher probability of mutations and translocations in lymphomas, lending further support to the potential role of chromatin architecture in cancer development. SUMMARY Chromosomal conformation is now recognized as a key feature in the development of a robust humoral immune response. Several examples from the literature show that dysregulation of chromosomal architecture may be a foundational event during malignancy. Therefore, understanding the mechanisms that regulate chromosomal folding and drive gene activation are instrumental for a better understanding of immune regulation and lymphomagenesis.
Collapse
Affiliation(s)
- Martin A Rivas
- Division of Hematology and Medical Oncology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Sandra and Edward Meyer Cancer Center, New York, New York, USA
| | | |
Collapse
|
74
|
Ryan RJH, Wilcox RA. Ontogeny, Genetics, Molecular Biology, and Classification of B- and T-Cell Non-Hodgkin Lymphoma. Hematol Oncol Clin North Am 2019; 33:553-574. [PMID: 31229154 DOI: 10.1016/j.hoc.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mature B- and T-cell lymphomas are diverse in their biology, etiology, genetics, clinical behavior, and response to specific therapies. Here, we review the principles of diagnostic classification for non-Hodgkin lymphomas, summarize the characteristic features of major entities, and place recent biological and molecular findings in the context of principles that are applicable across the spectrum of mature lymphoid cancers.
Collapse
Affiliation(s)
- Russell James Hubbard Ryan
- Department of Pathology, University of Michigan Medical School, 4306 Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5936, USA.
| | - Ryan Alan Wilcox
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, 4310 Rogel Cancer Center, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5936, USA
| |
Collapse
|
75
|
Liu Z, Guo Y, Tang S, Zhou L, Huang C, Cao Y, Huang H, Wu X, Meng D, Ye L, He H, Xie Z, Wu Y, Liu X, Zhou X. Cutting Edge: Transcription Factor BCL6 Is Required for the Generation, but Not Maintenance, of Memory CD8 + T Cells in Acute Viral Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:323-327. [PMID: 31175159 DOI: 10.4049/jimmunol.1900014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/23/2019] [Indexed: 11/19/2022]
Abstract
The differentiation of memory CD8+ T cells is critical to the long-term cellular immunity. The transcription factor BCL6 has been reportedly important for the generation and maintenance of memory CD8+ T cells; however, using the newly established BCL6 conditional knockout mouse model, we demonstrate that BCL6 is dispensable for the maintenance of established memory CD8+ T cell pool, although BCL6 is still required for the generation of CD8+ memory precursors upon acute viral infection. In addition, BCL6 promotes the expression of TCF-1 via directly binding to the Tcf7 (gene symbol for TCF-1) allele in CD8+ memory precursors and forced expression of TCF-1 restores the generation of BCL6-deficient memory precursors. Thus, our findings clarify that BCL6 is dispensable for the maintenance of memory CD8+ T cells, but functions as an important upstream of TCF-1 to regulate the generation of memory precursors in acute viral infection.
Collapse
Affiliation(s)
- Zhenyu Liu
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Yanyan Guo
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Shupei Tang
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Lan Zhou
- School of Biomedical Engineering and Medical Imaging, Third Military Medical University, Chongqing 400038, China
| | - Chunji Huang
- College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China; and
| | - Yi Cao
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Huang Huang
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Xiaoping Wu
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Dongwei Meng
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Haiyang He
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Zhunyi Xie
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Yuzhang Wu
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China;
| | - Xindong Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Xinyuan Zhou
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China;
| |
Collapse
|
76
|
The AKT kinase signaling network is rewired by PTEN to control proximal BCR signaling in germinal center B cells. Nat Immunol 2019; 20:736-746. [PMID: 31011187 PMCID: PMC6724213 DOI: 10.1038/s41590-019-0376-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 03/12/2019] [Indexed: 01/04/2023]
Abstract
Compared to naïve B cells (NBCs), both B cell antigen receptor (BCR) and CD40 signaling are rewired in germinal center (GC) B cells (GCBCs) to optimize selection for high-affinity B cells. The mechanism for BCR reprogramming in GCBCs remains unknown. We describe a GC-specific, AKT kinase-driven negative feedback loop that attenuates BCR signaling. A mass spectrometry proteomic approach revealed that AKT activity was retargeted in GCBCs compared to NBCs. Retargeting was linked to differential AKT T308 and S473 phosphorylation, in turn due to GC-specific upregulation of phosphoinositide-dependent protein kinase PDK1 and the phosphatase PTEN, which retuned phosphatidylinositol-3-OH kinase (PI3K) signals. In GCBCs, AKT preferentially targeted CSK, SHP-1 and HPK1, which are negative regulators of BCR signaling. Phosphorylation results in markedly increased enzymatic activity of these proteins, creating a negative-feedback loop that dampens upstream BCR signaling. Inhibiting AKT substantially enhanced activation of BCR proximal kinase LYN as well as downstream BCR signaling molecules in GCBCs, establishing the relevance of this pathway.
Collapse
|
77
|
Xu LS, Francis A, Turkistany S, Shukla D, Wong A, Batista CR, DeKoter RP. ETV6-RUNX1 interacts with a region in SPIB intron 1 to regulate gene expression in pre-B-cell acute lymphoblastic leukemia. Exp Hematol 2019; 73:50-63.e2. [PMID: 30986496 DOI: 10.1016/j.exphem.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 03/28/2019] [Accepted: 03/30/2019] [Indexed: 11/19/2022]
Abstract
The most frequently occurring genetic abnormality in pediatric B-lymphocyte-lineage acute lymphoblastic leukemia is the t(12;21) chromosomal translocation that results in a ETV6-RUNX1 (also known as TEL-AML1) fusion gene. Expression of ETV6-RUNX1 induces a preleukemic condition leading to acquisition of secondary driver mutations, but the mechanism is poorly understood. SPI-B (encoded by SPIB) is an important transcriptional activator of B-cell development and differentiation. We hypothesized that SPIB is directly transcriptionally repressed by ETV6-RUNX1. Using chromatin immunoprecipitation, we identified a regulatory region in the first intron of SPIB that interacts with ETV6-RUNX1. Mutation of the RUNX1 binding site in SPIB intron 1 prevented transcriptional repression in transient transfection assays. Next, we sought to determine to what extent gene expression in REH cells can be altered by ectopic SPI-B expression. SPI-B expression was forced using CRISPR-mediated gene activation and also using a retroviral vector. Forced expression of SPI-B resulted in altered gene expression and, at high levels, impaired cell proliferation and induced apoptosis. Finally, we identified CARD11 and CDKN1A (encoding p21) as transcriptional targets of SPI-B involved in regulation of proliferation and apoptosis. Taken together, this study identifies SPIB as an important target of ETV6-RUNX1 in regulation of B-cell gene expression in t(12;21) leukemia.
Collapse
MESH Headings
- Apoptosis/genetics
- CARD Signaling Adaptor Proteins/biosynthesis
- CARD Signaling Adaptor Proteins/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 12/metabolism
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Cyclin-Dependent Kinase Inhibitor p21/biosynthesis
- Cyclin-Dependent Kinase Inhibitor p21/genetics
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Leukemic
- Guanylate Cyclase/biosynthesis
- Guanylate Cyclase/genetics
- Humans
- Introns
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Response Elements
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Translocation, Genetic
Collapse
Affiliation(s)
- Li S Xu
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada
| | - Alyssa Francis
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Devanshi Shukla
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Alison Wong
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Carolina R Batista
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada
| | - Rodney P DeKoter
- Department of Microbiology & Immunology and the Centre for Human Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada; Division of Genetics and Development, Children's Health Research Institute, Lawson Research Institute, London, ON, Canada.
| |
Collapse
|
78
|
Mlynarczyk C, Fontán L, Melnick A. Germinal center-derived lymphomas: The darkest side of humoral immunity. Immunol Rev 2019; 288:214-239. [PMID: 30874354 PMCID: PMC6518944 DOI: 10.1111/imr.12755] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 02/06/2023]
Abstract
One of the unusual features of germinal center (GC) B cells is that they manifest many hallmarks of cancer cells. Accordingly, most B-cell neoplasms originate from the GC reaction, and characteristically display abundant point mutations, structural genomic lesions, and clonal diversity from the genetic and epigenetic standpoints. The dominant biological theme of GC-derived lymphomas is mutation of genes involved in epigenetic regulation and immune receptor signaling, which come into play at critical transitional stages of the GC reaction. Hence, mechanistic studies of these mutations reveal fundamental insight into the biology of the normal and malignant GC B cell. The BCL6 transcription factor plays a central role in establishing the GC phenotype in B cells, and most lymphomas are dependent on BCL6 to maintain survival, proliferation, and perhaps immune evasion. Many lymphoma mutations have the commonality of enhancing the oncogenic functions of BCL6, or overcoming some of its tumor suppressive effects. Herein, we discuss how unique features of the GC reaction create vulnerabilities that select for particular lymphoma mutations. We examine the interplay between epigenetic programming, metabolism, signaling, and immune regulatory mechanisms in lymphoma, and discuss how these are leading to novel precision therapy strategies to treat lymphoma patients.
Collapse
Affiliation(s)
- Coraline Mlynarczyk
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Lorena Fontán
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| | - Ari Melnick
- Department of MedicineDivision of Hematology & Medical OncologyWeill Cornell MedicineNew York CityNew York
| |
Collapse
|
79
|
Agirre X, Meydan C, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O, Mason CE, Prosper F, Melnick A. Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response. Nat Commun 2019; 10:821. [PMID: 30778059 PMCID: PMC6379396 DOI: 10.1038/s41467-019-08679-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/21/2019] [Indexed: 12/19/2022] Open
Abstract
lncRNAs make up a majority of the human transcriptome and have key regulatory functions. Here we perform unbiased de novo annotation of transcripts expressed during the human humoral immune response to find 30% of the human genome transcribed during this process, yet 58% of these transcripts manifest striking differential expression, indicating an lncRNA phylogenetic relationship among cell types that is more robust than that of coding genes. We provide an atlas of lncRNAs in naive and GC B-cells that indicates their partition into ten functionally categories based on chromatin features, DNase hypersensitivity and transcription factor localization, defining lncRNAs classes such as enhancer-RNAs (eRNA), bivalent-lncRNAs, and CTCF-associated, among others. Specifically, eRNAs are transcribed in 8.6% of regular enhancers and 36.5% of super enhancers, and are associated with coding genes that participate in critical immune regulatory pathways, while plasma cells have uniquely high levels of circular-RNAs accounted for by and reflecting the combinatorial clonal state of the Immunoglobulin loci. Long non-coding RNAs (lncRNA) constitute a large fraction of human transcriptome, and are reported, individually, for context-specific regulatory functions. Here the authors expand our understanding by providing a systemic, unbiased annotation of lncRNA to establish an atlas of lncRNA landscape during the induction of human humoral immune responses.
Collapse
Affiliation(s)
- Xabier Agirre
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA. .,Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain.
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Yanwen Jiang
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Leire Garate
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain.,Department of Hematology, Clínica Universidad de Navarra, IDISNA, Pamplona, 31008, Spain
| | - Ashley S Doane
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Zhuoning Li
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Akanksha Verma
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Bruno Paiva
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain
| | - José I Martín-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, 08036, Spain
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA. .,The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA. .,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Felipe Prosper
- Division of Hemato-Oncology, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Ciberonc, Pamplona, 31008, Spain. .,Department of Hematology, Clínica Universidad de Navarra, IDISNA, Pamplona, 31008, Spain.
| | - Ari Melnick
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, 10021, USA.
| |
Collapse
|
80
|
Hatzi K, Geng H, Doane AS, Meydan C, LaRiviere R, Cardenas M, Duy C, Shen H, Vidal MNC, Baslan T, Mohammad HP, Kruger RG, Shaknovich R, Haberman AM, Inghirami G, Lowe SW, Melnick AM. Histone demethylase LSD1 is required for germinal center formation and BCL6-driven lymphomagenesis. Nat Immunol 2019; 20:86-96. [PMID: 30538335 PMCID: PMC6294324 DOI: 10.1038/s41590-018-0273-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/31/2018] [Indexed: 01/03/2023]
Abstract
Germinal center (GC) B cells feature repression of many gene enhancers to establish their characteristic transcriptome. Here we show that conditional deletion of Lsd1 in GCs significantly impaired GC formation, associated with failure to repress immune synapse genes linked to GC exit, which are also direct targets of the transcriptional repressor BCL6. We found that BCL6 directly binds LSD1 and recruits it primarily to intergenic and intronic enhancers. Conditional deletion of Lsd1 suppressed GC hyperplasia caused by constitutive expression of BCL6 and significantly delayed BCL6-driven lymphomagenesis. Administration of catalytic inhibitors of LSD1 had little effect on GC formation or GC-derived lymphoma cells. Using a CRISPR-Cas9 domain screen, we found instead that the LSD1 Tower domain was critical for dependence on LSD1 in GC-derived B cells. These results indicate an essential role for LSD1 in the humoral immune response, where it modulates enhancer function by forming repression complexes with BCL6.
Collapse
Affiliation(s)
- Katerina Hatzi
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Dept. of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Reed LaRiviere
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Mariano Cardenas
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- High Throughput and Spectroscopy Resource Center, Rockefeller University, New York, NY, USA
| | - Cihangir Duy
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Hao Shen
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Maria Nieves Calvo Vidal
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helai P Mohammad
- Cancer Epigenetics Department, GlaxoSmithKline, Collegeville, PA, USA
| | - Ryan G Kruger
- Cancer Epigenetics Department, GlaxoSmithKline, Collegeville, PA, USA
| | - Rita Shaknovich
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Cancer Genetics Incorporated, Rutherford, NJ, USA
| | - Ann M Haberman
- Department of Laboratory Medicine, Department of Immunobiology Yale University School of Medicine, New Haven, CT, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
81
|
Dominguez PM, Ghamlouch H, Rosikiewicz W, Kumar P, Béguelin W, Fontán L, Rivas MA, Pawlikowska P, Armand M, Mouly E, Torres-Martin M, Doane AS, Calvo Fernandez MT, Durant M, Della-Valle V, Teater M, Cimmino L, Droin N, Tadros S, Motanagh S, Shih AH, Rubin MA, Tam W, Aifantis I, Levine RL, Elemento O, Inghirami G, Green MR, Figueroa ME, Bernard OA, Aoufouchi S, Li S, Shaknovich R, Melnick AM. TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis. Cancer Discov 2018; 8:1632-1653. [PMID: 30274972 PMCID: PMC6279514 DOI: 10.1158/2159-8290.cd-18-0657] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/26/2018] [Accepted: 09/26/2018] [Indexed: 01/04/2023]
Abstract
TET2 somatic mutations occur in ∼10% of diffuse large B-cell lymphomas (DLBCL) but are of unknown significance. Herein, we show that TET2 is required for the humoral immune response and is a DLBCL tumor suppressor. TET2 loss of function disrupts transit of B cells through germinal centers (GC), causing GC hyperplasia, impaired class switch recombination, blockade of plasma cell differentiation, and a preneoplastic phenotype. TET2 loss was linked to focal loss of enhancer hydroxymethylation and transcriptional repression of genes that mediate GC exit, such as PRDM1. Notably, these enhancers and genes are also repressed in CREBBP-mutant DLBCLs. Accordingly, TET2 mutation in patients yields a CREBBP-mutant gene-expression signature, CREBBP and TET2 mutations are generally mutually exclusive, and hydroxymethylation loss caused by TET2 deficiency impairs enhancer H3K27 acetylation. Hence, TET2 plays a critical role in the GC reaction, and its loss of function results in lymphomagenesis through failure to activate genes linked to GC exit signals. SIGNIFICANCE: We show that TET2 is required for exit of the GC, B-cell differentiation, and is a tumor suppressor for mature B cells. Loss of TET2 phenocopies CREBBP somatic mutation. These results advocate for sequencing TET2 in patients with lymphoma and for the testing of epigenetic therapies to treat these tumors.See related commentary by Shingleton and Dave, p. 1515.This article is highlighted in the In This Issue feature, p. 1494.
Collapse
Affiliation(s)
- Pilar M Dominguez
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Hussein Ghamlouch
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Parveen Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Wendy Béguelin
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Lorena Fontán
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Martín A Rivas
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Patrycja Pawlikowska
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marine Armand
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Enguerran Mouly
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Miguel Torres-Martin
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Ashley S Doane
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - María T Calvo Fernandez
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Matt Durant
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Veronique Della-Valle
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Matt Teater
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Luisa Cimmino
- Department of Pathology, Laura and Isaac Perlmutter Cancer Center, and The Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York
| | - Nathalie Droin
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Saber Tadros
- Department of Lymphoma/Myeloma and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Samaneh Motanagh
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Alan H Shih
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Wayne Tam
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York
| | - Iannis Aifantis
- Department of Pathology, Laura and Isaac Perlmutter Cancer Center, and The Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York
| | - Ross L Levine
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Giorgio Inghirami
- Pathology and Laboratory Medicine Department, Weill Cornell Medicine, New York, New York
| | - Michael R Green
- Department of Lymphoma/Myeloma and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida
| | - Olivier A Bernard
- INSERM U1170, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Said Aoufouchi
- CNRS UMR8200, équipe labelisée Ligue Nationale Contre le Cancer, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
- The Jackson Laboratory Cancer Center, Bar Harbor, Maine
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Rita Shaknovich
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.
- Cancer Genetics, Inc., Rutherford, New Jersey
| | - Ari M Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
82
|
Andrews JM, Payton JE. Epigenetic dynamics in normal and malignant B cells: die a hero or live to become a villain. Curr Opin Immunol 2018; 57:15-22. [PMID: 30342313 DOI: 10.1016/j.coi.2018.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/26/2018] [Indexed: 12/27/2022]
Abstract
Normal B cell development, activation, and terminal differentiation depend on the intricate dynamics of cooperating epigenetic and non-coding components to control the level and timing of expression of thousands of genes. Recent genome-wide studies have integratively mapped changes in the chromatin landscape, DNA methylome, 3-dimensional interactome, and coding and non-coding transcriptomes of normal and malignant B cells. Genetic ablation in human cells and mouse models has begun to elucidate the coordinated roles of essential epigenetic modifiers, key transcription factors, and long non-coding RNAs in B cell biology. Perturbation of these stewards of the epigenome drive B cell oncogenesis, but may be exploited to develop new avenues of therapy.
Collapse
Affiliation(s)
- Jared M Andrews
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| |
Collapse
|
83
|
Buxadé M, Huerga Encabo H, Riera-Borrull M, Quintana-Gallardo L, López-Cotarelo P, Tellechea M, Martínez-Martínez S, Redondo JM, Martín-Caballero J, Flores JM, Bosch E, Rodríguez-Fernández JL, Aramburu J, López-Rodríguez C. Macrophage-specific MHCII expression is regulated by a remote Ciita enhancer controlled by NFAT5. J Exp Med 2018; 215:2901-2918. [PMID: 30327417 PMCID: PMC6219740 DOI: 10.1084/jem.20180314] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/27/2018] [Accepted: 09/17/2018] [Indexed: 01/05/2023] Open
Abstract
NFAT5 regulates macrophage MHCII expression by controlling the transcription of its coactivator Ciita through a remote enhancer. This mechanism differs from those previously found in DCs and B lymphocytes and distinguishes macrophages from these APC lineages. MHCII in antigen-presenting cells (APCs) is a key regulator of adaptive immune responses. Expression of MHCII genes is controlled by the transcription coactivator CIITA, itself regulated through cell type–specific promoters. Here we show that the transcription factor NFAT5 is needed for expression of Ciita and MHCII in macrophages, but not in dendritic cells and other APCs. NFAT5-deficient macrophages showed defective activation of MHCII-dependent responses in CD4+ T lymphocytes and attenuated capacity to elicit graft rejection in vivo. Ultrasequencing analysis of NFAT5-immunoprecipitated chromatin uncovered an NFAT5-regulated region distally upstream of Ciita. This region was required for CIITA and hence MHCII expression, exhibited NFAT5-dependent characteristics of active enhancers such as H3K27 acetylation marks, and required NFAT5 to interact with Ciita myeloid promoter I. Our results uncover an NFAT5-regulated mechanism that maintains CIITA and MHCII expression in macrophages and thus modulates their T lymphocyte priming capacity.
Collapse
Affiliation(s)
- Maria Buxadé
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Hector Huerga Encabo
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Marta Riera-Borrull
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Lucía Quintana-Gallardo
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Pilar López-Cotarelo
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mónica Tellechea
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Sara Martínez-Martínez
- Gene Regulation in Cardiovascular Remodeling and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Juan Miguel Redondo
- Gene Regulation in Cardiovascular Remodeling and Inflammation Group, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Juan Martín-Caballero
- Parc Cientific de Barcelona/Barcelona Biomedical Research Park Animal Facilities, Barcelona, Spain
| | - Juana María Flores
- Department of Animal Medicine and Surgery, School of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (Spanish National Research Council), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - José Luis Rodríguez-Fernández
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jose Aramburu
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| | - Cristina López-Rodríguez
- Immunology Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, and Barcelona Biomedical Research Park, Barcelona, Spain
| |
Collapse
|
84
|
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells. Immunity 2018; 48:227-242.e8. [PMID: 29466755 DOI: 10.1016/j.immuni.2018.01.013] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/19/2017] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages.
Collapse
|
85
|
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] [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.
Collapse
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.
| |
Collapse
|
86
|
PRMT5 interacts with the BCL6 oncoprotein and is required for germinal center formation and lymphoma cell survival. Blood 2018; 132:2026-2039. [PMID: 30082494 DOI: 10.1182/blood-2018-02-831438] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
The germinal center (GC) reaction plays an important role in generating humoral immunity and is believed to give rise to most B-cell lymphomas. GC entry and exit are tightly regulated processes, controlled by the actions of transcription factors such as BCL6. Herein, we demonstrate that protein arginine methyltransferase 5 (PRMT5), a symmetric dimethyl arginine methyltransferase, is also necessary for GC formation and affinity maturation. PRMT5 contributes to GC formation and affinity maturation at least in part through its direct interaction with and methylation of BCL6 at arginine 305 (R305), a modification necessary for the full transcriptional repressive effects of BCL6. Inhibition of PRMT5 in B-cell lymphoma lines led to significant upregulation of BCL6 target genes, and the concomitant inhibition of both BCL6 and PRMT5 exhibited synergistic killing of BCL6-expressing lymphoma cells. Our studies identify PRMT5 as a novel regulator of the GC reaction and highlight the mechanistic rationale of cotargeting PRMT5 and BCL6 in lymphoma.
Collapse
|
87
|
Abstract
Enhancers are short noncoding segments of DNA (100-1000 bp) that control the temporal and spatial activity of genes in an orientation-independent manner. They can be separated from their target genes by large distances and are thus known as distal regulatory elements. One consequence of the variability in the distance separating enhancers and their target promoters is that it is difficult to determine which elements are involved in the regulation of a particular gene. Moreover, enhancers can be found in clusters in which multiple regulatory elements control expression of the same target gene. However, little is known about how the individual elements contribute to gene expression. Here, we describe how chromatin conformation promotes and constraints enhancer activity. Further, we discuss enhancer clusters and what is known about the contribution of individual elements to the regulation of target genes. Finally, we examine the reliability of different methods used to identify enhancers.
Collapse
Affiliation(s)
- Valentina Snetkova
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA.,MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA
| |
Collapse
|
88
|
Hnisz D, Schuijers J, Li CH, Young RA. Regulation and Dysregulation of Chromosome Structure in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018. [DOI: 10.1146/annurev-cancerbio-030617-050134] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer arises from genetic alterations that produce dysregulated gene expression programs. Normal gene regulation occurs in the context of chromosome loop structures called insulated neighborhoods, and recent studies have shown that these structures are altered and can contribute to oncogene dysregulation in various cancer cells. We review the types of genetic and epigenetic alterations that influence neighborhood structures and contribute to gene dysregulation in cancer, present models for insulated neighborhoods associated with the most prominent human oncogenes, and discuss how such models may lead to further advances in cancer diagnosis and therapy.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
| | - Charles H. Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;,
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
89
|
Boller S, Li R, Grosschedl R. Defining B Cell Chromatin: Lessons from EBF1. Trends Genet 2018; 34:257-269. [PMID: 29336845 DOI: 10.1016/j.tig.2017.12.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/11/2022]
Abstract
Hematopoiesis is regulated by signals from the microenvironment, transcription factor networks, and changes of the epigenetic landscape. Transcription factors interact with and shape chromatin to allow for lineage- and cell type-specific changes in gene expression. During B lymphopoiesis, epigenetic regulation is observed in multilineage progenitors in which a specific chromatin context is established, at the onset of the B cell differentiation when early B cell factor 1 (EBF1) induces lineage-specific changes in chromatin, during V(D)J recombination and after antigen-driven activation of B cells and terminal differentiation. In this review, we discuss the epigenetic changes underlying B cell differentiation, focusing on the role of transcription factor EBF1 in B cell lineage priming.
Collapse
Affiliation(s)
- Sören Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rui Li
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
| |
Collapse
|
90
|
Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| |
Collapse
|
91
|
Bessière C, Taha M, Petitprez F, Vandel J, Marin JM, Bréhélin L, Lèbre S, Lecellier CH. Probing instructions for expression regulation in gene nucleotide compositions. PLoS Comput Biol 2018; 14:e1005921. [PMID: 29293496 PMCID: PMC5766238 DOI: 10.1371/journal.pcbi.1005921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 12/10/2017] [Indexed: 01/22/2023] Open
Abstract
Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. Here, we probe sequence-level instructions for gene expression and develop a method to explain mRNA levels based solely on nucleotide features. Our method positions nucleotide composition as a critical component of gene expression. Moreover, our approach, able to rank regulatory regions according to their contribution, unveils a strong influence of the gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
Collapse
Affiliation(s)
- Chloé Bessière
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - May Taha
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
| | - Florent Petitprez
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jimmy Vandel
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- LIRMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Jean-Michel Marin
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
| | - Laurent Bréhélin
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- LIRMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Sophie Lèbre
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
- Univ. Paul-Valéry-Montpellier 3, Montpellier, France
| | - Charles-Henri Lecellier
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| |
Collapse
|
92
|
Wu P, Li T, Li R, Jia L, Zhu P, Liu Y, Chen Q, Tang D, Yu Y, Li C. 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations. Nat Commun 2017; 8:1937. [PMID: 29203764 PMCID: PMC5715138 DOI: 10.1038/s41467-017-01793-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 10/17/2017] [Indexed: 01/06/2023] Open
Abstract
The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the numbers of TADs increases by 25% in MM, the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid MM cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation. Chromosome conformation capture techniques enable the study of genome organization in cancer cells. Here, the authors use Hi-C, WGS, and RNA-seq to study the 3D genome of multiple myeloma and find that genome disorganization is associated with copy number variations and changes in gene expression.
Collapse
Affiliation(s)
- Pengze Wu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tingting Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ruifeng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Lumeng Jia
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ping Zhu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yifang Liu
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qing Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Daiwei Tang
- PKU-Tsinghua-NIBS Graduate Program, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuezhou Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China. .,Center for Statistical Science, Peking University, Beijing, 100871, China.
| |
Collapse
|
93
|
Solomon LA, Batista CR, DeKoter RP. Lenalidomide modulates gene expression in human ABC-DLBCL cells by regulating IKAROS interaction with an intronic control region of SPIB. Exp Hematol 2017; 56:46-57.e1. [DOI: 10.1016/j.exphem.2017.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 11/16/2022]
|
94
|
Abstract
Animal development depends on not only the linear genome sequence that embeds millions of cis-regulatory elements, but also the three-dimensional (3D) chromatin architecture that orchestrates the interplay between cis-regulatory elements and their target genes. Compared to our knowledge of the cis-regulatory sequences, the understanding of the 3D genome organization in human and other eukaryotes is still limited. Recent advances in technologies to map the 3D genome architecture have greatly accelerated the pace of discovery. Here, we review emerging concepts of chromatin organization in mammalian cells, discuss the dynamics of chromatin conformation during development, and highlight important roles for chromatin organization in cancer and other human diseases.
Collapse
Affiliation(s)
- Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, California 92093;
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, California 92093;
- Center for Epigenomics, Department of Cellular and Molecular Medicine, and Institute of Genomic Medicine, and Moores Cancer Center, University of California at San Diego, La Jolla, California 92093
| |
Collapse
|
95
|
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 2017; 67:566-578.e10. [PMID: 28803781 DOI: 10.1016/j.molcel.2017.07.013] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 04/25/2017] [Accepted: 07/10/2017] [Indexed: 11/23/2022]
Abstract
50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.
Collapse
|
96
|
CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation. Nat Commun 2017; 8:16067. [PMID: 28677680 PMCID: PMC5504274 DOI: 10.1038/ncomms16067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 05/22/2017] [Indexed: 11/25/2022] Open
Abstract
In germinal centres (GC) mature B cells undergo intense proliferation and immunoglobulin gene modification before they differentiate into memory B cells or long-lived plasma cells (PC). GC B-cell-to-PC transition involves a major transcriptional switch that promotes a halt in cell proliferation and the production of secreted immunoglobulins. Here we show that the CCCTC-binding factor (CTCF) is required for the GC reaction in vivo, whereas in vitro the requirement for CTCF is not universal and instead depends on the pathways used for B-cell activation. CTCF maintains the GC transcriptional programme, allows a high proliferation rate, and represses the expression of Blimp-1, the master regulator of PC differentiation. Restoration of Blimp-1 levels partially rescues the proliferation defect of CTCF-deficient B cells. Thus, our data reveal an essential function of CTCF in maintaining the GC transcriptional programme and preventing premature PC differentiation. Activated B cells differentiate into antibody-producing plasma cells in the germinal centre in secondary lymphoid organs. Here the authors show that this differentiation process and related transcription programs are modulated by the transcription factor CTCF, partly by suppressing the premature expression of Blimp-1.
Collapse
|
97
|
Enhancers and chromatin structures: regulatory hubs in gene expression and diseases. Biosci Rep 2017; 37:BSR20160183. [PMID: 28351896 PMCID: PMC5408663 DOI: 10.1042/bsr20160183] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/23/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression requires successful communication between enhancer and promoter regions, whose activities are regulated by a variety of factors and associated with distinct chromatin structures; in addition, functionally related genes and their regulatory repertoire tend to be arranged in the same subchromosomal regulatory domains. In this review, we discuss the importance of enhancers, especially clusters of enhancers (such as super-enhancers), as key regulatory hubs to integrate environmental cues and encode spatiotemporal instructions for genome expression, which are critical for a variety of biological processes governing mammalian development. Furthermore, we emphasize that the enhancer–promoter interaction landscape provides a critical context to understand the aetiologies and mechanisms behind numerous complex human diseases and provides new avenues for effective transcription-based interventions.
Collapse
|
98
|
Doane AS, Elemento O. Regulatory elements in molecular networks. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28093886 DOI: 10.1002/wsbm.1374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/06/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
Abstract
Regulatory elements determine the connectivity of molecular networks and mediate a variety of regulatory processes ranging from DNA looping to transcriptional, posttranscriptional, and posttranslational regulation. This review highlights our current understanding of the different types of regulatory elements found in molecular networks with a focus on DNA regulatory elements. We highlight technical advances and current challenges for the mapping of regulatory elements at the genome-wide scale, and describe new computational methods to uncover these elements via reconstructing regulatory networks from large genomic datasets. WIREs Syst Biol Med 2017, 9:e1374. doi: 10.1002/wsbm.1374 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Ashley S Doane
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
99
|
Hnisz D, Day DS, Young RA. Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control. Cell 2016; 167:1188-1200. [PMID: 27863240 PMCID: PMC5125522 DOI: 10.1016/j.cell.2016.10.024] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/22/2022]
Abstract
Understanding how transcriptional enhancers control over 20,000 protein-coding genes to maintain cell-type-specific gene expression programs in all human cells is a fundamental challenge in regulatory biology. Recent studies suggest that gene regulatory elements and their target genes generally occur within insulated neighborhoods, which are chromosomal loop structures formed by the interaction of two DNA sites bound by the CTCF protein and occupied by the cohesin complex. Here, we review evidence that insulated neighborhoods provide for specific enhancer-gene interactions, are essential for both normal gene activation and repression, form a chromosome scaffold that is largely preserved throughout development, and are perturbed by genetic and epigenetic factors in disease. Insulated neighborhoods are a powerful paradigm for gene control that provides new insights into development and disease.
Collapse
Affiliation(s)
- Denes Hnisz
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
| | - Daniel S Day
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
100
|
B cells: Genomic reorganization in germinal centres. Nat Rev Immunol 2016; 16:594-5. [PMID: 27670367 DOI: 10.1038/nri.2016.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|