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Willis TW, Gkrania-Klotsas E, Wareham NJ, McKinney EF, Lyons PA, Smith KGC, Wallace C. Leveraging pleiotropy identifies common-variant associations with selective IgA deficiency. Clin Immunol 2024; 268:110356. [PMID: 39241920 DOI: 10.1016/j.clim.2024.110356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Selective IgA deficiency (SIgAD) is the most common inborn error of immunity (IEI). Unlike many IEIs, evidence of a role for highly penetrant rare variants in SIgAD is lacking. Previous SIgAD studies have had limited power to identify common variants due to their small sample size. We overcame this problem first through meta-analysis of two existing GWAS. This identified four novel common-variant associations and enrichment of SIgAD-associated variants in genes linked to Mendelian IEIs. SIgAD showed evidence of shared genetic architecture with serum IgA and a number of immune-mediated diseases. We leveraged this pleiotropy through the conditional false discovery rate procedure, conditioning our SIgAD meta-analysis on large GWAS of asthma and rheumatoid arthritis, and our own meta-analysis of serum IgA. This identified an additional 18 variants, increasing the number of known SIgAD-associated variants to 27 and strengthening the evidence for a polygenic, common-variant aetiology for SIgAD.
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Affiliation(s)
- Thomas W Willis
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
| | - Effrossyni Gkrania-Klotsas
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK; Department of Infectious Diseases, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicholas J Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Chris Wallace
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
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2
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Yuan Z, Shu L, Fu J, Yang P, Wang Y, Sun J, Zheng M, Liu Z, Yang J, Song J, Song S, Cai Z. Single-Cell RNA Sequencing Deconstructs the Distribution of Immune Cells Within Abdominal Aortic Aneurysms in Mice. Arterioscler Thromb Vasc Biol 2024; 44:1986-2003. [PMID: 39051127 DOI: 10.1161/atvbaha.124.321129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Inflammation is a key component in the development of abdominal aortic aneurysm (AAA), yet insights into the roles of immune cells and their interactions in this process are limited. METHODS Using single-cell RNA transcriptomic analysis, we deconstructed the CD45+ cell population in elastase-induced murine AAA at the single-cell level. We isolated each group of immune cells from murine AAA tissue at different time points and divided them into several subtypes, listed the remarkable differentially expressed genes, explored the developmental trajectories of immune cells, and demonstrated the interactions among them. RESULTS Our findings reveal significant differences in several immune cell subsets, including macrophages, dendritic cells, and T cells, within the AAA microenvironment compared with the normal aorta. Especially, conventional dendritic cell type 1 exclusively existed in the AAA tissue rather than the normal aortas. Via CellChat analysis, we identified several intercellular communication pathways like visfatin, which targets monocyte differentiation and neutrophil extracellular trap-mediated interaction between neutrophils and dendritic cells, which might contribute to AAA development. Some of these pathways were validated in human AAA. CONCLUSIONS Despite the absence of external pathogenic stimuli, AAA tissues develop a complex inflammatory microenvironment involving numerous immune cells. In-depth studies of the inflammatory network shall provide new strategies for patients with AAA.
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MESH Headings
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/chemically induced
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Abdominal/metabolism
- Animals
- Single-Cell Analysis
- Disease Models, Animal
- Mice, Inbred C57BL
- Aorta, Abdominal/pathology
- Aorta, Abdominal/metabolism
- Aorta, Abdominal/immunology
- Mice
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Humans
- Macrophages/metabolism
- Macrophages/immunology
- Male
- Transcriptome
- RNA-Seq
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Gene Expression Profiling/methods
- Pancreatic Elastase
- Cell Communication
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Affiliation(s)
- Zhen Yuan
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Li Shu
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Jiantao Fu
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Peipei Yang
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Yidong Wang
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Jie Sun
- Pathology (J. Sun, M.Z.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengsha Zheng
- Pathology (J. Sun, M.Z.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhenjie Liu
- Vascular Surgery (Z.L.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jin Yang
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, China (J. Song, S.S.)
| | - Shen Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, China (J. Song, S.S.)
| | - Zhejun Cai
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
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3
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Mahla RS. TLR7 signaling: a central nexus in autoimmunity and cGVHD. Blood Adv 2024; 8:3186-3188. [PMID: 38696714 PMCID: PMC11225663 DOI: 10.1182/bloodadvances.2024012598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/04/2024] Open
Affiliation(s)
- Ranjeet Singh Mahla
- Kennedy Institute of Rheumatology, Medical Science Division, University of Oxford, Oxford, United Kingdom
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4
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Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN. Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients. Cancer Cell 2024; 42:444-463.e10. [PMID: 38428410 PMCID: PMC10966827 DOI: 10.1016/j.ccell.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.
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Affiliation(s)
- Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ziv Yaniv
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Bradley C Lowekamp
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Emily Speranza
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL 34987, USA
| | - Li Yao
- Li Yao Visuals, Rockville, MD 20855, USA
| | | | - Arthur L Shaffer
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA; Tumor Targeted Delivery, Heme Malignancy Target Discovery Group, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Danny Jonigk
- Institute of Pathology, Aachen Medical University, RWTH Aachen, 52074 Aachen, Germany; German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), 30625 Hannover, Germany
| | - James D Phelan
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Da Wei Huang
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | - Michael Kelly
- CCR Single Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Jagan Muppidi
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Jeremy L Davis
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jonathan M Hernandez
- Surgical Oncology Program, Metastasis Biology Section, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Elaine S Jaffe
- Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
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5
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Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M. An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinformatics 2023; 39:i413-i422. [PMID: 37387140 PMCID: PMC10311317 DOI: 10.1093/bioinformatics/btad271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post hoc analyses, and even then, one can often not explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called totally interpretable sequence-to-function model (tiSFM). tiSFM improves upon the performance of standard multilayer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multilayer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. RESULTS We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state-of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context-specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM's model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. AVAILABILITY AND IMPLEMENTATION The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv, implemented in Python.
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Affiliation(s)
- Ali Tuğrul Balcı
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Mark Maher Ebeid
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, United States
| | - Dennis Kostka
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Maria Chikina
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
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6
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Flerlage JE, Myers JR, Maciaszek JL, Oak N, Rashkin SR, Hui Y, Wang YD, Chen W, Wu G, Chang TC, Hamilton K, Tithi SS, Goldin LR, Rotunno M, Caporaso N, Vogt A, Flamish D, Wyatt K, Liu J, Tucker M, Hahn CN, Brown AL, Scott HS, Mullighan C, Nichols KE, Metzger ML, McMaster ML, Yang JJ, Rampersaud E. Discovery of novel predisposing coding and noncoding variants in familial Hodgkin lymphoma. Blood 2023; 141:1293-1307. [PMID: 35977101 PMCID: PMC10082357 DOI: 10.1182/blood.2022016056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Familial aggregation of Hodgkin lymphoma (HL) has been demonstrated in large population studies, pointing to genetic predisposition to this hematological malignancy. To understand the genetic variants associated with the development of HL, we performed whole genome sequencing on 234 individuals with and without HL from 36 pedigrees that had 2 or more first-degree relatives with HL. Our pedigree selection criteria also required at least 1 affected individual aged <21 years, with the median age at diagnosis of 21.98 years (3-55 years). Family-based segregation analysis was performed for the identification of coding and noncoding variants using linkage and filtering approaches. Using our tiered variant prioritization algorithm, we identified 44 HL-risk variants in 28 pedigrees, of which 33 are coding and 11 are noncoding. The top 4 recurrent risk variants are a coding variant in KDR (rs56302315), a 5' untranslated region variant in KLHDC8B (rs387906223), a noncoding variant in an intron of PAX5 (rs147081110), and another noncoding variant in an intron of GATA3 (rs3824666). A newly identified splice variant in KDR (c.3849-2A>C) was observed for 1 pedigree, and high-confidence stop-gain variants affecting IRF7 (p.W238∗) and EEF2KMT (p.K116∗) were also observed. Multiple truncating variants in POLR1E were found in 3 independent pedigrees as well. Whereas KDR and KLHDC8B have previously been reported, PAX5, GATA3, IRF7, EEF2KMT, and POLR1E represent novel observations. Although there may be environmental factors influencing lymphomagenesis, we observed segregation of candidate germline variants likely to predispose HL in most of the pedigrees studied.
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Affiliation(s)
- Jamie E. Flerlage
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Jason R. Myers
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jamie L. Maciaszek
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Sara R. Rashkin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yawei Hui
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kayla Hamilton
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Saima S. Tithi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Lynn R. Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | - Jia Liu
- Leidos Biomedical, Inc, Frederick, MD
| | - Margaret Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Christopher N. Hahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Anna L. Brown
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S. Scott
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
| | - Monika L. Metzger
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN
| | - Mary L. McMaster
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jun J. Yang
- Department of Oncology, St. Jude Children’s Research Hospital and the University of Tennessee Health Sciences Center, Memphis, TN
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
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7
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Das Gupta D, Lohoff M. Puppet masters of B-cell progenitor acute lymphoblastic leukemia: The preB cell receptor and the interleukin 7 receptor α. Eur J Immunol 2023; 53:e2250093. [PMID: 36805963 DOI: 10.1002/eji.202250093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/02/2022] [Accepted: 01/13/2023] [Indexed: 02/23/2023]
Abstract
B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) is enriched for a preB cell phenotype, hinting at a specific vulnerability of this cell stage. Two signaling pathways via the preB cell receptor (preBCR) and the interleukin 7 receptor α (IL-7Rα) chain govern the balance between differentiation and proliferation at this stage and both receptor pathways are routinely altered in human BCP-ALL. Here, we review the immunobiology of both the preBCR as well as the IL-7Rα and analyze the human BCP-ALL spectrum in the light of these signaling complexes. Finally, we present a terminology for preBCR signaling modules that distinguishes a pro-proliferative "phase-I" module from a pro-differentiative "phase-II" module. This terminology might serve as a framework to better address shared oncogenic mechanics of preB cell stage BCP-ALL.
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Affiliation(s)
- Dennis Das Gupta
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany.,Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Michael Lohoff
- Institute for Medical Microbiology & Hospital Hygiene, Philipps University Marburg, Marburg, Germany
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8
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Föh B, Buhre JS, Sina C, Ehlers M. Influence of nutrients and metabolites on the differentiation of plasma cells and implications for autoimmunity. Front Immunol 2022; 13:1004644. [PMID: 36466846 PMCID: PMC9716886 DOI: 10.3389/fimmu.2022.1004644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/04/2022] [Indexed: 09/10/2024] Open
Abstract
The modulation of inflammatory (auto)immune reactions by nutrients and gut bacterial metabolites is of great interest for potential preventive and therapeutic strategies. B cell-derived plasma cells are major players in inflammatory (auto)immune responses and can exhibit pro- or anti-inflammatory effects through (auto)antibody-dependent and -independent functions. Emerging evidence indicates a key role of nutrients and microbial metabolites in regulating the differentiation of plasma cells as well as their differentiation to pro- or anti-inflammatory phenotypes. These effects might be mediated indirectly by influencing other immune cells or directly through B cell-intrinsic mechanisms. Here, we provide an overview of nutrients and metabolites that influence B cell-intrinsic signaling pathways regulating B cell activation, plasma cell differentiation, and effector functions. Furthermore, we outline important inflammatory plasma cell phenotypes whose differentiation could be targeted by nutrients and microbial metabolites. Finally, we discuss possible implications for inflammatory (auto)immune conditions.
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Affiliation(s)
- Bandik Föh
- Department of Medicine I, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Jana Sophia Buhre
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Christian Sina
- Department of Medicine I, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Marc Ehlers
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Airway Research Center North, University of Lübeck, German Center for Lung Research Deutsches Zentrum für Lungenforschung (DZL), Lübeck, Germany
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9
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Donohue LK, Guo MG, Zhao Y, Jung N, Bussat RT, Kim DS, Neela PH, Kellman LN, Garcia OS, Meyers RM, Altman RB, Khavari PA. A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. CELL GENOMICS 2022; 2:100191. [PMID: 36742369 PMCID: PMC9894309 DOI: 10.1016/j.xgen.2022.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Gene expression is controlled by transcription factors (TFs) that bind cognate DNA motif sequences in cis-regulatory elements (CREs). The combinations of DNA motifs acting within homeostasis and disease, however, are unclear. Gene expression, chromatin accessibility, TF footprinting, and H3K27ac-dependent DNA looping data were generated and a random-forest-based model was applied to identify 7,531 cell-type-specific cis-regulatory modules (CRMs) across 15 diploid human cell types. A co-enrichment framework within CRMs nominated 838 cell-type-specific, recurrent heterotypic DNA motif combinations (DMCs), which were functionally validated using massively parallel reporter assays. Cancer cells engaged DMCs linked to neoplasia-enabling processes operative in normal cells while also activating new DMCs only seen in the neoplastic state. This integrative approach identifies cell-type-specific cis-regulatory combinatorial DNA motifs in diverse normal and diseased human cells and represents a general framework for deciphering cis-regulatory sequence logic in gene regulation.
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Affiliation(s)
- Laura K.H. Donohue
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA,These authors contributed equally
| | - Margaret G. Guo
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,These authors contributed equally
| | - Yang Zhao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Synthego, Redwood City, CA, USA
| | - Namyoung Jung
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Rose T. Bussat
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,23andMe, Inc., Sunnyvale, CA, USA
| | - Daniel S. Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Poornima H. Neela
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Fauna Bio, Emeryville, CA, USA
| | - Laura N. Kellman
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Omar S. Garcia
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robin M. Meyers
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Russ B. Altman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Biomedical Informatics, Stanford University, Stanford, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Paul A. Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA,Stanford Program in Cancer Biology, Stanford University, Stanford, CA, USA,Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA,Lead contact,Correspondence:
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10
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Yenamandra AK, Smith RB, Senaratne TN, Kang SHL, Fink JM, Corboy G, Hodge CA, Lu X, Mathew S, Crocker S, Fang M. Evidence-based review of genomic aberrations in diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS): Report from the cancer genomics consortium lymphoma working group. Cancer Genet 2022; 268-269:1-21. [PMID: 35970109 DOI: 10.1016/j.cancergen.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/26/2022] [Accepted: 07/31/2022] [Indexed: 01/25/2023]
Abstract
Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). The 2016 World Health Organization (WHO) classification defined DLBCL, NOS and its subtypes based on clinical findings, morphology, immunophenotype, and genetics. However, even within the WHO subtypes, it is clear that additional clinical and genetic heterogeneity exists. Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. We gathered an international group of experts to review the current literature on DLBCL, NOS, with respect to genomic aberrations and the role they may play in the diagnosis, prognosis and therapeutic decisions. We comprehensively surveyed clinical laboratory directors/professionals about their genetic testing practices for DLBCL, NOS. The survey results indicated that a variety of diagnostic approaches were being utilized and that there was an overwhelming interest in further standardization of routine genetic testing along with the incorporation of new genetic testing modalities to help guide a precision medicine approach. Additionally, we present a comprehensive literature summary on the most clinically relevant genomic aberrations in DLBCL, NOS. Based upon the survey results and literature review, we propose a standardized, tiered testing approach which will help laboratories optimize genomic testing in order to provide the maximum information to guide patient care.
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Affiliation(s)
- Ashwini K Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37215, United States.
| | | | - T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, United States
| | - Sung-Hae L Kang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, United States
| | - James M Fink
- Department of Pathology and Laboratory Medicine, Hennepin Healthcare, Minneapolis, MN, United States
| | - Gregory Corboy
- Haematology, Pathology Queensland, Herston, Queensland, Australia; Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; School of Clinical Sciences, Monash University, Clayton, Vic, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, Vic, Australia
| | - Casey A Hodge
- Department of Pathology and Immunology, Barnes Jewish Hospital, St. Louis, MO, United States
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Susan Mathew
- Department of Pathology, Weill Cornell Medicine, New York, NY, United States
| | - Susan Crocker
- Department of Pathology and Molecular Medicine, Kingston Health Sciences Centre, Queen's University, Kingston, ON, Canada
| | - Min Fang
- Fred Hutchinson Cancer Center and University of Washington, Seattle, WA, United States
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11
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Liu C, Omilusik K, Toma C, Kurd NS, Chang JT, Goldrath AW, Wang W. Systems-level identification of key transcription factors in immune cell specification. PLoS Comput Biol 2022; 18:e1010116. [PMID: 36156073 PMCID: PMC9536753 DOI: 10.1371/journal.pcbi.1010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/06/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
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12
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Föh B, Buhre JS, Lunding HB, Moreno-Fernandez ME, König P, Sina C, Divanovic S, Ehlers M. Microbial metabolite butyrate promotes induction of IL-10+IgM+ plasma cells. PLoS One 2022; 17:e0266071. [PMID: 35333906 PMCID: PMC8956175 DOI: 10.1371/journal.pone.0266071] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
The microbially-derived short-chain fatty acid butyrate is a central inhibitor of inflammatory innate and adaptive immune responses. Emerging evidence suggests that butyrate induces differentiation of IL-10-producing (IL-10+) regulatory B cells. However, the underlying mechanisms of butyrate-driven modulation of B cell differentiation are not fully defined. Given the dominant role of regulatory plasma cells (PCs) as the main source of anti-inflammatory cytokines including IL-10 and the observation that butyrate also induces the differentiation of PCs, we here investigated the effect of the microbial metabolite butyrate on the induction of regulatory IL-10+ PCs and underlying mechanisms. Here we show that butyrate induces the differentiation of IL-10+IgM+ PCs. Ex vivo, butyrate, but hardly propionate, another microbially-derived short-chain fatty acid, induced the differentiation of IL-10+IgM+ CD138high PCs from isolated splenic murine B cells. In vivo, administration of butyrate via drinking water or by daily intraperitoneal injection increased the number of IL-10+IgM+ CD138high PCs in the spleens of Ovalbumin (Ova)/complete Freund’s adjuvant-immunized mice. The induction of these regulatory PCs was associated with an increase of anti-Ova IgM, but a reduction of anti-Ova class-switched pathogenic IgG2b serum antibodies. Based on the knowledge that butyrate inhibits histone deacetylases (HDACs) thereby increasing histone acetylation, we identified here that HDAC3 inhibition was sufficient to induce PC differentiation and IL-10+ expression. Furthermore, reduced mitochondrial superoxide levels following butyrate treatment and HDAC3 inhibition were necessary for PC differentiation, but not IL-10 expression. In summary, the microbial metabolite butyrate promotes the differentiation of IgM+ PCs and their expression of IL-10. HDAC3 inhibition may be involved as an underlying pathway for both PC differentiation and IL-10 expression, while reduced mitochondrial superoxide levels are crucial only for PC differentiation. The induction of regulatory IL-10+IgM+ PCs and the inhibition of class switching to antigen-specific pathogenic IgG subclasses might represent important pathways of butyrate to limit inflammation.
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Affiliation(s)
- Bandik Föh
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Medicine I, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Jana Sophia Buhre
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Hanna B. Lunding
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Maria E. Moreno-Fernandez
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Medicine I, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Senad Divanovic
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
- Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Marc Ehlers
- Institute of Nutritional Medicine, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Airway Research Center North, University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
- * E-mail:
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13
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Zhu Y, Yang G. Molecular identification and functional characterization of IRF4 from common carp (Cyprinus carpio. L) in immune response: a negative regulator in the IFN and NF-κB signalling pathways. BMC Vet Res 2022; 18:106. [PMID: 35300694 PMCID: PMC8928632 DOI: 10.1186/s12917-022-03205-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background The interferon (IFN) regulatory factors (IRFs) were originally identified as transcription factors playing critical roles in the regulation of IFN-related genes in the signal pathway. In mammals, IRF4 plays a vital role in both the innate and adaptive immune system. This study aims to reveal the molecular characterization, phylogenetic analysis, expression profiles and the regulatory role in the IFN and NF-κB signalling pathways of IRF4 in common carp (Cyprinus carpio. L) (abbreviation, ccIRF4). Results Here, ccIRF4 was identified and characterized, it contained a DNA binding domain (DBD) which possess five tryptophans and an IRF-associated domain (IAD). The predicted protein sequence of the ccIRF4 showed higher identities with grass carp (Ctenopharyngodon idella) and zebrafish (Danio rerio). Phylogenetic analysis suggested that ccIRF4 has the closest relationship with zebrafish IRF4. Quantitative real-time PCR analysis showed that ccIRF4 was constitutively expressed in all investigated tissues with the highest expression level in the gonad. Polyinosinic:polycytidylic acid (poly I:C) stimulation up-regulated the ccIRF4 expressions in the liver, spleen, head kidney, skin, foregut and hindgut. Upon Aeromonas hydrophila injection, the expression level of ccIRF4 was up-regulated in all tissues with the exception of spleen. In addition, ccIRF4 was induced by lipopolysaccharide (LPS), peptidoglycan (PGN) and Flagellin in head kidney leukocytes (HKLs). Overexpression of the ccIRF4 gene in epithelioma papulosum cyprini cells (EPC) down regulated the expressions of IFN-related genes and proinflammatory factors. Dual-luciferase reporter assay revealed that ccIRF4 decreased the activation of NF-κB through MyD88. Conclusions These results indicate that ccIRF4 participates in both antiviral and antibacterial immune response and negatively regulates the IFN and NF-κB response. Overall, our study on ccIRF4 provides more new insights into the innate immune system of common carp as well as a theoretical basis for investigating the pathogenesis and prevention of fish disease.
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Affiliation(s)
- Yaoyao Zhu
- Key Laboratory of Tropical Marine Fishery Resources Protection and Utilization of Hainan Province, College of Fisheries and Life Science, Hainan Tropical Ocean University, No. 1 Yucai Road, Sanya, 572022, China. .,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China.
| | - Guiwen Yang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014, China.
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14
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Sundararaj S, Seneviratne S, Williams SJ, Enders A, Casarotto MG. The molecular basis for the development of Adult T-cell leukemia/lymphoma in patients with an IRF4 K59R mutation. Protein Sci 2021; 31:787-796. [PMID: 34913532 DOI: 10.1002/pro.4260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022]
Abstract
Interferon regulatory factor 4 (IRF4) is an essential regulator in the development of many immune cells, including B and T cells and has been implicated directly in numerous haematological malignancies, including Adult T-cell leukemia/lymphoma (ATLL). Recently, an activating mutation in the DNA binding domain of IRF4 (IRF4K59R ), was found as a recurrent somatic mutation in ATLL patients. However, it remains unknown how this mutation gives rise to the observed oncogenic effect. To understand the mode of IRF4K59R mediated gain of function in ATLL pathogenesis, we have determined the structural and affinity basis of IRF4K59R /DNA homodimer complex using X-ray crystallography and surface plasmon resonance. Our study shows that arginine substitution (R59) results in the reorientation of the side chain, enabling the guanidium group to interact with the phosphate backbone of the DNA helix. This markedly contrasts with the IRF4WT wherein the K59 interacts exclusively with DNA bases. Further, the arginine mutation causes enhanced DNA bending, enabling the IRF4K59R to interact more robustly with known DNA targets, as evidenced by increased binding affinity of the protein-DNA complex. Together, we demonstrate how key structural features underpin the basis for this activating mutation, thereby providing a molecular rationale for IRF4K59R -mediated ATLL development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Srinivasan Sundararaj
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Sandali Seneviratne
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Simon J Williams
- Research School of Biology, Australian National University, Canberra, Australia
| | - Anselm Enders
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Center for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Marco G Casarotto
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
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15
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Molecular interactions of IRF4 in B cell development and malignancies. Biophys Rev 2021; 13:1219-1227. [DOI: 10.1007/s12551-021-00825-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022] Open
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16
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Stetson LC, Balasubramanian D, Ribeiro SP, Stefan T, Gupta K, Xu X, Fourati S, Roe A, Jackson Z, Schauner R, Sharma A, Tamilselvan B, Li S, de Lima M, Hwang TH, Balderas R, Saunthararajah Y, Maciejewski J, LaFramboise T, Barnholtz-Sloan JS, Sekaly RP, Wald DN. Single cell RNA sequencing of AML initiating cells reveals RNA-based evolution during disease progression. Leukemia 2021; 35:2799-2812. [PMID: 34244611 PMCID: PMC8807029 DOI: 10.1038/s41375-021-01338-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/19/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The prognosis of most patients with AML is poor due to frequent disease relapse. The cause of relapse is thought to be from the persistence of leukemia initiating cells (LIC's) following treatment. Here we assessed RNA based changes in LICs from matched patient diagnosis and relapse samples using single-cell RNA sequencing. Previous studies on AML progression have focused on genetic changes at the DNA mutation level mostly in bulk AML cells and demonstrated the existence of DNA clonal evolution. Here we identified in LICs that the phenomenon of RNA clonal evolution occurs during AML progression. Despite the presence of vast transcriptional heterogeneity at the single cell level, pathway analysis identified common signaling networks involving metabolism, apoptosis and chemokine signaling that evolved during AML progression and become a signature of relapse samples. A subset of this gene signature was validated at the protein level in LICs by flow cytometry from an independent AML cohort and functional studies were performed to demonstrate co-targeting BCL2 and CXCR4 signaling may help overcome therapeutic challenges with AML heterogeneity. It is hoped this work will facilitate a greater understanding of AML relapse leading to improved prognostic biomarkers and therapeutic strategies to target LIC's.
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Affiliation(s)
- L C Stetson
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Tammy Stefan
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Kalpana Gupta
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Xuan Xu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Slim Fourati
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Anne Roe
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Zachary Jackson
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Schauner
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Ashish Sharma
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Samuel Li
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Marcos de Lima
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Tae Hyun Hwang
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | | | - Yogen Saunthararajah
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Jaroslaw Maciejewski
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Thomas LaFramboise
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Rafick-Pierre Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - David N Wald
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
- Department of Pathology, University Hospitals Cleveland Medical Center and Louis Stokes Cleveland VA Medical Center, Cleveland, OH, USA.
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17
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Sundararaj S, Seneviratne S, Williams SJ, Enders A, Casarotto MG. Structural determinants of the IRF4/DNA homodimeric complex. Nucleic Acids Res 2021; 49:2255-2265. [PMID: 33533913 PMCID: PMC7913761 DOI: 10.1093/nar/gkaa1287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/22/2020] [Accepted: 02/01/2021] [Indexed: 11/15/2022] Open
Abstract
Interferon regulatory factor 4 (IRF4) is a key transcription factor (TF) in the regulation of immune cells, including B and T cells. It acts by binding DNA as both a homodimer and, in conjunction with other TFs, as a heterodimer. The choice of homo and heterodimeric/ DNA interactions is a critical aspect in the control of the transcriptional program and cell fate outcome. To characterize the nature of this interaction in the homodimeric complex, we have determined the crystal structure of the IRF4/ISRE homodimeric complex. We show that the complex formation is aided by a substantial DNA deformation with co-operative binding achieved exclusively through protein–DNA contact. This markedly contrasts with the heterodimeric form where DNA bound IRF4 is shown to physically interact with PU.1 TF to engage EICE1. We also show that the hotspot residues (Arg98, Cys99 and Asn102) contact both consensus and non-consensus sequences with the L1 loop exhibiting marked flexibility. Additionally, we identified that IRF4L116R, a mutant associated with chronic lymphocytic leukemia, binds more robustly to DNA thereby providing a rationale for the observed gain of function. Together, we demonstrate key structural differences between IRF4 homo and heterodimeric complexes, thereby providing molecular insights into IRF4-mediated transcriptional regulation.
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Affiliation(s)
- Srinivasan Sundararaj
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2600, Australia
| | - Sandali Seneviratne
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2600, Australia
| | - Simon J Williams
- Research School of Biology, Australian National University, Canberra 2600, Australia
| | - Anselm Enders
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra 2600, Australia.,Center for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Canberra 2600, Australia
| | - Marco G Casarotto
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2600, Australia
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18
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Chetta M, Tarsitano M, Vicari L, Saracino A, Bukvic N. In Silico Analysis of Possible Interaction between Host Genomic Transcription Factors (TFs) and Zika Virus (ZikaSPH2015) Strain with Combinatorial Gene Regulation; Virus Versus Host-The Game Reloaded. Pathogens 2021; 10:pathogens10010069. [PMID: 33466592 PMCID: PMC7828653 DOI: 10.3390/pathogens10010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
In silico analysis is a promising approach for understanding biological events in complex diseases. Herein we report on the innovative computational workflow allowed to highlight new direct interactions between human transcription factors (TFs) and an entire genome of virus ZikaSPH2015 strain in order to identify the occurrence of specific motifs on a genomic Zika Virus sequence that is able to bind and, therefore, sequester host’s TFs. The analysis pipeline was performed using different bioinformatics tools available online (free of charge). According to obtained results of this in silico analysis, it is possible to hypothesize that these TFs binding motifs might be able to explain the complex and heterogeneous phenotype presentation in Zika-virus-affected fetuses/newborns, as well as the less severe condition in adults. Moreover, the proposed in silico protocol identified thirty-three different TFs identical to the distribution of TFBSs (Transcription Factor Binding Sites) on ZikaSPH2015 strain, potentially able to influence genes and pathways with biological functions confirming that this approach could find potential answers on disease pathogenesis.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
- Correspondence:
| | - Marina Tarsitano
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Laura Vicari
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Annalisa Saracino
- Clinica di Malattie Infettive, Dipartimento di Scienze Biomediche ed Oncologia Umana, Università degli Studi “Aldo Moro” di Bari, 70124 Bari, Italy;
| | - Nenad Bukvic
- Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
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19
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Oppezzo A, Rosselli F. The underestimated role of the microphthalmia-associated transcription factor (MiTF) in normal and pathological haematopoiesis. Cell Biosci 2021; 11:18. [PMID: 33441180 PMCID: PMC7805242 DOI: 10.1186/s13578-021-00529-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Haematopoiesis, the process by which a restrained population of stem cells terminally differentiates into specific types of blood cells, depends on the tightly regulated temporospatial activity of several transcription factors (TFs). The deregulation of their activity or expression is a main cause of pathological haematopoiesis, leading to bone marrow failure (BMF), anaemia and leukaemia. TFs can be induced and/or activated by different stimuli, to which they respond by regulating the expression of genes and gene networks. Most TFs are highly pleiotropic; i.e., they are capable of influencing two or more apparently unrelated phenotypic traits, and the action of a single TF in a specific setting often depends on its interaction with other TFs and signalling pathway components. The microphthalmia-associated TF (MiTF) is a prototype TF in multiple situations. MiTF has been described extensively as a key regulator of melanocyte and melanoma development because it acts mainly as an oncogene. Mitf-mutated mice show a plethora of pleiotropic phenotypes, such as microphthalmia, deafness, abnormal pigmentation, retinal degeneration, reduced mast cell numbers and osteopetrosis, revealing a greater requirement for MiTF activity in cells and tissue. A growing amount of evidence has led to the delineation of key roles for MiTF in haematopoiesis and/or in cells of haematopoietic origin, including haematopoietic stem cells, mast cells, NK cells, basophiles, B cells and osteoclasts. This review summarizes several roles of MiTF in cells of the haematopoietic system and how MiTFs can impact BM development.
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Affiliation(s)
- Alessia Oppezzo
- CNRS UMR9019, Équipe labellisée La Ligue contre le Cancer, Gustave Roussy, 114 rue Edouard Vaillant, 94805, Villejuif, France. .,Gustave Roussy Cancer Center, 94805, Villejuif, France. .,Université Paris Saclay - Paris Sud, Orsay, France.
| | - Filippo Rosselli
- CNRS UMR9019, Équipe labellisée La Ligue contre le Cancer, Gustave Roussy, 114 rue Edouard Vaillant, 94805, Villejuif, France. .,Gustave Roussy Cancer Center, 94805, Villejuif, France. .,Université Paris Saclay - Paris Sud, Orsay, France.
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20
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Yu Y, Cheng L, Xu Z, Zhang Y, Ou C, Wang Q, Gao P, Ma J. Tissue distribution and developmental changes of interferon regulatory factors in chickens and effects of infectious bursal disease virus infection. Microb Pathog 2020; 152:104601. [PMID: 33137404 DOI: 10.1016/j.micpath.2020.104601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Interferon regulatory factors (IRFs) are a family of transcription factors that play a role in a variety of biological processes including immune regulation of interferon and expression of inflammatory cytokines. However, the data on IRFs are rather limited in chickens. In the present study, qRT-PCR was used to study the tissue distribution of IRFs in chickens at D15 (the 15th day of raising) and developmental changes of all chIRFs (Chicken interferon regulatory factors) in BF from E15 (the 15th day of incubation) to D15. The effects of IBDV infection with chickens on the transcriptional level of chIRFs were also investigated. The results showed: (1) chIRF1 mRNA was expressed much more abundantly in intestinal tract, chIRF2, chIRF6, chIRF7, chIRF8 and chIRF10 distributed mainly in liver or/and kidney. The expression of chIRF5 was mainly in spleen and chIRF4 distributed uniquely abundantly in BF. (2) The mRNA expression levels of chIRF5, chIRF7, chIRF8 and chIRF10 was low before hatching of chicken and at D1 and increased significantly from D5 till to the experiment end and the fold change of chIRF5 at D10 and chIRF7 at D5 reached 41.0-fold and 15.7-fold compared to that of E15, respectively (P < 0.05). ChIRF4 mRNA level was always high during the whole experiment except for E15 and it was 11.9-fold at the highest time point than that of E15 (the lowest time point). (3) When chicken was infected with IBDV, the expression levels of chIRF2, chIRF7 and chIRF10 mRNA had the tendency of increasing first and then decreasing but they peaked at 1dpi, 2 dpi, and 3dpi, respectively. The expression of chIRF5 mRNA was suppressed obviously during the whole experiment stage in IBDV-infected chicken. And chIRF4 expression was up-regulated transitorily at 1dpi and then was suppressed on a very low level till to the experiment end. Conclusion: The chIRFs were constitutively expressed in different tissues examined and has tissue-specific expression. Of them, chIRF2, chIRF4, chIRF5, chIRF7, chIRF8 and chIRF10 were related closely with the development or immune response of BF, and when chicken was infected with IBDV, some of them were activated, earlier or later on, some of them were suppressed. These findings would help to sieve out a few antiviral chIRF candidate gene to improve the host's innate immune and provide a foundation of the further exploiting a new vaccine adjuvant.
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Affiliation(s)
- Yan Yu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Lingling Cheng
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Zhiyong Xu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Yanhong Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Changbo Ou
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Qiuxia Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Pei Gao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Jinyou Ma
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
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21
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Capitano ML. CXXC5: A novel regulator of myelopoiesis. J Leukoc Biol 2020; 108:451-453. [PMID: 32745327 DOI: 10.1002/jlb.1ce0420-106r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/21/2020] [Accepted: 04/29/2020] [Indexed: 11/07/2022] Open
Abstract
Discussion on how CXXC5 alters hematopoiesis by regulating the differentiation of hematopoietic stem and progenitor cells toward monocyte development.
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Affiliation(s)
- Maegan L Capitano
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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22
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Koh J, Jang I, Choi S, Kim S, Jang I, Ahn HK, Lee C, Paik JH, Kim CW, Lim MS, Kim K, Jeon YK. Discovery of Novel Recurrent Mutations and Clinically Meaningful Subgroups in Nodal Marginal Zone Lymphoma. Cancers (Basel) 2020; 12:cancers12061669. [PMID: 32585984 PMCID: PMC7352856 DOI: 10.3390/cancers12061669] [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: 05/19/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022] Open
Abstract
Nodal marginal zone lymphoma (NMZL) is a rare B-cell neoplasm, the genetic and transcriptomic landscape of which are unclear. Using high-throughput sequencing for whole-exome and transcriptome, we investigated the genetic characteristics of NMZL in a discovery cohort (n = 8) and validated their features in an extended cohort (n = 30). Novel mutations in NFKBIE and ITPR2 were found in 7.9% (3/38) and 13.9% (5/36), respectively, suggesting roles for the NF-κB pathway and B-cell-receptor-mediated calcium signaling pathway in the pathogenesis of NMZL. RNA-seq showed that NMZLs were characterized by an aberrant marginal zone differentiation, associated with an altered IRF4-NOTCH2 axis and the enrichment of various oncogenic pathways. Based on gene expression profile, two subgroups were identified. Compared with subgroup 1, subgroup 2 showed the following: the significant enrichment of cell cycle-associated and MYC-signaling pathways, a more diverse repertoire of upstream regulators, and higher Ki-67 proliferation indices. We designated two subgroups according to Ki-67 labeling, and subgroup 2 was significantly associated with a shorter progression-free survival (p = 0.014), a greater proportion of large cells (p = 0.009), and higher MYC expression (p = 0.026). We suggest that NMZL has unique features and, in this study, we provide information as to the heterogeneity of this enigmatic entity.
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Affiliation(s)
- Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea; (J.K.); (S.K.); (C.L.); (C.W.K.)
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Insoon Jang
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; (I.J.); (S.C.)
| | - Seongmin Choi
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; (I.J.); (S.C.)
- Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sehui Kim
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea; (J.K.); (S.K.); (C.L.); (C.W.K.)
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Ingeon Jang
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Hyun Kyung Ahn
- Cancer Research Institute, Seoul National University, Seoul 03080, Korea;
| | - Cheol Lee
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea; (J.K.); (S.K.); (C.L.); (C.W.K.)
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Jin Ho Paik
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam-si 46371, Korea;
| | - Chul Woo Kim
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea; (J.K.); (S.K.); (C.L.); (C.W.K.)
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Megan S. Lim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA;
| | - Kwangsoo Kim
- Division of Clinical Bioinformatics, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea; (I.J.); (S.C.)
- Correspondence: (K.K.); (Y.K.J.)
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea; (J.K.); (S.K.); (C.L.); (C.W.K.)
- Department of Pathology, Seoul National University College of Medicine, Seoul 03080, Korea;
- Cancer Research Institute, Seoul National University, Seoul 03080, Korea;
- Correspondence: (K.K.); (Y.K.J.)
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23
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Bigley V, Collin M. Insights from Patients with Dendritic Cell Immunodeficiency. Mol Immunol 2020; 122:116-123. [PMID: 32344243 DOI: 10.1016/j.molimm.2020.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/27/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022]
Abstract
Dendritic Cells (DCs), derived from haematopoietic stem cells, are critical to the dynamic and balanced functioning of the intact immune system and are of great interest as vehicles of immunotherapy. Genetically modified mouse models have proved powerful tools to map DC development and function in vivo but human studies have previously relied heavily on in vitro systems. Human dendritic cell immunodeficiency, resulting from single gene mutations, offers new opportunities to dissect the role of human DCs in vivo, determine the genetic requirements for their development and map their haematopoietic differentiation pathways. This review will summarise the clinical phenotypes of mutations in GATA2, IRF8 and IKZF1 genes which result in global or subset specific dendritic cell deficiencies, discuss the functional consequences of these cytopenias and how these syndromes have informed our knowledge of DC differentiation and human haematopoiesis.
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Affiliation(s)
- Venetia Bigley
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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24
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Regulation of B-cell function by NF-kappaB c-Rel in health and disease. Cell Mol Life Sci 2020; 77:3325-3340. [PMID: 32130429 DOI: 10.1007/s00018-020-03488-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/03/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
B cells mediate humoral immune response and contribute to the regulation of cellular immune response. Members of the Nuclear Factor kappaB (NF-κB) family of transcription factors play a major role in regulating B-cell functions. NF-κB subunit c-Rel is predominantly expressed in lymphocytes, and in B cells, it is required for survival, proliferation, and antibody production. Dysregulation of c-Rel expression and activation alters B-cell homeostasis and is associated with B-cell lymphomas and autoimmune pathologies. Based on its essential roles, c-Rel may serve as a potential prognostic and therapeutic target. This review summarizes the current understanding of the multifaceted role of c-Rel in B cells and B-cell diseases.
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25
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Enhancer jungles establish robust tissue-specific regulatory control in the human genome. Genomics 2019; 112:2261-2270. [PMID: 31887344 DOI: 10.1016/j.ygeno.2019.12.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 11/21/2022]
Abstract
An increasing number of studies suggest that functionally redundant enhancers safeguard development via buffering gene expression against environmental and genetic perturbations. Here, we identified over-represented clusters of enhancers (enhancer jungles or EJs) in human B lymphoblastoid cells. We found that EJs tend to associate with genes involved in the activation of the immune system response. Although spanning multiple genes, the enhancers within an EJ tend to collaborate with each other on regulating a single gene. The employment of homotypic transcription factor binding sites (TFBSs) in EJ enhancers and heterotypic TFBSs between constituent enhancers within an EJ may safeguard a robust transcriptional output of the target gene. EJ enhancers evolve under a weaker selective pressure compared to regular enhancers (REs), and approximately 35% of EJs do not have orthologues in the mouse genome. In GM12878, these human-specific EJs appear to regulate genes associated with the adaptive immune system response, while the conserved EJs are associated with innate immunity. Recently acquired human EJs are associated with the higher level of target gene expression compared with conserved EJs, thus facilitating the environmental adaptation of the organism during evolution. In short, the existence of EJs is a common regulatory architecture conferring a robust regulatory control for key lineage genes.
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26
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Speedy HE, Beekman R, Chapaprieta V, Orlando G, Law PJ, Martín-García D, Gutiérrez-Abril J, Catovsky D, Beà S, Clot G, Puiggròs M, Torrents D, Puente XS, Allan JM, López-Otín C, Campo E, Houlston RS, Martín-Subero JI. Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics. Nat Commun 2019; 10:3615. [PMID: 31399598 PMCID: PMC6689100 DOI: 10.1038/s41467-019-11582-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/23/2019] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies have provided evidence for inherited genetic predisposition to chronic lymphocytic leukemia (CLL). To gain insight into the mechanisms underlying CLL risk we analyze chromatin accessibility, active regulatory elements marked by H3K27ac, and DNA methylation at 42 risk loci in up to 486 primary CLLs. We identify that risk loci are significantly enriched for active chromatin in CLL with evidence of being CLL-specific or differentially regulated in normal B-cell development. We then use in situ promoter capture Hi-C, in conjunction with gene expression data to reveal likely target genes of the risk loci. Candidate target genes are enriched for pathways related to B-cell development such as MYC and BCL2 signalling. At 14 loci the analysis highlights 63 variants as the probable functional basis of CLL risk. By integrating genetic and epigenetic information our analysis reveals novel insights into the relationship between inherited predisposition and the regulatory chromatin landscape of CLL.
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MESH Headings
- B-Lymphocytes/metabolism
- Base Sequence
- Chromatin/metabolism
- DNA Methylation
- Epigenesis, Genetic/genetics
- Epigenesis, Genetic/physiology
- Epigenomics
- Gene Expression Regulation, Leukemic
- Genetic Predisposition to Disease/genetics
- Genome-Wide Association Study
- Genotype
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Polymorphism, Single Nucleotide
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors
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Affiliation(s)
- Helen E Speedy
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Renée Beekman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Vicente Chapaprieta
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain
| | - Giulia Orlando
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - David Martín-García
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Jesús Gutiérrez-Abril
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Daniel Catovsky
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Montserrat Puiggròs
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
| | - David Torrents
- Programa Conjunto de Biología Computacional, Barcelona Supercomputing Center (BSC), Institut de Recerca Biomèdica (IRB), Spanish National Bioinformatics Institute, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Carlos López-Otín
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain
- Hematopathology Section, Hospital Clinic of Barcelona, 08036, Barcelona, Spain
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SW7 3RP, UK.
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, 08036, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
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27
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Kaur A, Lee LH, Chow SC, Fang CM. IRF5-mediated immune responses and its implications in immunological disorders. Int Rev Immunol 2018; 37:229-248. [PMID: 29985675 DOI: 10.1080/08830185.2018.1469629] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transcription factors are gene regulators that activate or repress target genes. One family of the transcription factors that have been extensively studied for their crucial role in regulating gene network in the immune system is the interferon regulatory factors (IRFs). IRFs possess a novel turn-helix turn motif that recognizes a specific DNA consensus found in the promoters of many genes that are involved in immune responses. IRF5, a member of IRFs has recently gained much attention for its role in regulating inflammatory responses and autoimmune diseases. Here, we discuss the role of IRF5 in regulating immune cells functions and how the dysregulation of IRF5 contributes to the pathogenesis of immune disorders. We also review the latest findings of potential IRF5 inhibitors that modulate IRF5 activity in the effort of developing therapeutic approaches for treating inflammatory disorders.
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Affiliation(s)
- Ashwinder Kaur
- a School of Pharmacy, Faculty of Science , The University of Nottingham Malaysia Campus , Selangor Darul , Ehsan , Malaysia
| | - Learn-Han Lee
- c School of Pharmacy , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia.,e Jeffrey Cheah School of Medicine and Health Sciences , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia
| | - Sek-Chuen Chow
- d School of Science , Monash University Malaysia , Selangor Darul , Ehsan , Malaysia
| | - Chee-Mun Fang
- b Department of Biomedical Sciences, Faculty of Science , The University of Nottingham Malaysia Campus , Selangor Darul , Ehsan , Malaysia
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28
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Bigley V, Maisuria S, Cytlak U, Jardine L, Care MA, Green K, Gunawan M, Milne P, Dickinson R, Wiscombe S, Parry D, Doffinger R, Laurence A, Fonseca C, Stoevesandt O, Gennery A, Cant A, Tooze R, Simpson AJ, Hambleton S, Savic S, Doody G, Collin M. Biallelic interferon regulatory factor 8 mutation: A complex immunodeficiency syndrome with dendritic cell deficiency, monocytopenia, and immune dysregulation. J Allergy Clin Immunol 2018; 141:2234-2248. [PMID: 29128673 PMCID: PMC5986711 DOI: 10.1016/j.jaci.2017.08.044] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND The homozygous K108E mutation of interferon regulatory factor 8 (IRF8) is reported to cause dendritic cell (DC) and monocyte deficiency. However, more widespread immune dysfunction is predicted from the multiple roles ascribed to IRF8 in immune cell development and function. OBJECTIVE We sought to describe the effect on hematopoiesis and immunity of the compound heterozygous R83C/R291Q mutation of IRF8, which is present in a patient with recurrent viral infection, granuloproliferation, and intracerebral calcification. METHODS Variant IRF8 alleles were identified by means of exome sequencing, and their function was tested by using reporter assays. The cellular phenotype was studied in detail by using flow cytometry, functional immunologic assay transcriptional profiling, and antigen receptor profiling. RESULTS Both mutations affected conserved residues, and R291Q is orthologous to R294, which is mutated in the BXH2 IRF8-deficient mouse. R83C showed reduced nuclear translocation, and neither mutant was able to regulate the Ets/IRF composite element or interferon-stimulated response element, whereas R291Q retained BATF/JUN interactions. DC deficiency and monocytopenia were observed in blood, dermis, and lung lavage fluid. Granulocytes were consistently increased, dysplastic, and hypofunctional. Natural killer cell development and maturation were arrested. TH1, TH17, and CD8+ memory T-cell differentiation was significantly reduced, and T cells did not express CXCR3. B-cell development was impaired, with fewer memory cells, reduced class-switching, and lower frequency and complexity of somatic hypermutation. Cell-specific gene expression was widely disturbed in interferon- and IRF8-regulated transcripts. CONCLUSIONS This analysis defines the clinical features of human biallelic IRF8 deficiency, revealing a complex immunodeficiency syndrome caused by DC and monocyte deficiency combined with widespread immune dysregulation.
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Affiliation(s)
- Venetia Bigley
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
| | - Sheetal Maisuria
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, United Kingdom
| | - Urszula Cytlak
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Matthew A Care
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Merry Gunawan
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul Milne
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Rachel Dickinson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sarah Wiscombe
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Parry
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Arian Laurence
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Claudia Fonseca
- Cambridge Protein Arrays, Babraham Research Campus, Cambridge, United Kingdom
| | - Oda Stoevesandt
- Cambridge Protein Arrays, Babraham Research Campus, Cambridge, United Kingdom
| | - Andrew Gennery
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Andrew Cant
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Reuben Tooze
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - A John Simpson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sophie Hambleton
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sinisa Savic
- National Institute for Health Research-Leeds Musculoskeletal Biomedical Research Unit and Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, United Kingdom
| | - Gina Doody
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Matthew Collin
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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29
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Zhong W, Xu X, Zhu Z, Du Q, Du H, Yang L, Ling Y, Xiong H, Li Q. Increased expression of IRF8 in tumor cells inhibits the generation of Th17 cells and predicts unfavorable survival of diffuse large B cell lymphoma patients. Oncotarget 2018; 8:49757-49772. [PMID: 28537908 PMCID: PMC5564805 DOI: 10.18632/oncotarget.17693] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/18/2017] [Indexed: 01/08/2023] Open
Abstract
The immunological pathogenesis of diffuse large B cell lymphoma (DLBCL) remains elusive. Searching for new prognostic markers of DLBCL is a crucial focal point for clinical scientists. The aim of the present study was to examine the prognostic value of interferon regulatory factor 8 (IRF8) expression and its effect on the development of Th17 cells in the tumor microenvironment of DLBCL patients. Flow cytometry, immunohistochemistry, and quantitative real-time PCR were used to detect the distribution of Th17 cells and related cytokines and IRF8 in tumor tissues from DLBCL patients. Two DLBCL cell lines (OCI-LY10 and OCI-LY1) with IRF8 knockdown or overexpression and two human B lymphoblast cell lines were co-cultured with peripheral blood mononuclear cells (PBMCs) in vitro to determine the effect of IRF8 on the generation of Th17 cells. Quantitative real-time PCR and Western blotting were used to investigate the involvement of retinoic acid receptor-related orphan receptor gamma t (RORγt) in the effect of IRF8 on Th17 cell generation. The survival of 67 DLBCL patients was estimated using the Kaplan-Meier method and log-rank analysis. The percentage of Th17 cells was lower in DLBCL tumor tissues than in PBMCs and corresponding adjacent benign tissues. Relative expression of interleukin (IL)-17A was lower, whereas that of interferon (IFN)-γ was higher in tumor tissues than in benign tissues. Co-culture with DLBCL cell lines inhibited the generation of Th17 cells in vitro. IRF8 upregulation was detected in DLBCL tumor tissues, and it was associated with decreased DLBCL patient survival. Investigation of the underlying mechanism suggested that IRF8 upregulation in DLBCL, through an unknown mechanism, inhibited Th17 cell generation by suppressing RORγt in neighboring CD4+ T cells. Tumor cells may express soluble or membrane-bound factors that inhibit the expression of RORγt in T cells within the tumor microenvironment. Our findings suggest that IRF8 expression could be a prognostic factor for DLBCL.
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Affiliation(s)
- Weijie Zhong
- Department of Hematology & Oncology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- Department of Hematology & Oncology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Immunology Institute, Mount Sinai School of Medicine, New York, NY, USA
| | - Zhigang Zhu
- Department of Hematology & Oncology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qinghua Du
- Department of Hematology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hong Du
- Department of Pathology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Li Yang
- Department of Hematology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Guangdong Esophageal Cancer Institute, Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Yanying Ling
- Department of Laboratory, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Huabao Xiong
- Immunology Institute, Mount Sinai School of Medicine, New York, NY, USA
| | - Qingshan Li
- Department of Hematology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
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30
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Laghari ZA, Li L, Chen SN, Huo HJ, Huang B, Zhou Y, Nie P. Composition and transcription of all interferon regulatory factors (IRFs), IRF1‒11 in a perciform fish, the mandarin fish, Siniperca chuatsi. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:127-140. [PMID: 29180032 DOI: 10.1016/j.dci.2017.11.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/23/2017] [Accepted: 11/23/2017] [Indexed: 06/07/2023]
Abstract
Interferon regulatory factors (IRFs) are a family of mediators in various biological processes including immune modulation of interferon (IFN) and proinflammatory cytokine expression. However, the data on the complete composition of IRFs is rather limited in teleost fish. In the present study, all IRF members, i.e. IRF1‒11 with two IRF4, IRF4a and IRF4b have been characterised in an aquaculture species of fish, the mandarin fish, Siniperca chuatsi, in addition to the previous report of IRF1, IRF2, IRF3 and IRF7 from the fish. These IRFs are constitutively expressed in various organs/tissues of the fish, and their expression can be induced following the stimulation of polyinosinic:polycytidylic acid (poly(I:C)) and the infection of infectious spleen and kidney necrosis virus (ISKNV), a viral pathogen of mandarin fish in aquaculture. The ISKNV infection induced the significant increase in the expression of some IRF genes, i.e. IRF2, IRF4a, IRF7, IRF9, IRF10 at 24 or 36 h post-infection (hpi) in spleen and head-kidney, and the significant increase of some other IRF genes, e.g. IRF1, IRF3, IRF4b, IRF5, IRF6, IRF8 at later stage of infection from 72, or 96, or even 120 hpi, which may imply the inhibitory effect of ISKNV on fish immune response. It is considered that the present study provides the first detailed analysis on all IRF members in an aquaculture species of fish, and can be served as the base for further investigation on the role of IRFs in teleost fish.
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Affiliation(s)
- Zubair Ahmed Laghari
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Hui Jun Huo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Bei Huang
- College of Fisheries, Jimei University, Xiamen, Fujian Province, 361021, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - P Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China.
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31
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Zhang Y, Jia X, Xia Y, Li H, Chen F, Zhu J, Zhang X, Zhang Y, Wang Y, Xu Y, Pan M, Huang X, Yu T, Fu L, Xiao C, Geng D. Altered expression of transcription factors IRF4 and IRF8 in peripheral blood B cells is associated with clinical severity and circulating plasma cells frequency in patients with myasthenia gravis. Autoimmunity 2018; 51:126-134. [PMID: 29569949 DOI: 10.1080/08916934.2018.1454913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Zhang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao Jia
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Xia
- Department of Rehabilitation, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hao Li
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Fei Chen
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jie Zhu
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiuying Zhang
- Department of Neurology, Shenzhen Guangming New District Central Hospital, Shenzhen, China
| | - Yanyan Zhang
- Department of Neurology, The Third People’s Hospital of Xuzhou, Xuzhou, Jiangsu, China
| | - YuZhong Wang
- Department of Neurology, Affiliated Hospital of Jining Medical college, Jining, Shandong, China
| | - Yanan Xu
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Meng Pan
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaoyu Huang
- Class 2014, Excellent Physician Class of Clinical Medicine Department, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tingyan Yu
- Class 2014, Excellent Physician Class of Clinical Medicine Department, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Linlin Fu
- Department of Pathogenic Biology, Laboratory of Infection and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chenghua Xiao
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Deqin Geng
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
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32
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Bigley V, Cytlak U, Collin M. Human dendritic cell immunodeficiencies. Semin Cell Dev Biol 2018; 86:50-61. [PMID: 29452225 DOI: 10.1016/j.semcdb.2018.02.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/28/2017] [Accepted: 02/10/2018] [Indexed: 12/21/2022]
Abstract
The critical functions of dendritic cells (DCs) in immunity and tolerance have been demonstrated in many animal models but their non-redundant roles in humans are more difficult to probe. Human primary immunodeficiency (PID), resulting from single gene mutations, may result in DC deficiency or dysfunction. This relatively recent recognition illuminates the in vivo role of human DCs and the pathophysiology of the associated clinical syndromes. In this review, the development and function of DCs as established in murine models and human in vitro systems, discussed. This forms the basis of predicting the effects of DC deficiency in vivo and understanding the consequences of specific mutations on DC development and function. DC deficiency syndromes are associated with heterozygous GATA2 mutation, bi-allelic and heterozygous IRF8 mutation and heterozygous IKZF1 mutation. The intricate involvement of DCs in the balance between immunity and tolerance is leading to increased recognition of their involvement in a number of other immunodeficiencies and autoimmune conditions. Owing to the precise control of transcription factor gene expression by super-enhancer elements, phenotypic anomalies are relatively commonly caused by heterozygous mutations.
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Affiliation(s)
- Venetia Bigley
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Urszula Cytlak
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Collin
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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33
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Shukla V, Shukla A, Joshi SS, Lu R. Interferon regulatory factor 4 attenuates Notch signaling to suppress the development of chronic lymphocytic leukemia. Oncotarget 2018; 7:41081-41094. [PMID: 27232759 PMCID: PMC5173044 DOI: 10.18632/oncotarget.9596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/14/2016] [Indexed: 11/25/2022] Open
Abstract
Molecular pathogenesis of Chronic Lymphocytic Leukemia (CLL) is not fully elucidated. Genome wide association studies have linked Interferon Regulatory Factor 4 (IRF4) to the development of CLL. We recently established a causal relationship between low levels of IRF4 and development of CLL. However, the molecular mechanism through which IRF4 suppresses CLL development remains unclear. Deregulation of Notch signaling pathway has been identified as one of the most recurrent molecular anomalies in the pathogenesis of CLL. Yet, the role of Notch signaling as well as its regulation during CLL development remains poorly understood. Previously, we demonstrated that IRF4 deficient mice expressing immunoglobulin heavy chain Vh11 (IRF4−/−Vh11) developed spontaneous CLL with complete penetrance. In this study, we show that elevated Notch2 expression and the resulting hyperactivation of Notch signaling are common features of IRF4−/−Vh11 CLL cells. Our studies further reveal that Notch signaling is indispensable for CLL development in the IRF4−/−Vh11 mice. Moreover, we identify E3 ubiquitin ligase Nedd4, which targets Notch for degradation, as a direct target of IRF4 in CLL cells and their precursors. Collectively, our studies provide the first in vivo evidence for an essential role of Notch signaling in the development of CLL and establish IRF4 as a critical regulator of Notch signaling during CLL development.
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Affiliation(s)
- Vipul Shukla
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ashima Shukla
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shantaram S Joshi
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Runqing Lu
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
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34
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Li S, Hu G, Chen Z, Song L, Wang G, Liu D, Liu Q. Cloning and expression study of an IRF4a gene and its two transcript variants in turbot, Scophthalmus maximus. FISH & SHELLFISH IMMUNOLOGY 2018; 72:389-398. [PMID: 29054828 DOI: 10.1016/j.fsi.2017.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/09/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
Interferon regulatory factor 4 (IRF4) is known to be involved in antiviral response as well as regulation of functional and developmental processes in lymphomyeloid cell lineages in mammals. In this study, the gene of IRF4a and its two transcript variants (named IRF4a1 and -2) were cloned from turbot, Scophthalmus maximus, the tissue distributions and in vivo immune responsive expression patterns of the two transcripts were subsequently examined. The Scophthalmus maximus (Sm)IRF4a gene is 8367 nucleotide (nt) in length, consisting of eight exons and seven introns. The SmIRF4a1 transcript is 3185 nt long, containing an open reading frame (ORF) of 1401 nt that encodes a polypeptide of 466 amino acids (aa). The SmIRF4a2 transcript is 2265 nt long and identical with the SmIRF4a1 from position 1 to 1171, containing an ORF of 1164 nt that encodes a truncated protein of 387 aa as a result of a frame shift in exon 6 which introduces a premature stop codon. The deduced aa sequence of SmIRF4a1 posses a DNA-binding domain (DBD), a nuclear localization signal (NLS), a serine-rich domain (SRD) and an IRF association domain (IAD), while SmIRF4a2 lacks the C-terminal 52 residues of the IAD and the downstream C-terminal extension, instead, they are replaced by a 8-aa segment although the three upstream domains are intact. Quantitative real-time PCR analysis revealed a broad tissue expression for both SmIRF4a1 and -2 with the former showing a significantly higher expression in all examined tissues except skin. Expressions of two transcript variants after stimulation with polyinosinic:polycytidylic acid [poly(I:C)] and turbot reddish body iridovirus (TRBIV) were tested in gills, spleen, head kidney and muscle. A two-wave of induced expression pattern was observed for both transcripts with either stimulus treatment during a 7-day time course. SmIRF4a2 responded more promptly to the stimuli and showed a higher level of inducibility in the early phase while SmIRF4a1 was strongly detected in the later phase. These data suggest an important role of SmIRF4a2 in the fast immune response under a background of SmIRF4a1-dominant antiviral response in the IRF4a system of turbot.
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Affiliation(s)
- Song Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
| | - Zhipeng Chen
- College of Fisheries, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lianfei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Guanjie Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Dahai Liu
- First Institute of Oceanography, State Oceanic Administration of China, Qingdao 266061, China
| | - Qiuming Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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35
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Haljasorg U, Dooley J, Laan M, Kisand K, Bichele R, Liston A, Peterson P. Irf4 Expression in Thymic Epithelium Is Critical for Thymic Regulatory T Cell Homeostasis. THE JOURNAL OF IMMUNOLOGY 2017; 198:1952-1960. [DOI: 10.4049/jimmunol.1601698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022]
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36
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Almamun M, Kholod O, Stuckel AJ, Levinson BT, Johnson NT, Arthur GL, Davis JW, Taylor KH. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2017; 58:1-12. [PMID: 28094574 DOI: 10.1080/10428194.2016.1272683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Olha Kholod
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Alexei J Stuckel
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Benjamin T Levinson
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Nathan T Johnson
- b Bioinformatics and Computational Biology , Worcester Polytechnic Institute , Worcester , MA , USA
| | - Gerald L Arthur
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - J Wade Davis
- c Department of Health Management and Informatics , University of Missouri-Columbia , Columbia , MO , USA
| | - Kristen H Taylor
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
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Ai K, Luo K, Li Y, Hu W, Gao W, Fang L, Tian G, Ruan G, Xu Q. Expression pattern analysis of IRF4 and its related genes revealed the functional differentiation of IRF4 paralogues in teleost. FISH & SHELLFISH IMMUNOLOGY 2017; 60:59-64. [PMID: 27856326 DOI: 10.1016/j.fsi.2016.11.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 11/09/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
In mammals, interferon regulatory factor 4 (IRF4) plays an important role in the process of development and differentiation of B cells, T cells and dendritic cells. It can regulate immune pathway through IRF5, MyD88, IL21, PGC1α, and NOD2. In the present study, we investigated the expression pattern of IRF4 paralogues and these related genes for the first time in teleosts. The results showed that these genes were all expressed predominantly in known immune tissues while IRF5 was also relatively highly expressed in muscle. IRF4b, IL21, MyD88, IRF5 and NOD2 showed maternal expression in the oocyte and the higher expression of IRF4a, Mx and PGC1α before hatching might be involved in the embryonic innate defense system. Zebrafish embryonic fibroblast (ZF4) cells were infected with GCRV and SVCV. During GCRV infection, the expression of Mx was significantly up-regulated from 3 h to 24 h, reaching the highest level at 12 h (101.5-fold over the controls, P < 0.001). And the expression of IRF4a was significantly up-regulated from 3 h to 48 h, reaching the highest level at 12 h (13.75-fold over the controls, P < 0.001). While the expression of IRF4b was only slightly up-regulated at 12 h and 24 h (3.39-fold, 1.93-fold) above control levels, respectively. Whereas the expression of Mx was significantly up-regulated during SVCV infection from 1 h to 48 h, reaching the highest level at 24 h (11.49-fold over the controls, P < 0.001). IRF4a transcripts were significantly up-regulated from 6 h to 24 h, reaching the highest level at 24 h (41-fold over the controls, P < 0.01). IRF4b only showed a slightly up-regulation by SVCV at 24 h (3.2-fold over the controls, P < 0.01). IRF4a and IRF4b displayed a distinct tissue expression pattern, embryonic stages expression and inducible expression in vivo and in vitro, suggesting that IRF4 paralogues might play different roles in immune system.
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Affiliation(s)
- Kete Ai
- School of Animal Science, Yangtze University, Jingzhou, 434020, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Kai Luo
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Youshen Li
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Weihua Gao
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Liu Fang
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Guangming Tian
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Guoliang Ruan
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Qiaoqing Xu
- School of Animal Science, Yangtze University, Jingzhou, 434020, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China.
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Liu D, Chen J, Zhang H, Hu M, Lou H, Liu Q, Zhang S, Hu G. Interferon regulatory factor 4b (IRF4b) in Japanese flounder, Paralichthys olivaceus: Sequencing, ubiquitous tissue distribution and inducible expression by poly(I:C) and DNA virus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 62:127-133. [PMID: 27084058 DOI: 10.1016/j.dci.2016.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 04/10/2016] [Accepted: 04/10/2016] [Indexed: 06/05/2023]
Abstract
Interferon regulatory factor 4 (IRF4) in mammals is known to be critical in regulation of development and functions of lymphomyeloid cell lineages. Recent studies have demonstrated its involvement in immune responses to bacterial and viral challenges in teleosts. In this study, an IRF4 gene was cloned from Japanese flounder (Paralichthys olivaceus) and its expression in response to polyinosinic:polycytidylic acid [poly(I:C)] and lymphocystis disease virus (LCDV) stimulations was studied in vivo. The cloned gene spans over 5.9 kb, comprises eight exons and seven introns and encodes a putative protein of 456 amino acids. The deduced amino acid sequence possesses a conserved DNA-binding domain (DBD), an IRF-association domain (IAD) and a nuclear localization signal (NLS). Phylogenetic analysis clustered it into the teleost IRF4b clade and, thus, it was named Paralichthys olivaceus (Po)IRF4b. The constitutive expression of PoIRF4b transcripts was detectable in all examined organs, with highest levels found in lymphomyeloid-rich tissues. They were induced by both poly(I:C) and LCDV with a similar inducibility in immune or non-immune organs. Two waves of induced expression of PoIRF4b were observed with the two stimuli during a 7-day time course in the immune organs, with the early-phase induction being stronger. The maximum increases of PoIRF4b transcript levels ranged from 1.3 to 4.0-fold and appeared at day 1-5 post-injection depending on different organs and stimuli. In both stimulation cases, the strongest induction was detected in spleen and the weakest in muscle. These results indicate that PoIRF4b may participate in regulation of immune responses of flounders to both RNA and DNA virus infections.
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Affiliation(s)
- Dahai Liu
- First Institute of Oceanography, State Oceanic Administration of China, Qingdao 266061, China
| | - Jinjing Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haiyan Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mengzhu Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huimin Lou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Qiuming Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shicui Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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39
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Smith SM, Carew NT, Milcarek C. RNA polymerases in plasma cells trav-ELL2 the beat of a different drum. World J Immunol 2015; 5:99-112. [DOI: 10.5411/wji.v5.i3.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/19/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
There is a major transformation in gene expression between mature B cells (including follicular, marginal zone, and germinal center cells) and antibody secreting cells (ASCs), i.e., ASCs, (including plasma blasts, splenic plasma cells, and long-lived bone marrow plasma cells). This significant change-over occurs to accommodate the massive amount of secretory-specific immunoglobulin that ASCs make and the export processes itself. It is well known that there is an up-regulation of a small number of ASC-specific transcription factors Prdm1 (B-lymphocyte-induced maturation protein 1), interferon regulatory factor 4, and Xbp1, and the reciprocal down-regulation of Pax5, Bcl6 and Bach2, which maintain the B cell program. Less well appreciated are the major alterations in transcription elongation and RNA processing occurring between B cells and ASCs. The three ELL family members ELL1, 2 and 3 have different protein sequences and potentially distinct cellular roles in transcription elongation. ELL1 is involved in DNA repair and small RNAs while ELL3 was previously described as either testis or stem-cell specific. After B cell stimulation to ASCs, ELL3 levels fall precipitously while ELL1 falls off slightly. ELL2 is induced at least 10-fold in ASCs relative to B cells. All of these changes cause the RNA Polymerase II in ASCs to acquire different properties, leading to differences in RNA processing and histone modifications.
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Xu Y, Jiang L, Fang J, Fang R, Morse HC, Ouyang G, Zhou JX. Loss of IRF8 Inhibits the Growth of Diffuse Large B-cell Lymphoma. J Cancer 2015; 6:953-61. [PMID: 26316891 PMCID: PMC4543755 DOI: 10.7150/jca.12067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022] Open
Abstract
IRF8 is a transcription factor with a critical role in B lymphocyte development and functions. Its role in human diffuse large B-cell lymphoma (DLBCL), however, remained elusive. In this study, using shRNA-mediated knockdown of IRF8 expression, we found that the loss of IRF8 significantly reduced the proliferation of DLBCL cells (P<0.05). Mechanistically, decreasing the levels of IRF8 led to a suppression of the phosphorylation of p38 and ERK, molecules critical for B cell proliferation. Furthermore, using a xenograft lymphoma mouse model, we found that the loss of IRF8 significantly inhibited the growth of lymphomas in vivo (P<0.05). Immunohistochemical analysis of human DLBCL tissues revealed that the levels of IRF8 were significantly greater in non-germinal center B-cell-like (non-GCB) subtype than that in GCB subtype (P<0.05). Analysis of public available data also suggested that the expression levels of IRF8 mRNA in human DLBCL tissues were inversely correlated with patients' overall survival time. Taken together, this study suggested that IRF8 may play an oncogenic role in human DLBCL by promoting cell proliferation.
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Affiliation(s)
- Yulian Xu
- 1. Department of Pathology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Lei Jiang
- 1. Department of Pathology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Jianchen Fang
- 2. The Pathology Service Center, Ningbo, Zhejiang, China
| | - Rong Fang
- 1. Department of Pathology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Herbert C Morse
- 3. The National Institute of Allergy and Infectious Diseases, the National Institutes of Health, Rockville, MD, USA
| | - Guifang Ouyang
- 4. Department of Hematology, Ningbo University Affiliated First Hospital, Ningbo, Zhejiang, China
| | - Jeff X Zhou
- 1. Department of Pathology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
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