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He T, Xiao L, Qiao Y, Klingbeil O, Young E, Wu XS, Mannan R, Mahapatra S, Eyunni S, Ching-Yi Tien J, Wang X, Zheng Y, Kim N, Zheng H, Hou S, Su F, Miner SJ, Mehra R, Cao X, Abbineni C, Samajdar S, Ramachandra M, Parolia A, Vakoc CR, Chinnaiyan AM. Targeting the mSWI/SNF Complex in POU2F-POU2AF Transcription Factor-Driven Malignancies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576669. [PMID: 38328238 PMCID: PMC10849552 DOI: 10.1101/2024.01.22.576669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The POU2F3-POU2AF2/3 (OCA-T1/2) transcription factor complex is the master regulator of the tuft cell lineage and tuft cell-like small cell lung cancer (SCLC). Here, we found that the POU2F3 molecular subtype of SCLC (SCLC-P) exhibits an exquisite dependence on the activity of the mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complex. SCLC-P cell lines were sensitive to nanomolar levels of a mSWI/SNF ATPase proteolysis targeting chimera (PROTAC) degrader when compared to other molecular subtypes of SCLC. POU2F3 and its cofactors were found to interact with components of the mSWI/SNF complex. The POU2F3 transcription factor complex was evicted from chromatin upon mSWI/SNF ATPase degradation, leading to attenuation of downstream oncogenic signaling in SCLC-P cells. A novel, orally bioavailable mSWI/SNF ATPase PROTAC degrader, AU-24118, demonstrated preferential efficacy in the SCLC-P relative to the SCLC-A subtype and significantly decreased tumor growth in preclinical models. AU-24118 did not alter normal tuft cell numbers in lung or colon, nor did it exhibit toxicity in mice. B cell malignancies which displayed a dependency on the POU2F1/2 cofactor, POU2AF1 (OCA-B), were also remarkably sensitive to mSWI/SNF ATPase degradation. Mechanistically, mSWI/SNF ATPase degrader treatment in multiple myeloma cells compacted chromatin, dislodged POU2AF1 and IRF4, and decreased IRF4 signaling. In a POU2AF1-dependent, disseminated murine model of multiple myeloma, AU-24118 enhanced survival compared to pomalidomide, an approved treatment for multiple myeloma. Taken together, our studies suggest that POU2F-POU2AF-driven malignancies have an intrinsic dependence on the mSWI/SNF complex, representing a therapeutic vulnerability.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- These authors contributed equally
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoli S. Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sanjana Eyunni
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jean Ching-Yi Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
- Lead contact
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Yanagi M, Ikegami I, Kamekura R, Sato T, Sato T, Kamiya S, Murayama K, Jitsukawa S, Ito F, Yorozu A, Kihara M, Abe T, Takaki H, Kawata K, Shigehara K, Miyajima S, Nishikiori H, Sato A, Tohse N, Takano KI, Chiba H, Ichimiya S. Bob1 maintains T follicular helper cells for long-term humoral immunity. Commun Biol 2024; 7:185. [PMID: 38360857 PMCID: PMC10869348 DOI: 10.1038/s42003-024-05827-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Humoral immunity is vital for host protection, yet aberrant antibody responses can trigger harmful inflammation and immune-related disorders. T follicular helper (Tfh) cells, central to humoral immunity, have garnered significant attention for unraveling immune mechanisms. This study shows the role of B-cell Oct-binding protein 1 (Bob1), a transcriptional coactivator, in Tfh cell regulation. Our investigation, utilizing conditional Bob1-deficient mice, suggests that Bob1 plays a critical role in modulating inducible T-cell costimulator expression and cellular respiration in Tfh cells. This regulation maintains the long-term functionality of Tfh cells, enabling their reactivation from central memory T cells to produce antibodies during recall responses. In a bronchial asthma model induced by house dust mite (HDM) inhalation, Bob1 is observed to enhance HDM-specific antibodies, including IgE, highlighting its pivotal function in Tfh cell regulation. Further exploration of Bob1-dependent mechanisms in Tfh cells holds promise for governing protective immunity and addressing immune-related disorders.
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Affiliation(s)
- Masahiro Yanagi
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ippei Ikegami
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ryuta Kamekura
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Tatsuya Sato
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Taiki Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shiori Kamiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Kosuke Murayama
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Sumito Jitsukawa
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Fumie Ito
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akira Yorozu
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, 650-0047, Japan
| | - Hiromi Takaki
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Koji Kawata
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Katsunori Shigehara
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Satsuki Miyajima
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirotaka Nishikiori
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Akinori Sato
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
- Department of Rehabilitation, Faculty of Healthcare and Science, Hokkaido Bunkyo University, Eniwa, 061-1449, Japan
| | - Noritsugu Tohse
- Department of Cellular Physiology and Signal Transduction, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Ken-Ichi Takano
- Department of Otolaryngology-Head and Neck Surgery, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Hirofumi Chiba
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan
| | - Shingo Ichimiya
- Department of Human Immunology, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, 060-8556, Japan.
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Tawfik A, Kawaguchi T, Takahashi M, Setoh K, Yamaguchi I, Tabara Y, Van Steen K, Sakuntabhai A, Matsuda F. Transcriptomic Analysis Reveals Sixteen Potential Genes Associated with the Successful Differentiation of Antibody-Secreting Cells through the Utilization of Unfolded Protein Response Mechanisms in Robust Responders to the Influenza Vaccine. Vaccines (Basel) 2024; 12:136. [PMID: 38400120 PMCID: PMC10892001 DOI: 10.3390/vaccines12020136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The seasonal influenza vaccine remains one of the vital recommended infection control measures for the elderly with chronic illnesses. We investigated the immunogenicity of a single dose of influenza vaccine in 123 seronegative participants and classified them into four distinct groups, determined by the promptness of vaccine response, the longevity of humoral immunity, and the likelihood of exhibiting cross-reactivity. Subsequently, we used transcriptional profiling and differential gene expression analysis to identify potential genes directly associated with the robust response to the vaccine. The group of exemplary vaccine responders differentially expressed 16 genes, namely: MZB1, MYDGF, TXNDC5, TXNDC11, HSP90B1, FKBP11, PDIA5, PRDX4, CD38, SDC1, TNFRSF17, TNFRSF13B, PAX5, POU2AF1, IRF4, and XBP1. Our findings point out a list of expressed proteins that are related to B cell proliferation, unfolded protein response, and cellular haemostasis, as well as a linkage of these expressions to the survival of long-lived plasma cells.
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Affiliation(s)
- Ahmed Tawfik
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, CNRS UMR2000, 75015 Paris, France;
- Pasteur International Unit at Center for Genomic Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
| | - Meiko Takahashi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
| | - Kazuya Setoh
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
| | - Izumi Yamaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
| | - Yasuharu Tabara
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
| | - Kristel Van Steen
- BIO3—Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Liège, 4000 Liège, Belgium
- BIO3—Laboratory for Systems Genetics, GIGA-R Medical Genomics, University of Leuven, 3000 Leuven, Belgium
| | - Anavaj Sakuntabhai
- Pasteur International Unit at Center for Genomic Medicine, Kyoto University, Kyoto 606-8507, Japan
- Ecology and Emergence of Arthropod-Borne Pathogens Unit, Institut Pasteur, CNRS UMR2000, 75015 Paris, France
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (I.Y.)
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4
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Szczepanski AP, Tsuboyama N, Watanabe J, Hashizume R, Zhao Z, Wang L. POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity. SCIENCE ADVANCES 2022; 8:eabq2403. [PMID: 36197978 PMCID: PMC9534498 DOI: 10.1126/sciadv.abq2403] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Small cell lung cancer (SCLC), accounting for around 13% of all lung cancers, often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. The POU class 2 homeobox 3 (POU2F3) is a master regulator of tuft cell identity and defines the SCLC-P subtype that lacks the neuroendocrine markers. Here, we have identified a previously uncharacterized protein, C11orf53, which is coexpressed with POU2F3 in both SCLC cell lines and patient samples. Mechanistically, C11orf53 directly interacts with POU2F3 and is recruited to chromatin by POU2F3. Depletion of C11orf53 reduced enhancer H3K27ac levels and chromatin accessibility, resulting in a reduction of POU2F3-dependent gene expression. On the basis of the molecular function of C11orf53, we renamed it as "POU Class 2 Homeobox Associating Factor 2" (POU2AF2). In summary, our study has identified a new coactivator of POU2F3 and sheds light on the therapeutic potential of targeting POU2AF2/POU2F3 heterodimer in human SCLC.
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Affiliation(s)
- Aileen Patricia Szczepanski
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Natsumi Tsuboyama
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jun Watanabe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL 60611, USA
- Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 303 East Superior St., Chicago, IL 60611, USA
- Division of Hematology, Oncology, Neuro-Oncology & Stem Cell Transplantation, Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 East Chicago Avenue, Box 205, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Corresponding author. Email (Z.Z.); (L.W.)
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Corresponding author. Email (Z.Z.); (L.W.)
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5
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Shirai Y, Nakanishi Y, Suzuki A, Konaka H, Nishikawa R, Sonehara K, Namba S, Tanaka H, Masuda T, Yaga M, Satoh S, Izumi M, Mizuno Y, Jo T, Maeda Y, Nii T, Oguro-Igashira E, Morisaki T, Kamatani Y, Nakayamada S, Nishigori C, Tanaka Y, Takeda Y, Yamamoto K, Kumanogoh A, Okada Y. Multi-trait and cross-population genome-wide association studies across autoimmune and allergic diseases identify shared and distinct genetic component. Ann Rheum Dis 2022; 81:1301-1312. [PMID: 35753705 PMCID: PMC9380494 DOI: 10.1136/annrheumdis-2022-222460] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Autoimmune and allergic diseases are outcomes of the dysregulation of the immune system. Our study aimed to elucidate differences or shared components in genetic backgrounds between autoimmune and allergic diseases. METHODS We estimated genetic correlation and performed multi-trait and cross-population genome-wide association study (GWAS) meta-analysis of six immune-related diseases: rheumatoid arthritis, Graves' disease, type 1 diabetes for autoimmune diseases and asthma, atopic dermatitis and pollinosis for allergic diseases. By integrating large-scale biobank resources (Biobank Japan and UK biobank), our study included 105 721 cases and 433 663 controls. Newly identified variants were evaluated in 21 778 cases and 712 767 controls for two additional autoimmune diseases: psoriasis and systemic lupus erythematosus. We performed enrichment analyses of cell types and biological pathways to highlight shared and distinct perspectives. RESULTS Autoimmune and allergic diseases were not only mutually classified based on genetic backgrounds but also they had multiple positive genetic correlations beyond the classifications. Multi-trait GWAS meta-analysis newly identified six allergic disease-associated loci. We identified four loci shared between the six autoimmune and allergic diseases (rs10803431 at PRDM2, OR=1.07, p=2.3×10-8, rs2053062 at G3BP1, OR=0.90, p=2.9×10-8, rs2210366 at HBS1L, OR=1.07, p=2.5×10-8 in Japanese and rs4529910 at POU2AF1, OR=0.96, p=1.9×10-10 across ancestries). Associations of rs10803431 and rs4529910 were confirmed at the two additional autoimmune diseases. Enrichment analysis demonstrated link to T cells, natural killer cells and various cytokine signals, including innate immune pathways. CONCLUSION Our multi-trait and cross-population study should elucidate complex pathogenesis shared components across autoimmune and allergic diseases.
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Affiliation(s)
- Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshimitsu Nakanishi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita,Japan, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Department of Advanced Clinical and Translational Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hachirou Konaka
- Department of Respiratory Medicine and Clinical Immunology, Public Interest Incorporated Foundation, Nippon Life Saiseikai, Nippon Life Hospital, Osaka, Japan
| | - Rika Nishikawa
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hiroaki Tanaka
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- The First Department of Internal Medicine, University of Occupational and Environmental Health, School of Medicine, Kitakyushu, Fukuoka, Japan
| | - Tatsuo Masuda
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Suita, Japan
- StemRIM Institute of Regeneration-Inducing Medicine, Osaka University, Suita, Japan
| | - Moto Yaga
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mayuko Izumi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yumiko Mizuno
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsunori Jo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Internal Medicine, Institute of Medical Science, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Nakayamada
- The First Department of Internal Medicine, University of Occupational and Environmental Health, School of Medicine, Kitakyushu, Fukuoka, Japan
| | - Chikako Nishigori
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, University of Occupational and Environmental Health, School of Medicine, Kitakyushu, Fukuoka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita,Japan, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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6
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Lombard‐Vadnais F, Lacombe J, Chabot‐Roy G, Ferron M, Lesage S. OCA‐B does not act as a transcriptional coactivator in T cells. Immunol Cell Biol 2022; 100:338-351. [DOI: 10.1111/imcb.12543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/14/2022] [Accepted: 03/09/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Félix Lombard‐Vadnais
- Immunologie‐oncologie Centre de recherche de l’Hôpital Maisonneuve‐Rosemont Montréal QC H1T 2M4 Canada
- Department of Microbiology & Immunology McGill University Montreal QC H3A 0G4 Canada
| | - Julie Lacombe
- Molecular Physiology Research Unit Institut de recherches cliniques de Montréal Montréal QC H2W 1R7 Canada
| | - Geneviève Chabot‐Roy
- Immunologie‐oncologie Centre de recherche de l’Hôpital Maisonneuve‐Rosemont Montréal QC H1T 2M4 Canada
| | - Mathieu Ferron
- Molecular Physiology Research Unit Institut de recherches cliniques de Montréal Montréal QC H2W 1R7 Canada
- Département de médecine Université de Montréal Montréal QC H3T 1J4 Canada
- Division of Experimental Medicine McGill University Montreal QC H3A 0G4 Canada
| | - Sylvie Lesage
- Immunologie‐oncologie Centre de recherche de l’Hôpital Maisonneuve‐Rosemont Montréal QC H1T 2M4 Canada
- Département de microbiologie, infectiologie et immunologie Université de Montréal Montréal QC H3T 1J4 Canada
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7
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Zhang DW, Ye JJ, Sun Y, Ji S, Kang JY, Wei YY, Fei GH. CD19 and POU2AF1 are Potential Immune-Related Biomarkers Involved in the Emphysema of COPD: On Multiple Microarray Analysis. J Inflamm Res 2022; 15:2491-2507. [PMID: 35479834 PMCID: PMC9035466 DOI: 10.2147/jir.s355764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/05/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Emphysema is the main cause of the progression of chronic obstructive pulmonary disease (COPD). This study aimed to identify the key genes involved in COPD-related emphysema. Patients and Methods GSE76925 was downloaded from Gene Expression Omnibus database. Protein–protein interaction networks of differentially expressed genes (DEGs) between control and COPD groups were constructed to identify hub genes using Cytoscape. Diagnostic performance of hub genes was evaluated using receiver operating characteristic analysis. Correlation analysis was performed to identify the key genes by analyzing the relationship between the hub genes and lung function and computed tomography (CT) indexes of emphysema. COPD patients were then divided into two groups based on the median expression of key genes and DEGs between these two groups were identified. Enrichment analysis of DEGs and correlation analysis between key genes and the infiltration of the immune cells were also analyzed. Finally, the role of key genes was evaluated in a lung tissues dataset (GSE47460) and a blood dataset (GSE76705). Additionally, the expression of key genes was validated by quantitative real-time polymerase chain reaction and immunohistochemistry. Results CD19 and POU2AF1 had diagnostic efficacy for COPD and were significantly correlated with lung function and CT indexes of emphysema. Enrichment and immune analyses revealed that CD19 and POU2AF1 were correlated with the B cells in COPD. These results were consistent in GSE47460. The expression of CD19 and POU2AF1 in blood was the opposite of that in lung tissues, and CD19 and POU2AF1 were both significantly upregulated in COPD lung tissues at both the mRNA and protein levels. Conclusion CD19 and POU2AF1 may serve as key regulators of emphysema and contribute to the progression of COPD by regulating the B-cell immunology. Targeting B cells may be a promising strategy for treating COPD.
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Affiliation(s)
- Da-Wei Zhang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jing-Jing Ye
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Ying Sun
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Shuang Ji
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Jia-Ying Kang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Yuan-Yuan Wei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
| | - Guang-He Fei
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China
- Key Laboratory of Respiratory Diseases Research and Medical Transformation of Anhui Province, Hefei, 230022, Anhui Province, People’s Republic of China
- Correspondence: Guang-He Fei, Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui Province, People’s Republic of China, Tel +86 551 6292 2013, Fax +86 551 6363 5578, Email
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8
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Betzler AC, Fiedler K, Hoffmann TK, Fehling HJ, Wirth T, Brunner C. BOB.1/OBF.1 is required during B-cell ontogeny for B-cell differentiation and germinal center function. Eur J Immunol 2021; 52:404-417. [PMID: 34918350 DOI: 10.1002/eji.202149333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/28/2021] [Accepted: 11/26/2021] [Indexed: 11/06/2022]
Abstract
BOB.1/OBF.1 is a lymphocyte-specific transcriptional co-activator of octamer-dependent transcription. It regulates the expression of genes important for lymphocyte physiology together with the Oct-1 and Oct-2 transcription factors. So far, BOB.1/OBF.1 has been studied in conventional knockout mice, whereby a function of BOB.1/OBF.1 in B but also in T cells was described. The main characteristic of BOB.1/OBF.1-deficient mice is the complete absence of germinal centers. However, it is entirely unsolved at which stage of B-cell development BOB.1/OBF.1 expression is essential for germinal center formation. Still, it is not known whether defects observed late in B-cell development of BOB.1/OBF.1-deficient mice are merely a consequence of defective early B-cell development. To answer the question, whether BOB.1/OBF.1 expression is required before or during the process of germinal center formation, we established a mouse system, which allows the conditional deletion of BOB.1/OBF.1 at different stages of B-cell development. Our data reveal a requirement for BOB.1/OBF.1 during both early antigen-independent and late antigen-dependent B-cell development, and further a requirement for efficient germinal center reaction during complete B-cell ontogeny. By specifically deleting BOB.1/OBF.1 in germinal center B cells, we provide evidence that the failure to form germinal centers is a germinal center B-cell intrinsic defect and not exclusively a consequence of defective early B-cell maturation.
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Affiliation(s)
- Annika C Betzler
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany
| | - Katja Fiedler
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany.,Department of Physiological Chemistry, Ulm University, Ulm, Germany
| | - Thomas K Hoffmann
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany
| | | | - Thomas Wirth
- Department of Physiological Chemistry, Ulm University, Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Ulm University Medical Center, Ulm, Germany
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9
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Sleiman S, Marshall AE, Dong X, Mhanni A, Alidou-D'Anjou I, Frosk P, Marin SE, Stark Z, Del Bigio MR, McBride A, Sadedin S, Gallacher L, Christodoulou J, Boycott KM, Dragon F, Kernohan KD. Compound heterozygous variants in SHQ1 are associated with a spectrum of neurological features, including early-onset dystonia. Hum Mol Genet 2021; 31:614-624. [PMID: 34542157 DOI: 10.1093/hmg/ddab247] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/06/2021] [Accepted: 08/23/2021] [Indexed: 01/29/2023] Open
Abstract
SHQ1 is essential for biogenesis of H/ACA ribonucleoproteins, a class of molecules important for processing ribosomal RNAs, modifying spliceosomal small nuclear RNAs, and stabilizing telomerase. Components of the H/ACA ribonucleoprotein complex have been linked to neurological developmental defects. Here we report two sibling pairs from unrelated families with compound heterozygous variants in SHQ1. Exome sequencing was used to detect disease causing variants which were submitted to 'matching' platforms linked to MatchMaker Exchange. Phenotype comparisons supported these matches. The affected individuals present with early-onset dystonia, with individuals from one family displaying additional neurological phenotypes, including neurodegeneration. As a result of CSF studies suggesting possible abnormal dopamine metabolism, a trial of levodopa replacement therapy was started but no clear response was noted. We show that fibroblasts from affected individuals have dramatic loss of SHQ1 protein. Variants from both families were expressed in S. cerevisiae, resulting in a strong reduction in H/ACA snoRNA production and remarkable defects in rRNA processing and ribosome formation. Our study identifies SHQ1 as associated with neurological disease, including early-onset dystonia, and begins to delineate the molecular etiology of this novel condition.
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Affiliation(s)
- Sophie Sleiman
- Centre d'excellence en recherche sur les maladies orphelines - Fondation Courtois (CERMO-FC), Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, H3C 3P8, Canada
| | - Aren E Marshall
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Xiaomin Dong
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Aziz Mhanni
- Departments of Pediatrics and Child Health.,Biochemistry and Medical Genetics
| | - Ismaël Alidou-D'Anjou
- Centre d'excellence en recherche sur les maladies orphelines - Fondation Courtois (CERMO-FC), Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, H3C 3P8, Canada
| | - Patrick Frosk
- Departments of Pediatrics and Child Health.,Biochemistry and Medical Genetics
| | | | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marc R Del Bigio
- Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Simon Sadedin
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Lyndon Gallacher
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | | | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - François Dragon
- Centre d'excellence en recherche sur les maladies orphelines - Fondation Courtois (CERMO-FC), Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, H3C 3P8, Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada.,Newborn Screening Ontario, Ottawa, Canada, K1H 8L1
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10
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OBF1 and Oct factors control the germinal center transcriptional program. Blood 2021; 137:2920-2934. [PMID: 33512466 DOI: 10.1182/blood.2020010175] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
OBF1 is a specific coactivator of the POU family transcription factors OCT1 and OCT2. OBF1 and OCT2 are B cell-specific and indispensable for germinal center (GC) formation, but their mechanism of action is unclear. Here, we show by chromatin immunoprecipitation-sequencing that OBF1 extensively colocalizes with OCT1 and OCT2. We found that these factors also often colocalize with transcription factors of the ETS family. Furthermore, we showed that OBF1, OCT2, and OCT1 bind widely to the promoters or enhancers of genes involved in GC formation in mouse and human GC B cells. Short hairpin RNA knockdown experiments demonstrated that OCT1, OCT2, and OBF1 regulate each other and are essential for proliferation of GC-derived lymphoma cell lines. OBF1 downregulation disrupts the GC transcriptional program: genes involved in GC maintenance, such as BCL6, are downregulated, whereas genes related to exit from the GC program, such as IRF4, are upregulated. Ectopic expression of BCL6 does not restore the proliferation of GC-derived lymphoma cells depleted of OBF1 unless IRF4 is also depleted, indicating that OBF1 controls an essential regulatory node in GC differentiation.
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11
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Yeremenko N, Danger R, Baeten D, Tomilin A, Brouard S. Transcriptional regulator BOB.1: Molecular mechanisms and emerging role in chronic inflammation and autoimmunity. Autoimmun Rev 2021; 20:102833. [PMID: 33864944 DOI: 10.1016/j.autrev.2021.102833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
Lymphocytes constitute an essential and potent effector compartment of the immune system. Therefore, their development and functions must be strictly regulated to avoid inappropriate immune responses, such as autoimmune reactions. Several lines of evidence from genetics (e.g. association with multiple sclerosis and primary biliary cirrhosis), human expression studies (e.g. increased expression in target tissues and draining lymph nodes of patients with autoimmune diseases), animal models (e.g. loss of functional protein protects animals from the development of collagen-induced arthritis, experimental autoimmune encephalomyelitis, type 1 diabetes, bleomycin-induced fibrosis) strongly support a causal link between the aberrant expression of the lymphocyte-restricted transcriptional regulator BOB.1 and the development of autoimmune diseases. In this review, we summarize the current knowledge of unusual structural and functional plasticity of BOB.1, stringent regulation of its expression, and the pivotal role that BOB.1 plays in shaping B- and T-cell responses. We discuss recent developments highlighting the significant contribution of BOB.1 to the pathogenesis of autoimmune diseases and how to leverage our knowledge to target this regulator to treat autoimmune tissue inflammation.
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Affiliation(s)
- Nataliya Yeremenko
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France; Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.
| | - Richard Danger
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Dominique Baeten
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Alexey Tomilin
- Institute of Cytology, Russian Academy of Sciences, St-Petersburg, Russian Federation
| | - Sophie Brouard
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
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12
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Chen Y, Kim J, Yang S, Wang H, Wu CJ, Sugimoto H, LeBleu VS, Kalluri R. Type I collagen deletion in αSMA + myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer. Cancer Cell 2021; 39:548-565.e6. [PMID: 33667385 PMCID: PMC8423173 DOI: 10.1016/j.ccell.2021.02.007] [Citation(s) in RCA: 248] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/23/2020] [Accepted: 02/10/2021] [Indexed: 12/11/2022]
Abstract
Stromal desmoplastic reaction in pancreatic ductal adenocarcinoma (PDAC) involves significant accumulation of type I collagen (Col1). However, the precise molecular and mechanistic contribution of Col1 in PDAC progression remains unknown. Activated pancreatic stellate cells/αSMA+ myofibroblasts are major contributors of Col1 in the PDAC stroma. We use a dual-recombinase genetic mouse model of spontaneous PDAC to delete Col1 specifically in myofibroblasts. This results in significant reduction of total stromal Col1 content and accelerates the emergence of PanINs and PDAC, decreasing overall survival. Col1 deletion leads to Cxcl5 upregulation in cancer cells via SOX9. Increase in Cxcl5 is associated with recruitment of myeloid-derived suppressor cells and suppression of CD8+ T cells, which can be attenuated with combined targeting of CXCR2 and CCR2 to restrain accelerated PDAC progression in the setting of stromal Col1 deletion. Our results unravel the fundamental role of myofibroblast-derived Co1l in regulating tumor immunity and restraining PDAC progression.
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Affiliation(s)
- Yang Chen
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jiha Kim
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sujuan Yang
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Huamin Wang
- Department of Anatomical Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Hikaru Sugimoto
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Valerie S LeBleu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Raghu Kalluri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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13
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Kennedy DE, Clark MR. Compartments and Connections Within the Germinal Center. Front Immunol 2021; 12:659151. [PMID: 33868306 PMCID: PMC8045557 DOI: 10.3389/fimmu.2021.659151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protective high affinity antibody responses emerge through an orchestrated developmental process that occurs in germinal centers (GCs). While GCs have been appreciated since 1930, a wealth of recent progress provides new insights into the molecular and cellular dynamics governing humoral immunity. In this review, we highlight advances that demonstrate that fundamental GC B cell function, selection, proliferation and SHM occur within distinct cell states. The resulting new model provides new opportunities to understand the evolution of immunity in infectious, autoimmune and neoplastic diseases.
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Affiliation(s)
| | - Marcus R. Clark
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, United States
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14
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Song S, Matthias PD. The Transcriptional Regulation of Germinal Center Formation. Front Immunol 2018; 9:2026. [PMID: 30233601 PMCID: PMC6134015 DOI: 10.3389/fimmu.2018.02026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022] Open
Abstract
Germinal centers (GCs) are essential structures of the humoral immune response, which form in the periphery in response to T cell dependent antigens. During the GC reaction, B cells undergo critical differentiation steps, which ultimately lead to the generation of antibodies with altered effector function and higher affinity for the selected antigen. Remarkably, many of the B cell tumors have their origin in the GCs; thus, understanding how the formation of these structures is regulated or deregulated is of high medical importance. This review gives an overview of the transcription factors that have been linked to the generation of GCs, and of their roles in the process.
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Affiliation(s)
- Shuang Song
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Patrick D Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
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15
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Carter S, Miard S, Caron A, Sallé-Lefort S, St-Pierre P, Anhê FF, Lavoie-Charland E, Blais-Lecours P, Drolet MC, Lefebvre JS, Lacombe J, Deshaies Y, Couet J, Laplante M, Ferron M, Bossé Y, Marette A, Richard D, Marsolais D, Picard F. Loss of OcaB Prevents Age-Induced Fat Accretion and Insulin Resistance by Altering B-Lymphocyte Transition and Promoting Energy Expenditure. Diabetes 2018; 67:1285-1296. [PMID: 29496744 DOI: 10.2337/db17-0558] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 02/19/2018] [Indexed: 11/13/2022]
Abstract
The current demographic shift toward an aging population has led to a robust increase in the prevalence of age-associated metabolic disorders. Recent studies have demonstrated that the etiology of obesity-related insulin resistance that develops with aging differs from that induced by high-calorie diets. Whereas the role of adaptive immunity in changes in energy metabolism driven by nutritional challenges has recently gained attention, its impact on aging remains mostly unknown. Here we found that the number of follicular B2 lymphocytes and expression of the B-cell-specific transcriptional coactivator OcaB increase with age in spleen and in intra-abdominal epididymal white adipose tissue (eWAT), concomitantly with higher circulating levels of IgG and impaired glucose homeostasis. Reduction of B-cell maturation and Ig production-especially that of IgG2c-by ablation of OcaB prevented age-induced glucose intolerance and insulin resistance and promoted energy expenditure by stimulating fatty acid utilization in eWAT and brown adipose tissue. Transfer of wild-type bone marrow in OcaB-/- mice replenished the eWAT B2-cell population and IgG levels, which diminished glucose tolerance, insulin sensitivity, and energy expenditure while increasing body weight gain in aged mice. Thus these findings demonstrate that upon aging, modifications in B-cell-driven adaptive immunity contribute to glucose intolerance and fat accretion.
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Affiliation(s)
- Sophie Carter
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC, Canada
| | - Stéphanie Miard
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Alexandre Caron
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Sandrine Sallé-Lefort
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC, Canada
| | - Philippe St-Pierre
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Institute for Nutrition and Functional Foods, Québec, QC, Canada
| | - Fernando Forato Anhê
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Institute for Nutrition and Functional Foods, Québec, QC, Canada
| | - Emilie Lavoie-Charland
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Pascale Blais-Lecours
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Marie-Claude Drolet
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Julie S Lefebvre
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Julie Lacombe
- Integrative and Molecular Physiology Research Unit, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
| | - Yves Deshaies
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Jacques Couet
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Mathieu Laplante
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Mathieu Ferron
- Integrative and Molecular Physiology Research Unit, Institut de recherches cliniques de Montréal, Montréal, QC, Canada
- Department of Medicine and Biochemistry, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Yohan Bossé
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - André Marette
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
- Institute for Nutrition and Functional Foods, Québec, QC, Canada
| | - Denis Richard
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - David Marsolais
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Frédéric Picard
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC, Canada
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16
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Pankratova EV, Stepchenko AG, Portseva T, Mogila VA, Georgieva SG. Different N-terminal isoforms of Oct-1 control expression of distinct sets of genes and their high levels in Namalwa Burkitt's lymphoma cells affect a wide range of cellular processes. Nucleic Acids Res 2016; 44:9218-9230. [PMID: 27407111 PMCID: PMC5100579 DOI: 10.1093/nar/gkw623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/03/2023] Open
Abstract
Oct-1 transcription factor has various functions in gene regulation. Its expression level is increased in several types of cancer and is associated with poor survival prognosis. Here we identified distinct Oct-1 protein isoforms in human cells and compared gene expression patterns and functions for Oct-1A, Oct-1L, and Oct-1X isoforms that differ by their N-terminal sequences. The longest isoform, Oct-1A, is abundantly expressed and is the main Oct-1 isoform in most of human tissues. The Oct-1L and the weakly expressed Oct-1X regulate the majority of Oct-1A targets as well as additional sets of genes. Oct-1X controls genes involved in DNA replication, DNA repair, RNA processing, and cellular response to stress. The high level of Oct-1 isoforms upregulates genes related to cell cycle progression and activates proliferation both in Namalwa Burkitt's lymphoma cells and primary human fibroblasts. It downregulates expression of genes related to antigen processing and presentation, cytokine-cytokine receptor interaction, oxidative metabolism, and cell adhesion, thus facilitating pro-oncogenic processes.
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Affiliation(s)
- Elizaveta V Pankratova
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991 Russia
| | - Alexander G Stepchenko
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991 Russia
| | - Tatiana Portseva
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991 Russia
| | - Vladic A Mogila
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991 Russia
| | - Sofia G Georgieva
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991 Russia
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17
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Madsen MB, Kogelman LJA, Kadarmideen HN, Rasmussen HB. Systems genetics analysis of pharmacogenomics variation during antidepressant treatment. THE PHARMACOGENOMICS JOURNAL 2016; 18:144-152. [PMID: 27752142 DOI: 10.1038/tpj.2016.68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/17/2016] [Accepted: 08/25/2016] [Indexed: 12/24/2022]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel the involved genetic components. Moreover, we investigated the potential difference in the genetic interaction networks underlying SSRI treatment response over time. We found four hub genes (ASCC3, PPARGC1B, SCHIP1 and TMTC2) with different connectivity in the initial SSRI treatment period (baseline to week 4) compared with the subsequent period (4-8 weeks after initiation), suggesting that different genetic networks are important at different times during SSRI treatment. The strongest interactions in the initial SSRI treatment period involved genes encoding transcriptional factors, and in the subsequent period genes involved in calcium homeostasis. In conclusion, we suggest a difference in genetic interaction networks between initial and subsequent SSRI response.
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Affiliation(s)
- M B Madsen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Capital Region of Denmark, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - L J A Kogelman
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - H N Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - H B Rasmussen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Capital Region of Denmark, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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18
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Yin L, Xu J, Li M, Reddy V, Zhou Q, Liu H, Chu P, Zhang Q, Huang Q, Gao Z, Liang X, Wang HY, Pan Z. Oct2 and Bob1 are sensitive and specific markers in lineage determination of B cell lymphomas with no expression of conventional B cell markers. Histopathology 2016; 69:775-783. [PMID: 27319306 DOI: 10.1111/his.13017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
AIMS Rare cases of B cell lymphomas do not express conventional B cell markers (CD20, CD79a and PAX5), and these types of lymphomas include anaplastic lymphoma kinase (ALK)-positive large B cell lymphoma, plasmablastic lymphoma, primary effusion lymphoma and the solid variant of primary effusion lymphoma, extracavitary human herpesvirus 8 (HHV8)-positive large B cell lymphoma. Establishing accurate diagnoses of these B cell lymphomas can be challenging, and often requires a large panel of immunohistochemical stains, molecular assays and cytogenetic studies. B cell-specific transcription factors, Oct2 and Bob1, have been shown to be expressed consistently in most, if not all, B cell lymphomas, and therefore we investigated the utility of Oct2 and Bob1 immunohistochemistry in lineage determination of the aforementioned B cell lymphomas. METHODS AND RESULTS We selected 34 cases of previously diagnosed B cell lymphomas with no or weak expression of CD20, CD79a and PAX5. Oct2 and Bob1 were positive in 74% (25 of 34) and 85% (29 of 34) of the cases, respectively. When we combined the results of these two immunostains, 94% (32 of 34) cases expressed at least one of these two markers. We also included 51 control cases of non-B cell neoplasms, and none of them expressed either Oct2 or Bob1. CONCLUSIONS Oct2 and Bob1 are very reliable in determining B cell lineage in the absence of expression of other pan-B cell markers, and it should provide great diagnostic benefit to include them both in a panel of immunohistochemistry to assess undifferentiated malignant neoplasms.
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Affiliation(s)
- Liqun Yin
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA
| | - Jie Xu
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Min Li
- Department of Pathology, Peking University Health Science Center, Beijing, China
| | - Vishnu Reddy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Quan Zhou
- Department of Pathology, Zhejiang Wujing General Hospital, Zhejiang, China
| | - Huanxin Liu
- Department of Pathology, Guangdong Wujing General Hospital, Guangdong, China
| | - Peiguo Chu
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Qianyun Zhang
- Department of Pathology, University of New Mexico, Albuquerque, NM, USA
| | - Qin Huang
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zifen Gao
- Department of Pathology, Peking University Health Science Center, Beijing, China
| | - Xiayuan Liang
- Department of Pathology, Children's Hospital Colorado, Aurora, CO, USA
| | - Huan-You Wang
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Zenggang Pan
- Department of Pathology, University of Colorado Denver, Aurora, CO, USA.
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19
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Regulatory roles of Oct proteins in the mammary gland. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:812-9. [PMID: 27044595 DOI: 10.1016/j.bbagrm.2016.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/07/2016] [Accepted: 03/24/2016] [Indexed: 11/21/2022]
Abstract
The expression of Oct-1 and -2 and their binding to the octamer motif in the mammary gland are developmentally and hormonally regulated, consistent with the expression of milk proteins. Both of these transcription factors constitutively bind to the proximal promoter of the milk protein gene β-casein and might be involved in the inhibition or activation of promoter activity via interactions with other transcription factors or cofactors at different developmental stages. In particular, the lactogenic hormone prolactin and glucocorticoids induce Oct-1 and Oct-2 binding and interaction with both the signal transducer and activator of transcription 5 (STAT5) and the glucocorticoid receptor on the β-casein promoter to activate β-casein expression. In addition, increasing evidence has shown the involvement of another Oct factor, Oct-3/4, in mammary tumorigenesis, making Oct-3/4 an emerging prognostic marker of breast cancer and a molecular target for the gene-directed therapeutic intervention, prevention and treatment of breast cancer. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
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20
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Meira M, Sievers C, Hoffmann F, Haghikia A, Rasenack M, Décard BF, Kuhle J, Derfuss T, Kappos L, Lindberg RLP. Natalizumab-induced POU2AF1/Spi-B upregulation: A possible route for PML development. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2016; 3:e223. [PMID: 27088119 PMCID: PMC4821666 DOI: 10.1212/nxi.0000000000000223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/10/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVES To assess messenger RNA (mRNA) expression of POU2AF1 and Spi-B and their potential regulatory microRNAs (miRNAs) in natalizumab-treated patients with multiple sclerosis and in therapy-associated progressive multifocal leukoencephalopathy (PML). METHODS Expression of POU2AF1/Spi-B was analyzed by using real-time reverse transcription PCR assays on isolated B/CD8(+) T lymphocytes and peripheral blood mononuclear cells (PBMCs) from cohorts of untreated and natalizumab-treated patients with and without PML. Longitudinal expression analysis was performed on CD4(+), CD8(+) T and B cells from 14 patients who interrupted natalizumab therapy for 8 weeks. The miRNA profiling was conducted in PBMCs from 5 untreated and 5 natalizumab-treated patients using low-density arrays followed by validation with single miRNAs assays in untreated and natalizumab-treated patients. RESULTS POU2AF1 and Spi-B mRNAs were upregulated in B and CD8(+) T cells from natalizumab-treated patients, which was validated in PBMCs from different cohorts of natalizumab-treated patients with and without PML, with a noteworthy higher expression of Spi-B in patients with PML. In contrast, downregulation of POU2AF1/Spi-B expression was measured in B and CD8(+) T cells after natalizumab discontinuation. Seventeen differentially expressed miRNAs including miR-10b, a regulator of POU2AF1 mRNA, were identified in long-term natalizumab-treated patients compared with untreated ones. CONCLUSIONS Upregulation of POU2AF1 and Spi-B, known transactivators of the JC virus, the causative agent for PML, and its association with occurrence of PML in natalizumab-treated patients, corroborates POU2AF1/Spi-B as potential biomarkers for PML risk, which merits further evaluation.
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Affiliation(s)
- Maria Meira
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Claudia Sievers
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Francine Hoffmann
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Aiden Haghikia
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Maria Rasenack
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Bernhard F Décard
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Jens Kuhle
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Tobias Derfuss
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Ludwig Kappos
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Raija L P Lindberg
- Clinical Neuroimmunology (M.M., C.S., F.H., M.R., B.F.D., J.K., T.D., L.K., R.L.P.L.), Departments of Biomedicine and Neurology, University Hospital Basel, Switzerland; and Department of Neurology (A.H.), St. Josef-Hospital, Ruhr-University Bochum, Germany
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21
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Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2. Proc Natl Acad Sci U S A 2016; 113:E2039-46. [PMID: 26993806 DOI: 10.1073/pnas.1600557113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The requirement for the B-cell transcription factor OCT2 (octamer-binding protein 2, encoded by Pou2f2) in germinal center B cells has proved controversial. Here, we report that germinal center B cells are formed normally after depletion of OCT2 in a conditional knockout mouse, but their proliferation is reduced and in vivo differentiation to antibody-secreting plasma cells is blocked. This finding led us to examine the role of OCT2 in germinal center-derived lymphomas. shRNA knockdown showed that almost all diffuse large B-cell lymphoma (DLBCL) cell lines are addicted to the expression of OCT2 and its coactivator OCA-B. Genome-wide chromatin immunoprecipitation (ChIP) analysis and gene-expression profiling revealed the broad transcriptional program regulated by OCT2 that includes the expression of STAT3, IL-10, ELL2, XBP1, MYC, TERT, and ADA. Importantly, genetic alteration of OCT2 is not a requirement for cellular addiction in DLBCL. However, we detected amplifications of the POU2F2 locus in DLBCL tumor biopsies and a recurrent mutation of threonine 223 in the DNA-binding domain of OCT2. This neomorphic mutation subtly alters the DNA-binding preference of OCT2, leading to the transactivation of noncanonical target genes including HIF1a and FCRL3 Finally, by introducing mutations designed to disrupt the OCT2-OCA-B interface, we reveal a requirement for this protein-protein interface that ultimately might be exploited therapeutically. Our findings, combined with the predominantly B-cell-restricted expression of OCT2 and the absence of a systemic phenotype in our knockout mice, suggest that an OCT2-targeted therapeutic strategy would be efficacious in both major subtypes of DLBCL while avoiding systemic toxicity.
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22
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Differential expression of immune-related genes between healthy volunteers and type 2 diabetic patients with spleen-deficiency pattern. J TRADIT CHIN MED 2016; 35:646-52. [PMID: 26742309 DOI: 10.1016/s0254-6272(15)30154-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To investigate the clinical differentia tion of spleen-deficiency pattern (SDP), a group of symptoms and signs defined in terms of Traditional Chinese Medicine for its clinical practice. METHODS Peripheral venous blood (> 3 mL) was collected from each of six type 2 diabetes mellitus (T2DM)-SDP patients and six healthy volunteers. After the isolation of peripheral white blood cells (PWBCs), total RNA was extracted, and quality control was performed on all RNA samples. Microarray experiments were conducted using the Agilent human whole genome gene chip, and genes demonstrating differential expression were screened. Bioinformatics analysis was conducted on these genes using several online databases. RESULTS We screened a total of 175 differentially expressed genes (DEGs), of which 111 (63%) were down-regulated and 64 (37%) were up-regulated in T2DM-SDP patients compared with healthy controls. Among the 175 genes, 158 had biological function annotations: 46 (29%) were directly related to an individual's immune regulation or response, 25 (16%) were associated with substance and energy metabolism of PWBCs which could also indirectly influence immunity, and the remaining 87 (55%) were involved in a variety of PWBC biological processes that might eventually influence the immune function. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the DEGs were predominantly enriched in seven immune-related pathways. Hierarchical cluster analysis identified gene expression patterns that were distinguishable between the two study groups. CONCLUSION Our results suggest that T2DM-SDP patients experience significant hypoimmunity and/or immune dysfunctions, and possess a specific gene expression profile. These findings offer new insights into SDP and the clinical pattern differentiation of T2DM-SDP.
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Abstract
Genome-wide association studies (GWASs) have been a significant technological advance in our ability to evaluate the genetic architecture of complex diseases such as primary biliary cirrhosis (PBC). To date, six large-scale studies have been performed that have identified 27 risk loci in addition to human leukocyte antigen (HLA) associated with PBC. The identified risk variants emphasize important disease concepts; namely, that disturbances in immunoregulatory pathways are important in the pathogenesis of PBC and that such perturbations are shared among a diverse number of autoimmune diseases-suggesting the risk architecture may confer a generalized propensity to autoimmunity not necessarily specific to PBC. Furthermore, the impact of non-HLA risk variants, particularly in genes involved with interleukin-12 signaling, and ethnic variation in conferring susceptibility to PBC have been highlighted. Although GWASs have been a critical stepping stone in understanding common genetic variation contributing to PBC, limitations pertaining to power, sample availability, and strong linkage disequilibrium across genes have left us with an incomplete understanding of the genetic underpinnings of disease pathogenesis. Future efforts to gain insight into this missing heritability, the genetic variation that contributes to important disease outcomes, and the functional consequences of associated variants will be critical if practical clinical translation is to be realized.
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Affiliation(s)
- Aliya F. Gulamhusein
- Division of Gastroenterology and Hepatology and the Mayo Clinic Center for Cell Signaling, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology and the Mayo Clinic Center for Cell Signaling, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905
| | - Konstantinos N. Lazaridis
- Division of Gastroenterology and Hepatology and the Mayo Clinic Center for Cell Signaling, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905. Phone: (507) 538-4877. Fax: (507) 284-0762
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24
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Kilzheimer M, Quandt J, Langhans J, Weihrich P, Wirth T, Brunner C. NF-κB-dependent signals control BOB.1/OBF.1 and Oct2 transcriptional activity in B cells. Eur J Immunol 2015; 45:3441-53. [DOI: 10.1002/eji.201545475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 07/30/2015] [Accepted: 09/12/2015] [Indexed: 12/18/2022]
Affiliation(s)
| | - Jasmin Quandt
- Institute of Physiological Chemistry; Ulm University; Ulm Germany
| | - Julia Langhans
- Department of Otorhinolaryngology; Ulm University; Ulm Germany
| | - Petra Weihrich
- Institute of Physiological Chemistry; Ulm University; Ulm Germany
- Department of Otorhinolaryngology; Ulm University; Ulm Germany
| | - Thomas Wirth
- Institute of Physiological Chemistry; Ulm University; Ulm Germany
| | - Cornelia Brunner
- Institute of Physiological Chemistry; Ulm University; Ulm Germany
- Department of Otorhinolaryngology; Ulm University; Ulm Germany
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25
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de Almeida CR, Hendriks RW, Stadhouders R. Dynamic Control of Long-Range Genomic Interactions at the Immunoglobulin κ Light-Chain Locus. Adv Immunol 2015; 128:183-271. [DOI: 10.1016/bs.ai.2015.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Litvinov IV, Netchiporouk E, Cordeiro B, Zargham H, Pehr K, Gilbert M, Zhou Y, Moreau L, Woetmann A, Ødum N, Kupper TS, Sasseville D. Ectopic expression of embryonic stem cell and other developmental genes in cutaneous T-cell lymphoma. Oncoimmunology 2014; 3:e970025. [PMID: 25941598 DOI: 10.4161/21624011.2014.970025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a potentially devastating malignancy. The pathogenesis of this cancer remains poorly elucidated. Previous studies focused on analysis of expression and function of known oncogenes and tumor suppressor genes. However, emerging reports highlight that it is also important to analyze the expression of genes that are ectopically expressed in CTCL (e.g., embryonic stem cell genes (ESC), cancer testis (CT) genes, etc.). Currently, it is not known whether ESC genes are expressed in CTCL. In the current work, we analyze by RT-PCR the expression of 26 ESC genes, many of which are known to regulate pluripotency and promote cancer stem cell-like phenotype, in a historic cohort of 60 patients from Boston and in a panel of 11 patient-derived CTCL cell lines and compare such expression to benign inflammatory dermatoses that often clinically mimic CTCL. Our findings document that many critical ESC genes including NANOG, SOX2, OCT4 (POU5F1) and their upstream and downstream signaling members are expressed in CTCL. Similarly, polycomb repressive complex 2 (PRC2) genes (i.e., EZH2, EED, and SUZ12) are also expressed in CTCL lesional skin. Furthermore, select ESC genes (OCT4, EED, TCF3, THAP11, CHD7, TIP60, TRIM28) are preferentially expressed in CTCL samples when compared to benign skin biopsies. Our work suggests that ESC genes are ectopically expressed together with CT genes, thymocyte development genes and B cell-specific genes and may be working in concert to promote tumorigenesis. Specifically, while ESC genes may be promoting cancer stem cell-like phenotype, CT genes may be contributing to aneuploidy and genomic instability by producing aberrant chromosomal translocations. Further analysis of ESC expression and function in this cancer will greatly enhance our fundamental understanding of CTCL and will help us identify novel therapeutic targets.
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Key Words
- ALCL, Anaplastic Large Cell Lymphoma
- BLK, B-lymphoid kinase
- C-ALCL, Cutaneous Anaplastic Large Cell Lymphoma
- CSC, Cancer Stem Cell
- CTCL, Cutaneous T-Cell Lymphoma
- DMC1, Disrupted Meiotic cDNA 1
- ESC, Embryonic Stem Cell
- EVA1, Epithelial C-like antigen 1
- MF, Mycosis Fungoides
- PBMC, Peripheral Blood Mononucleated Cells
- PLS3, Plastin-3
- PRC1, Polycomb Repressive Complex 1
- PRC2, Polycomb Repressive Complex 2
- SS, Sézary Syndrome
- SYCP1, Synaptonemal Complex Protein 1
- TOX, Thymocyte selection–associated high mobility group box
- ZFX, Zinc finger protein X-linked
- cancer testis genes
- cutaneous T cell lymphoma (CTCL)
- embryonic stem cell genes
- mycosis fungoides (MF)
- polycomb repressive complex 2 (PRC2)
- sézary syndrome (SS)
- thymocyte development genes
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Affiliation(s)
- Ivan V Litvinov
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Elena Netchiporouk
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Brendan Cordeiro
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Hanieh Zargham
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Kevin Pehr
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Martin Gilbert
- Division of Dermatology; Université Laval ; Québec City, QC Canada
| | - Youwen Zhou
- Department of Dermatology and Skin Science; University of British Columbia ; Vancouver, BC Canada
| | - Linda Moreau
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
| | - Anders Woetmann
- Department of International Health, Immunology, and Microbiology; University of Copenhagen ; Copenhagen, Denmark
| | - Niels Ødum
- Department of International Health, Immunology, and Microbiology; University of Copenhagen ; Copenhagen, Denmark
| | - Thomas S Kupper
- Department of Dermatology; Harvard Skin Disease Research Center; Brigham and Women's Hospital; Harvard University ; Boston, MA USA
| | - Denis Sasseville
- Division of Dermatology; McGill University Health Centre ; Montréal, QC Canada
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Hematopoietic overexpression of FOG1 does not affect B-cells but reduces the number of circulating eosinophils. PLoS One 2014; 9:e92836. [PMID: 24747299 PMCID: PMC3991581 DOI: 10.1371/journal.pone.0092836] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 02/26/2014] [Indexed: 12/31/2022] Open
Abstract
We have identified expression of the gene encoding the transcriptional coactivator FOG-1 (Friend of GATA-1; Zfpm1, Zinc finger protein multitype 1) in B lymphocytes. We found that FOG-1 expression is directly or indirectly dependent on the B cell-specific coactivator OBF-1 and that it is modulated during B cell development: expression is observed in early but not in late stages of B cell development. To directly test in vivo the role of FOG-1 in B lymphocytes, we developed a novel embryonic stem cell recombination system. For this, we combined homologous recombination with the FLP recombinase activity to rapidly generate embryonic stem cell lines carrying a Cre-inducible transgene at the Rosa26 locus. Using this system, we successfully generated transgenic mice where FOG-1 is conditionally overexpressed in mature B-cells or in the entire hematopoietic system. While overexpression of FOG-1 in B cells did not significantly affect B cell development or function, we found that enforced expression of FOG-1 throughout all hematopoietic lineages led to a reduction in the number of circulating eosinophils, confirming and extending to mammals the known function of FOG-1 in this lineage.
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28
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Corcoran L, Emslie D, Kratina T, Shi W, Hirsch S, Taubenheim N, Chevrier S. Oct2 and Obf1 as Facilitators of B:T Cell Collaboration during a Humoral Immune Response. Front Immunol 2014; 5:108. [PMID: 24688485 PMCID: PMC3960507 DOI: 10.3389/fimmu.2014.00108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 03/03/2014] [Indexed: 11/16/2022] Open
Abstract
The Oct2 protein, encoded by the Pou2f2 gene, was originally predicted to act as a DNA binding transcriptional activator of immunoglobulin (Ig) in B lineage cells. This prediction flowed from the earlier observation that an 8-bp sequence, the “octamer motif,” was a highly conserved component of most Ig gene promoters and enhancers, and evidence from over-expression and reporter assays confirmed Oct2-mediated, octamer-dependent gene expression. Complexity was added to the story when Oct1, an independently encoded protein, ubiquitously expressed from the Pou2f1 gene, was characterized and found to bind to the octamer motif with almost identical specificity, and later, when the co-activator Obf1 (OCA-B, Bob.1), encoded by the Pou2af1 gene, was cloned. Obf1 joins Oct2 (and Oct1) on the DNA of a subset of octamer motifs to enhance their transactivation strength. While these proteins variously carried the mantle of determinants of Ig gene expression in B cells for many years, such a role has not been borne out for them by characterization of mice lacking functional copies of the genes, either as single or as compound mutants. Instead, we and others have shown that Oct2 and Obf1 are required for B cells to mature fully in vivo, for B cells to respond to the T cell cytokines IL5 and IL4, and for B cells to produce IL6 normally during a T cell dependent immune response. We show here that Oct2 affects Syk gene expression, thus influencing B cell receptor signaling, and that Oct2 loss blocks Slamf1 expression in vivo as a result of incomplete B cell maturation. Upon IL4 signaling, Stat6 up-regulates Obf1, indirectly via Xbp1, to enable plasma cell differentiation. Thus, Oct2 and Obf1 enable B cells to respond normally to antigen receptor signals, to express surface receptors that mediate physical interaction with T cells, or to produce and respond to cytokines that are critical drivers of B cell and T cell differentiation during a humoral immune response.
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Affiliation(s)
- Lynn Corcoran
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Dianne Emslie
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Tobias Kratina
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Wei Shi
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Susanne Hirsch
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Nadine Taubenheim
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
| | - Stephane Chevrier
- Molecular Immunology Division, Walter and Eliza Hall Institute of Medical Research , Melbourne, VIC , Australia ; Department of Medical Biology, The University of Melbourne , Melbourne, VIC , Australia
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Meira M, Sievers C, Hoffmann F, Derfuss T, Kuhle J, Kappos L, Lindberg RLP. MiR-126: a novel route for natalizumab action? Mult Scler 2014; 20:1363-70. [DOI: 10.1177/1352458514524998] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background: MicroRNAs (miRNAs) have emerged as a family of post-transcriptional regulators of gene expression that mediate diverse aspects of immunity. MiRNA dysregulation has been found in multiple sclerosis (MS), reflecting the growing need to identify disease-specific miRNA expression signatures. Our previous low-density array studies reveal differential miR-126 expression in the CD4+T cells of untreated relapsing–remitting MS (RRMS) patients. Here, we investigated miR-126 expression in natalizumab-treated patients. Methods: We isolated CD4+ T cells from untreated ( n = 12) and natalizumab-treated MS patients ( n = 24), and from healthy volunteers ( n = 12). We analyzed the expression of miRNAs and potential targets by real time reverse transcription polymerase chain reaction (RT-PCR). We assessed specific inhibition of miR-126, in vitro. Results: MiR-126 was down-regulated in cells of patients under natalizumab treatment and up-regulated during relapse, supporting a regulatory role in MS immunopathogenesis. MiR-126 expression correlated with the expression of POU2AF1, a regulator of Spi-B that binds to the promoter/enhancer sequences of JC virus (JCV), the pathogen of progressive multifocal leukoencephalopathy (PML), a rare complication of natalizumab treatment. The same trend was found for Spi-B. Strong up-regulation of both genes appeared to be treatment duration-dependent. Specific inhibition experiments supported the link between the expression of miR-126 and POU2AF1/Spi-B. Conclusions: Our findings provided deeper insight into the mode of action of natalizumab, with possible implications for understanding both the effects of natalizumab on MS activity and its specific adverse event profile.
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Affiliation(s)
- Maria Meira
- University Hospital Basel, University of Basel, Switzerland
| | | | | | - Tobias Derfuss
- University Hospital Basel, University of Basel, Switzerland
| | - Jens Kuhle
- University Hospital Basel, University of Basel, Switzerland
| | - Ludwig Kappos
- University Hospital Basel, University of Basel, Switzerland
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Nakamura M. Analysis of disease-pathways by susceptibility genes in primary biliary cirrhosis. Inflamm Regen 2014. [DOI: 10.2492/inflammregen.34.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Heydarian M, Luperchio TR, Cutler J, Mitchell CJ, Kim MS, Pandey A, Sollner-Webb B, Reddy K. Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis. ACTA ACUST UNITED AC 2014; 7. [PMID: 25544807 PMCID: PMC4276347 DOI: 10.4172/jpb.1000302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An increasingly common method for predicting gene activity is genome-wide chromatin immuno-precipitation of ‘active’ chromatin modifications followed by massively parallel sequencing (ChIP-seq). In order to understand better the relationship between developmentally regulated chromatin landscapes and regulation of early B cell development, we determined how differentially active promoter regions were able to predict relative RNA and protein levels at the pre-pro-B and pro-B stages. Herein, we describe a novel ChIP-seq quantification method (cRPKM) to identify active promoters and a multi-omics approach that compares promoter chromatin status with ongoing active transcription (GRO-seq), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ). We demonstrate that active chromatin modifications at promoters are good indicators of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted the differential abundance of proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in abundance of their cognate proteins. As expected, this large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Strikingly, the most differentially abundant protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by a micro-RNA. These data highlight how this integrated multi-omics data set can be a useful resource in uncovering regulatory mechanisms. This data can be accessed at: https://usegalaxy.org/u/thereddylab/p/prediction-of-gene-activity-based-on-an-integrative-multi-omics-analysis
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Affiliation(s)
- Mohammad Heydarian
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, Center for Epigenetics, 855 North Wolfe Street, Baltimore, USA
| | - Teresa Romeo Luperchio
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, Center for Epigenetics, 855 North Wolfe Street, Baltimore, USA
| | - Jevon Cutler
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, Center for Epigenetics, 855 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, McKusick-Nathans Institute of Genetic Medicine, 733 North, Broadway Avenue, Baltimore, USA
| | - Christopher J Mitchell
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, McKusick-Nathans Institute of Genetic Medicine, 733 North, Broadway Avenue, Baltimore, USA
| | - Min-Sik Kim
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, McKusick-Nathans Institute of Genetic Medicine, 733 North, Broadway Avenue, Baltimore, USA
| | - Akhilesh Pandey
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, McKusick-Nathans Institute of Genetic Medicine, 733 North, Broadway Avenue, Baltimore, USA
| | - Barbara Sollner-Webb
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA
| | - Karen Reddy
- Johns Hopkins University, Department of Biological Chemistry, 725 North Wolfe Street, Baltimore, USA ; Johns Hopkins University, Center for Epigenetics, 855 North Wolfe Street, Baltimore, USA
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Anti-inflammatory cytokine interleukin-4 inhibits inducible nitric oxide synthase gene expression in the mouse macrophage cell line RAW264.7 through the repression of octamer-dependent transcription. Mediators Inflamm 2013; 2013:369693. [PMID: 24459328 PMCID: PMC3891534 DOI: 10.1155/2013/369693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/30/2013] [Accepted: 12/02/2013] [Indexed: 11/17/2022] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a signature molecule involved in the classical activation of M1 macrophages and is induced by the Nos2 gene upon stimulation with Th1-cell derived interferon-gamma (IFNγ) and bacterial lipopolysaccharide (LPS). Although the anti-inflammatory cytokine IL-4 is known to inhibit Nos2 gene expression, the molecular mechanism involved in the negative regulation of Nos2 by IL-4 remains to be fully elucidated. In the present study, we investigated the mechanism of IL-4-mediated Nos2 transcriptional repression in the mouse macrophage-like cell line RAW264.7. Signal transducer and activator of transcription 6 (Stat6) knockdown by siRNA abolished the IL-4-mediated inhibition of Nos2 induced by IFNγ/LPS. Transient transfection of a luciferase reporter gene containing the 5′-flanking region of the Nos2 gene demonstrated that an octamer transcription factor (OCT) binding site in the promoter region is required for both positive regulation by IFNγ/LPS and negative regulation by IL-4. Although IL-4 had no inhibitory effect on the DNA-binding activity of constitutively expressed Oct-1, IL-4-induced Nos2-reporter transcriptional repression was partially attenuated by overexpression of the coactivator CREB-binding protein (CBP). These results suggest that a coactivator/cofactor that functionally interacts with Oct-1 is a molecular target for the IL-4-mediated inhibition of Nos2 and that IL-4-activated Stat6 represses Oct-1-dependent transcription by competing with this coactivator/cofactor.
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A C-terminal acidic domain regulates degradation of the transcriptional coactivator Bob1. Mol Cell Biol 2013; 33:4628-40. [PMID: 24061476 DOI: 10.1128/mcb.01590-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bob1 (Obf-1 or OCA-B) is a 34-kDa transcriptional coactivator encoded by the Pou2af1 gene that is essential for normal B-cell development and immune responses in mice. During lymphocyte activation, Bob1 protein levels dramatically increase independently of mRNA levels, suggesting that the stability of Bob1 is regulated. We used a fluorescent protein-based reporter system to analyze protein stability in response to genetic and physiological perturbations and show that, while Bob1 degradation is proteasome mediated, it does not require ubiquitination of Bob1. Furthermore, degradation of Bob1 in B cells appears to be largely independent of the E3 ubiquitin ligase Siah. We propose a novel mechanism of Bob1 turnover in B cells, whereby an acidic region in the C terminus of Bob1 regulates the activity of degron signals elsewhere in the protein. Changes that make the C terminus more acidic, including tyrosine phosphorylation-mimetic mutations, stabilize the instable murine Bob1 protein, indicating that B cells may regulate Bob1 stability and activity via signaling pathways. Finally, we show that expressing a stable Bob1 mutant in B cells suppresses cell proliferation and induces changes in surface marker expression commonly seen during B-cell differentiation.
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Mueller K, Quandt J, Marienfeld RB, Weihrich P, Fiedler K, Claussnitzer M, Laumen H, Vaeth M, Berberich-Siebelt F, Serfling E, Wirth T, Brunner C. Octamer-dependent transcription in T cells is mediated by NFAT and NF-κB. Nucleic Acids Res 2013; 41:2138-54. [PMID: 23293002 PMCID: PMC3575799 DOI: 10.1093/nar/gks1349] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The transcriptional co-activator BOB.1/OBF.1 was originally identified in B cells and is constitutively expressed throughout B cell development. BOB.1/OBF.1 associates with the transcription factors Oct1 and Oct2, thereby enhancing octamer-dependent transcription. In contrast, in T cells, BOB.1/OBF.1 expression is inducible by treatment of cells with PMA/Ionomycin or by antigen receptor engagement, indicating a marked difference in the regulation of BOB.1/OBF.1 expression in B versus T cells. The molecular mechanisms underlying the differential expression of BOB.1/OBF.1 in T and B cells remain largely unknown. Therefore, the present study focuses on mechanisms controlling the transcriptional regulation of BOB.1/OBF.1 and Oct2 in T cells. We show that both calcineurin- and NF-κB-inhibitors efficiently attenuate the expression of BOB.1/OBF.1 and Oct2 in T cells. In silico analyses of the BOB.1/OBF.1 promoter revealed the presence of previously unappreciated combined NFAT/NF-κB sites. An array of genetic and biochemical analyses illustrates the involvement of the Ca2+/calmodulin-dependent phosphatase calcineurin as well as NFAT and NF-κB transcription factors in the transcriptional regulation of octamer-dependent transcription in T cells. Conclusively, impaired expression of BOB.1/OBF.1 and Oct2 and therefore a hampered octamer-dependent transcription may participate in T cell-mediated immunodeficiency caused by the deletion of NFAT or NF-κB transcription factors.
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Affiliation(s)
- Kerstin Mueller
- Institute of Physiological Chemistry, University Ulm, D-89081 Ulm, Germany, Institute of Pathology, University Ulm, D-89081 Ulm, Germany
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Shakoori AR, Hoessli DC, Nasir-ud-Din. Post-translational modifications in activation and inhibition of oct-1-DNA binding complex in H2B and other diverse gene regulation: Prediction of interplay sites. J Cell Biochem 2012; 114:266-74. [DOI: 10.1002/jcb.24382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/08/2022]
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Karnowski A, Chevrier S, Belz GT, Mount A, Emslie D, D'Costa K, Tarlinton DM, Kallies A, Corcoran LM. B and T cells collaborate in antiviral responses via IL-6, IL-21, and transcriptional activator and coactivator, Oct2 and OBF-1. ACTA ACUST UNITED AC 2012; 209:2049-64. [PMID: 23045607 PMCID: PMC3478936 DOI: 10.1084/jem.20111504] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transcriptional activator Oct2 and cofactor OBF-1 regulate B cell IL-6 to induce T cell production of IL-21, to support Tfh cell development in antiviral immunity. A strong humoral response to infection requires the collaboration of several hematopoietic cell types that communicate via antigen presentation, surface coreceptors and their ligands, and secreted factors. The proinflammatory cytokine IL-6 has been shown to promote the differentiation of activated CD4+ T cells into T follicular helper cells (TFH cells) during an immune response. TFH cells collaborate with B cells in the formation of germinal centers (GCs) during T cell–dependent antibody responses, in part through secretion of critical cytokines such as IL-21. In this study, we demonstrate that loss of either IL-6 or IL-21 has marginal effects on the generation of TFH cells and on the formation of GCs during the response to acute viral infection. However, mice lacking both IL-6 and IL-21 were unable to generate a robust TFH cell–dependent immune response. We found that IL-6 production in follicular B cells in the draining lymph node was an important early event during the antiviral response and that B cell–derived IL-6 was necessary and sufficient to induce IL-21 from CD4+ T cells in vitro and to support TFH cell development in vivo. Finally, the transcriptional activator Oct2 and its cofactor OBF-1 were identified as regulators of Il6 expression in B cells.
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Affiliation(s)
- Alex Karnowski
- Molecular Immunology Division and 2 Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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Nakamura M, Nishida N, Kawashima M, Aiba Y, Tanaka A, Yasunami M, Nakamura H, Komori A, Nakamuta M, Zeniya M, Hashimoto E, Ohira H, Yamamoto K, Onji M, Kaneko S, Honda M, Yamagiwa S, Nakao K, Ichida T, Takikawa H, Seike M, Umemura T, Ueno Y, Sakisaka S, Kikuchi K, Ebinuma H, Yamashiki N, Tamura S, Sugawara Y, Mori A, Yagi S, Shirabe K, Taketomi A, Arai K, Monoe K, Ichikawa T, Taniai M, Miyake Y, Kumagi T, Abe M, Yoshizawa K, Joshita S, Shimoda S, Honda K, Takahashi H, Hirano K, Takeyama Y, Harada K, Migita K, Ito M, Yatsuhashi H, Fukushima N, Ota H, Komatsu T, Saoshiro T, Ishida J, Kouno H, Kouno H, Yagura M, Kobayashi M, Muro T, Masaki N, Hirata K, Watanabe Y, Nakamura Y, Shimada M, Hirashima N, Komeda T, Sugi K, Koga M, Ario K, Takesaki E, Maehara Y, Uemoto S, Kokudo N, Tsubouchi H, Mizokami M, Nakanuma Y, Tokunaga K, Ishibashi H. Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population. Am J Hum Genet 2012; 91:721-8. [PMID: 23000144 DOI: 10.1016/j.ajhg.2012.08.010] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 06/03/2012] [Accepted: 08/08/2012] [Indexed: 01/12/2023] Open
Abstract
For the identification of susceptibility loci for primary biliary cirrhosis (PBC), a genome-wide association study (GWAS) was performed in 963 Japanese individuals (487 PBC cases and 476 healthy controls) and in a subsequent replication study that included 1,402 other Japanese individuals (787 cases and 615 controls). In addition to the most significant susceptibility region, human leukocyte antigen (HLA), we identified two significant susceptibility loci, TNFSF15 (rs4979462) and POU2AF1 (rs4938534) (combined odds ratio [OR] = 1.56, p = 2.84 × 10(-14) for rs4979462, and combined OR = 1.39, p = 2.38 × 10(-8) for rs4938534). Among 21 non-HLA susceptibility loci for PBC identified in GWASs of individuals of European descent, three loci (IL7R, IKZF3, and CD80) showed significant associations (combined p = 3.66 × 10(-8), 3.66 × 10(-9), and 3.04 × 10(-9), respectively) and STAT4 and NFKB1 loci showed suggestive association with PBC (combined p = 1.11 × 10(-6) and 1.42 × 10(-7), respectively) in the Japanese population. These observations indicated the existence of ethnic differences in genetic susceptibility loci to PBC and the importance of TNF signaling and B cell differentiation for the development of PBC in individuals of European descent and Japanese individuals.
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Keating GL, Turner EC, Kinsella BT. Regulation of the human prostacyclin receptor gene in megakaryocytes: Major roles for C/EBPδ and PU.1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:428-45. [DOI: 10.1016/j.bbagrm.2012.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/03/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
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Ren X, Siegel R, Kim U, Roeder RG. Direct interactions of OCA-B and TFII-I regulate immunoglobulin heavy-chain gene transcription by facilitating enhancer-promoter communication. Mol Cell 2011; 42:342-55. [PMID: 21549311 DOI: 10.1016/j.molcel.2011.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 02/16/2011] [Accepted: 04/16/2011] [Indexed: 02/07/2023]
Abstract
B cell-specific coactivator OCA-B, together with Oct-1/2, binds to octamer sites in promoters and enhancers to activate transcription of immunoglobulin (Ig) genes, although the mechanisms underlying their roles in enhancer-promoter communication are unknown. Here, we demonstrate a direct interaction of OCA-B with transcription factor TFII-I, which binds to DICE elements in Igh promoters, that affects transcription at two levels. First, OCA-B relieves HDAC3-mediated Igh promoter repression by competing with HDAC3 for binding to promoter-bound TFII-I. Second, and most importantly, Igh 3' enhancer-bound OCA-B and promoter-bound TFII-I mediate promoter-enhancer interactions, in both cis and trans, that are important for Igh transcription. These and other results reveal an important function for OCA-B in Igh 3' enhancer function in vivo and strongly favor an enhancer mechanism involving looping and facilitated factor recruitment rather than a tracking mechanism.
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Affiliation(s)
- Xiaodi Ren
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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40
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Poretti G, Kwee I, Bernasconi B, Rancoita PMV, Rinaldi A, Capella C, Zucca E, Neri A, Tibiletti MG, Bertoni F. Chromosome 11q23.1 is an unstable region in B-cell tumor cell lines. Leuk Res 2011; 35:808-13. [PMID: 21420167 DOI: 10.1016/j.leukres.2010.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/18/2010] [Accepted: 10/31/2010] [Indexed: 01/08/2023]
Abstract
Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.
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Affiliation(s)
- Giulia Poretti
- Laboratory of Experimental Oncology and Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
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41
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Toman I, Loree J, Klimowicz AC, Bahlis N, Lai R, Belch A, Pilarski L, Reiman T. Expression and prognostic significance of Oct2 and Bob1 in multiple myeloma: implications for targeted therapeutics. Leuk Lymphoma 2011; 52:659-67. [DOI: 10.3109/10428194.2010.548535] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Sebastiano V, Dalvai M, Gentile L, Schubart K, Sutter J, Wu GM, Tapia N, Esch D, Ju JY, Hübner K, Bravo MJA, Schöler HR, Cavaleri F, Matthias P. Oct1 regulates trophoblast development during early mouse embryogenesis. Development 2010; 137:3551-60. [PMID: 20876643 DOI: 10.1242/dev.047027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Oct1 (Pou2f1) is a transcription factor of the POU-homeodomain family that is unique in being ubiquitously expressed in both embryonic and adult mouse tissues. Although its expression profile suggests a crucial role in multiple regions of the developing organism, the only essential function demonstrated so far has been the regulation of cellular response to oxidative and metabolic stress. Here, we describe a loss-of-function mouse model for Oct1 that causes early embryonic lethality, with Oct1-null embryos failing to develop beyond the early streak stage. Molecular and morphological analyses of Oct1 mutant embryos revealed a failure in the establishment of a normal maternal-embryonic interface due to reduced extra-embryonic ectoderm formation and lack of the ectoplacental cone. Oct1(-/-) blastocysts display proper segregation of trophectoderm and inner cell mass lineages. However, Oct1 loss is not compatible with trophoblast stem cell derivation. Importantly, the early gastrulation defect caused by Oct1 disruption can be rescued in a tetraploid complementation assay. Oct1 is therefore primarily required for the maintenance and differentiation of the trophoblast stem cell compartment during early post-implantation development. We present evidence that Cdx2, which is expressed at high levels in trophoblast stem cells, is a direct transcriptional target of Oct1. Our data also suggest that Oct1 is required in the embryo proper from late gastrulation stages onwards.
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Affiliation(s)
- Vittorio Sebastiano
- Max Planck Institute for Molecular Biomedicine, Department of Cell and Developmental Biology, Röntgenstrasse, 20 48149 Münster, Germany
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Divergent transcriptional activities determine limb identity. Nat Commun 2010; 1:35. [PMID: 20975709 DOI: 10.1038/ncomms1036] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 06/16/2010] [Indexed: 11/09/2022] Open
Abstract
Limbs develop using a common genetic programme despite widely differing morphologies. This programme is modulated by limb-restricted regulators such as hindlimb (HL) transcription factors Pitx1 and Tbx4 and the forelimb (FL) Tbx5. Both Tbx factors have been implicated in limb patterning and growth, but their relative activities and underlying mechanisms remain unclear. In this paper, we show that Tbx4 and Tbx5 harbour conserved and divergent transcriptional regulatory domains that account for their roles in limb development. In particular, both factors share an activator domain and the ability to stimulate limb growth. However, we find that Tbx4 is the primary effector of HL identity for both skeletal and muscle development; this activity relies on a repressor domain that is inactivated by a human TBX4 small-patella syndrome mutation. We propose that limb identity is largely achieved by default in FL, whereas a specific repressor activity unique to Tbx4 determines HL identity.
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Hecker M, Goertsches RH, Engelmann R, Thiesen HJ, Guthke R. Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics 2009; 10:262. [PMID: 19703281 PMCID: PMC2757030 DOI: 10.1186/1471-2105-10-262] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 08/24/2009] [Indexed: 12/29/2022] Open
Abstract
Background The investigation of gene regulatory networks is an important issue in molecular systems biology and significant progress has been made by combining different types of biological data. The purpose of this study was to characterize the transcriptional program induced by etanercept therapy in patients with rheumatoid arthritis (RA). Etanercept is known to reduce disease symptoms and progression in RA, but the underlying molecular mechanisms have not been fully elucidated. Results Using a DNA microarray dataset providing genome-wide expression profiles of 19 RA patients within the first week of therapy we identified significant transcriptional changes in 83 genes. Most of these genes are known to control the human body's immune response. A novel algorithm called TILAR was then applied to construct a linear network model of the genes' regulatory interactions. The inference method derives a model from the data based on the Least Angle Regression while incorporating DNA-binding site information. As a result we obtained a scale-free network that exhibits a self-regulating and highly parallel architecture, and reflects the pleiotropic immunological role of the therapeutic target TNF-alpha. Moreover, we could show that our integrative modeling strategy performs much better than algorithms using gene expression data alone. Conclusion We present TILAR, a method to deduce gene regulatory interactions from gene expression data by integrating information on transcription factor binding sites. The inferred network uncovers gene regulatory effects in response to etanercept and thus provides useful hypotheses about the drug's mechanisms of action.
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Affiliation(s)
- Michael Hecker
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena, Germany.
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A far-upstream Oct-1 motif regulates cytokine-induced transcription of the human inducible nitric oxide synthase gene. J Mol Biol 2009; 390:595-603. [PMID: 19467240 DOI: 10.1016/j.jmb.2009.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 05/18/2009] [Accepted: 05/20/2009] [Indexed: 11/22/2022]
Abstract
Transcriptional regulation of the human inducible nitric oxide synthase (hiNOS) gene is highly complex and requires an orchestrated flow of positive and negative transcription factors that bind to specific cis-acting upstream response elements. Very little specific information exists about the far-upstream region of the hiNOS gene. Oct-1 protein belongs to the Pit-Oct-Unc domain transcription factor family and is constitutively expressed in all dividing cells. It is essential for proliferation, differentiation, and other key cell processes. However, the role of Oct-1 in regulating hiNOS gene expression has not been reported. In this work, the octamer sequence 5'-ATGCAAAT-3' at -10.2 kb in the hiNOS promoter was identified as high-affinity Oct-1 binding by electrophoretic mobility shift assay in vitro and chromatin immunoprecipitation assay in vivo. Mutation of Oct-1 motif at -10.2 kb in the hiNOS promoter decreased cytokine-induced hiNOS promoter activity by 40%. Cytokine-induced hiNOS promoter activity was also significantly reduced by Oct-1 small interfering RNA targeting. Overexpression of Oct-1 increased cytokine-induced hiNOS protein expression in primary human hepatocytes. Furthermore, the Oct-1 motif at -10.2 kb of the hiNOS promoter conferred increased transcriptional activity to the heterologous thymidine kinase promoter irrespective of cytokine induction. Taken together, this work identifies a far-upstream functional Oct-1 enhancer motif at -10.2 kb in the hiNOS promoter that regulates cytokine-induced hiNOS gene transcription and further underscores tight control mechanisms regulating the expression of the hiNOS gene.
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Role of defective Oct-2 and OCA-B expression in immunoglobulin production and Kaposi's sarcoma-associated herpesvirus lytic reactivation in primary effusion lymphoma. J Virol 2009; 83:4308-15. [PMID: 19224997 DOI: 10.1128/jvi.02196-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Primary effusion lymphoma (PEL) is a distinct type of B-cell non-Hodgkin lymphoma characterized by the presence of Kaposi's sarcoma-associated herpesvirus (KSHV/human herpesvirus 8). Despite having a genotype and gene expression signature of highly differentiated B cells, PEL does not usually express surface or cytoplasmic immunoglobulin (Ig). We show the lack of Oct-2 and OCA-B transcription factors to be responsible, at least in part, for this defect in Ig production. Like Ig genes, ORF50, the key regulator of the switch from latency to lytic reactivation, contains an octamer motif within its promoter. We therefore examined the impact of Oct-2 and OCA-B on ORF50 activation. The binding of Oct-1 to the ORF50 promoter has been shown to significantly enhance ORF50 transactivation. We found that Oct-2, on the other hand, inhibited ORF50 expression and consequently lytic reactivation by competing with Oct-1 for the octamer motif in the ORF50 promoter. Our data suggest that Oct-2 downregulation in infected cells would be favorable to KSHV in allowing for efficient viral reactivation.
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Trahan C, Dragon F. Dyskeratosis congenita mutations in the H/ACA domain of human telomerase RNA affect its assembly into a pre-RNP. RNA (NEW YORK, N.Y.) 2009; 15:235-243. [PMID: 19095616 PMCID: PMC2648702 DOI: 10.1261/rna.1354009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 10/30/2008] [Indexed: 05/27/2023]
Abstract
Dyskeratosis congenita (DC) is an inherited disorder that implicates defects in the biology of telomeres, which are maintained by telomerase, a ribonucleoprotein with reverse transcriptase activity. Like all H/ACA RNAs, the H/ACA domain of nascent human telomerase RNA (hTR) forms a pre-RNP with H/ACA proteins NAF1, dyskerin, NOP10, and NHP2 in vivo. To assess the pre-RNP assembly of hTR mutants that poorly accumulate in vivo, we developed an in vitro system that uses components of human origin. Pre-RNPs were reconstituted with synthetic (32)P-labeled RNAs and (35)S-labeled proteins produced in rabbit reticulocyte lysate, and immunoprecipitations were carried out to analyze RNP formation. We show that human NAF1 cannot bind directly to the H/ACA domain of hTR, and requires the core trimer dyskerin-NOP10-NHP2 to be efficiently incorporated into the pre-RNP. This order of assembly seems common to H/ACA RNAs since it was observed with snoRNA ACA36 and scaRNA U92, which are predicted to guide pseudouridylation of 18S rRNA and U2 snRNA, respectively. However, the processing H/ACA snoRNA U17 did not conform to this rule, as NAF1 alone was able to bind it. We also provide the first evidence that DC-related mutations of hTR C408G and Delta378-451 severely impair pre-RNP assembly. Integrity of boxes H and ACA of hTR are also crucial for pre-RNP assembly, while the CAB box is dispensable. Our results offer new insights into the defects caused by some mutations located in the H/ACA domain of hTR.
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Affiliation(s)
- Christian Trahan
- Département des Sciences Biologiques and Centre de Recherche BioMed, Université du Québec à Montréal, Canada
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Bordon A, Bosco N, Du Roure C, Bartholdy B, Kohler H, Matthias G, Rolink AG, Matthias P. Enforced expression of the transcriptional coactivator OBF1 impairs B cell differentiation at the earliest stage of development. PLoS One 2008; 3:e4007. [PMID: 19104664 PMCID: PMC2603323 DOI: 10.1371/journal.pone.0004007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 11/19/2008] [Indexed: 02/06/2023] Open
Abstract
OBF1, also known as Bob.1 or OCA-B, is a B lymphocyte-specific transcription factor which coactivates Oct1 and Oct2 on B cell specific promoters. So far, the function of OBF1 has been mainly identified in late stage B cell populations. The central defect of OBF1 deficient mice is a severely reduced immune response to T cell-dependent antigens and a lack of germinal center formation in the spleen. Relatively little is known about a potential function of OBF1 in developing B cells. Here we have generated transgenic mice overexpressing OBF1 in B cells under the control of the immunoglobulin heavy chain promoter and enhancer. Surprisingly, these mice have greatly reduced numbers of follicular B cells in the periphery and have a compromised immune response. Furthermore, B cell differentiation is impaired at an early stage in the bone marrow: a first block is observed during B cell commitment and a second differentiation block is seen at the large preB2 cell stage. The cells that succeed to escape the block and to differentiate into mature B cells have post-translationally downregulated the expression of transgene, indicating that expression of OBF1 beyond the normal level early in B cell development is deleterious. Transcriptome analysis identified genes deregulated in these mice and Id2 and Id3, two known negative regulators of B cell differentiation, were found to be upregulated in the EPLM and preB cells of the transgenic mice. Furthermore, the Id2 and Id3 promoters contain octamer-like sites, to which OBF1 can bind. These results provide evidence that tight regulation of OBF1 expression in early B cells is essential to allow efficient B lymphocyte differentiation.
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Affiliation(s)
- Alain Bordon
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel, Switzerland
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Lopez F, Textoris J, Bergon A, Didier G, Remy E, Granjeaud S, Imbert J, Nguyen C, Puthier D. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One 2008; 3:e4001. [PMID: 19104654 PMCID: PMC2602602 DOI: 10.1371/journal.pone.0004001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 11/25/2008] [Indexed: 11/18/2022] Open
Abstract
Background As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data. Methodology We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms. Conclusions/Significance As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.
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Affiliation(s)
- Fabrice Lopez
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - Julien Textoris
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
- Service d'Anesthésie et de Réanimation, hôpital Nord - Assistance Publique, Hôpitaux de Marseille, Marseille, France
| | - Aurélie Bergon
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - Gilles Didier
- Université de la Méditerranée, Marseille, France
- Institut de Mathématiques de Luminy, Campus de Luminy, Marseille, France
| | - Elisabeth Remy
- Université de la Méditerranée, Marseille, France
- Institut de Mathématiques de Luminy, Campus de Luminy, Marseille, France
| | - Samuel Granjeaud
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - Jean Imbert
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - Catherine Nguyen
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - Denis Puthier
- Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France
- ESIL, Université de Provence et de la Méditerranée, Marseille, France
- * E-mail:
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Richard MLL, Hikima JI, Wilson MR, Miller NW, Cunningham C, Warr GW. BOB.1 of the channel catfish, Ictalurus punctatus: not a transcriptional coactivator? Mol Immunol 2008; 46:481-91. [PMID: 19041136 DOI: 10.1016/j.molimm.2008.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 10/05/2008] [Accepted: 10/08/2008] [Indexed: 10/21/2022]
Abstract
Expression of the immunoglobulin heavy chain (IGH) locus of the channel catfish (Ictalurus punctatus) is driven by the Emu3' enhancer, whose core region contains two octamer motifs and a muE5 site. Orthologues of the Oct1 and Oct2 transcription factors have been cloned in the channel catfish and shown to bind to the octamer motifs within the core enhancer. While catfish Oct2 is an activator of transcription, catfish Oct1 failed to drive transcription and may act as a negative regulator of IGH transcription. In mammals, the Oct co-activator BOB.1 (B cell Oct-binding protein1, also known as OCA-B and OBF-1) greatly enhances the transcriptional activity of Oct factors and plays an important role in the development of the immune system. An orthologue of BOB.1 has been cloned in the catfish, and its function characterized. The POU binding domain of the catfish BOB.1 was found to be 95% identical at the amino acid level with the binding domain of human BOB.1, and all the residues directly involved in binding to the Oct-DNA complex were conserved. Despite this conservation, catfish BOB.1 failed to enhance transcriptional activation mediated by endogenous or co-transfected catfish Oct2, and failed to rescue the activity of the inactive catfish Oct1. Electrophoretic mobility shift assays showed that catfish BOB.1 was capable of binding both catfish Oct1 and Oct2 when they formed a complex with the Oct motif. Analysis of recombinant chimeric catfish and human BOB.1 proteins demonstrated that the failure to drive transcription was due to the lack of a functional activation domain within the catfish BOB.1.
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Affiliation(s)
- Mara L Lennard Richard
- Marine Biomedicine and Environmental Sciences Center, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
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