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Sumida TS, Lincoln MR, He L, Park Y, Ota M, Oguchi A, Son R, Yi A, Stillwell HA, Leissa GA, Fujio K, Murakawa Y, Kulminski AM, Epstein CB, Bernstein BE, Kellis M, Hafler DA. An autoimmune transcriptional circuit drives FOXP3 + regulatory T cell dysfunction. Sci Transl Med 2024; 16:eadp1720. [PMID: 39196959 DOI: 10.1126/scitranslmed.adp1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/02/2024] [Indexed: 08/30/2024]
Abstract
Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. Although CD4+FOXP3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptomic and epigenomic profiling of Tregs in the autoimmune disease multiple sclerosis (MS) to identify critical transcriptional programs regulating human autoimmunity. We found that up-regulation of a primate-specific short isoform of PR domain zinc finger protein 1 (PRDM1-S) induces expression of serum and glucocorticoid-regulated kinase 1 (SGK1) independent from the evolutionarily conserved long PRDM1, which led to destabilization of forkhead box P3 (FOXP3) and Treg dysfunction. This aberrant PRDM1-S/SGK1 axis is shared among other autoimmune diseases. Furthermore, the chromatin landscape profiling in Tregs from individuals with MS revealed enriched activating protein-1 (AP-1)/interferon regulatory factor (IRF) transcription factor binding as candidate upstream regulators of PRDM1-S expression and Treg dysfunction. Our study uncovers a mechanistic model where the evolutionary emergence of PRDM1-S and epigenetic priming of AP-1/IRF may be key drivers of dysfunctional Tregs in autoimmune diseases.
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Affiliation(s)
- Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON M6R 1B5, Canada
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON M6R 1B5, Canada
| | - Liang He
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | - Yongjin Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Raku Son
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alice Yi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Helen A Stillwell
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Greta A Leissa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8303, Japan
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27705, USA
| | | | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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2
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He J, Gao L, Wang P, Chan WK, Zheng Y, Zhang Y, Sun J, Li X, Wang J, Li XH, Chen H, Yang Z, Wang Y. Prdm1 positively regulates liver Group 1 ILCs cancer immune surveillance and preserves functional heterogeneity. eLife 2024; 13:RP92948. [PMID: 39133873 PMCID: PMC11318973 DOI: 10.7554/elife.92948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
Group 1 innate lymphoid cells (ILCs) comprise conventional natural killer (cNK) cells and type 1 innate lymphoid cells (ILC1s). The main functions of liver cNK cells and ILC1s not only include directly killing target cells but also regulating local immune microenvironment of the liver through the secretion of cytokines. Uncovering the intricate mechanisms by which transcriptional factors regulate and influence the functions of liver cNK cells and ILC1s, particularly within the context of liver tumors, presents a significant opportunity to amplify the effectiveness of immunotherapies against liver malignancies. Using Ncr1-drived conditional knockout mouse model, our study reveals the regulatory role of Prdm1 in shaping the composition and maturation of cNK cells. Although Prdm1 did not affect the killing function of cNK cells in an in vivo cytotoxicity model, a significant increase in cancer metastasis was observed in Prdm1 knockout mice. Interferon-gamma (IFN-γ), granzyme B, and perforin secretion decreased significantly in Prdm1-deficient cNK cells and liver ILC1s. Single-cell RNA sequencing (scRNA-seq) data also provided evidences that Prdm1 maintains functional subsets of cNK cells and liver ILC1s and facilitates communications between cNK cells, liver ILC1s, and macrophages. The present study unveiled a novel regulatory mechanism of Prdm1 in cNK cells and liver ILC1s, showing promising potential for developing innovative immune therapy strategies against liver cancer.
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Affiliation(s)
- Jitian He
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
- Organ Transplant Center, The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhouChina
| | - Le Gao
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Peiying Wang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Wing Keung Chan
- Department of Internal Medicine, Division of Hematology, The Ohio State UniversityColumbusUnited States
| | - Yiran Zheng
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Yumo Zhang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Jiaman Sun
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Xue Li
- Department of Basic Medicine, Haihe Hospital, Tianjin UniversityTianjinChina
| | - Jiming Wang
- Tianjin Economic-Technological Development Area (TEDA) HospitalTianjinChina
| | - Xiao-Hong Li
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
| | - Huaiyong Chen
- Department of Basic Medicine, Haihe Hospital, Tianjin UniversityTianjinChina
- College of Pulmonary and Critical Care Medicine, 8th Medical Center, Chinese PLA General HospitalBeijingChina
- Tianjin Key Laboratory of Lung Regenerative MedicineTianjinChina
| | - Zhouxin Yang
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Zhejiang HospitalHangzhouChina
| | - Youwei Wang
- Institute of Medical Engineering & Translational Medicine, Tianjin UniversityTianjinChina
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3
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Katsura Y, Shigenobu S, Satta Y. Adaptive Evolution and Functional Differentiation of Testis-Expressed Genes in Theria. Animals (Basel) 2024; 14:2316. [PMID: 39199849 PMCID: PMC11350913 DOI: 10.3390/ani14162316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024] Open
Abstract
Gene expression patterns differ in different tissues, and the expression pattern of genes in the mammalian testis is known to be extremely variable in different species. To clarify how the testis transcriptomic pattern has evolved in particular species, we examined the evolution of the adult testis transcriptome in Theria using 10 species: two marsupials (opossum and Tasmanian devil), six eutherian (placental) mammals (human, chimpanzee, bonobo, gorilla, rhesus macaque, and mouse), and two outgroup species (platypus and chicken). We show that 22 testis-expressed genes are marsupial-specific, suggesting their acquisition in the stem lineage of marsupials after the divergence from eutherians. Despite the time length of the eutherian stem lineage being similar to that of the marsupial lineage, acquisition of testis-expressed genes was not found in the stem lineage of eutherians; rather, their expression patterns differed by species, suggesting rapid gene evolution in the eutherian ancestors. Fifteen testis-expressed genes are therian-specific, and for three of these genes, the evolutionary tempo is markedly faster in eutherians than in marsupials. Our phylogenetic analysis of Rho GTPase-activating protein 28 (ARHGAP28) suggests the adaptive evolution of this gene in the eutherians, probably together with the expression pattern differentiation.
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Affiliation(s)
- Yukako Katsura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama 484-8506, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki 444-0867, Japan;
| | - Yoko Satta
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193, Japan;
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4
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Hu X, Chen J, Dai W, Xiao Y, Chen X, Chen Z, Zhang S, Hu Y. PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cells. Cell Mol Life Sci 2024; 81:305. [PMID: 39012348 PMCID: PMC11335229 DOI: 10.1007/s00018-024-05279-z] [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: 12/11/2023] [Revised: 03/30/2024] [Accepted: 05/13/2024] [Indexed: 07/17/2024]
Abstract
Lentiviral vectors have markedly enhanced gene therapy efficiency in treating congenital diseases, but their long-term safety remains controversial. Most gene therapies for congenital eye diseases need to be carried out at early ages, yet the assessment of related risks to ocular development posed by lentiviral vectors is challenging. Utilizing single-cell transcriptomic profiling on human retinal organoids, this study explored the impact of lentiviral vectors on the retinal development and found that lentiviral vectors can cause retinal precursor cells to shift toward photoreceptor fate through the up-regulation of key fate-determining genes such as PRDM1. Further investigation demonstrated that the intron and intergenic region of PRDM1 was bound by PHLDA1, which was also up-regulated by lentiviral vectors exposure. Importantly, knockdown of PHLDA1 successfully suppressed the lentivirus-induced differentiation bias of photoreceptor cells. The findings also suggest that while lentiviral vectors may disrupt the fate determination of retinal precursor cells, posing risks in early-stage retinal gene therapy, these risks could potentially be reduced by inhibiting the PHLDA1-PRDM1 axis.
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Affiliation(s)
- Xing Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Wangxuan Dai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Yuhua Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Xu Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Zheyao Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Shuyao Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Youjin Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
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5
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Xiang M, Li H, Zhan Y, Ma D, Gao Q, Fang Y. Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies. Mol Cancer 2024; 23:73. [PMID: 38581063 PMCID: PMC10996278 DOI: 10.1186/s12943-024-01987-z] [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: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
T cells are fundamental components in tumour immunity and cancer immunotherapies, which have made immense strides and revolutionized cancer treatment paradigm. However, recent studies delineate the predicament of T cell dysregulation in tumour microenvironment and the compromised efficacy of cancer immunotherapies. CRISPR screens enable unbiased interrogation of gene function in T cells and have revealed functional determinators, genetic regulatory networks, and intercellular interactions in T cell life cycle, thereby providing opportunities to revamp cancer immunotherapies. In this review, we briefly described the central roles of T cells in successful cancer immunotherapies, comprehensively summarised the studies of CRISPR screens in T cells, elaborated resultant master genes that control T cell activation, proliferation, fate determination, effector function, and exhaustion, and highlighted genes (BATF, PRDM1, and TOX) and signalling cascades (JAK-STAT and NF-κB pathways) that extensively engage in multiple branches of T cell responses. In conclusion, this review bridged the gap between discovering element genes to a specific process of T cell activities and apprehending these genes in the global T cell life cycle, deepened the understanding of T cell biology in tumour immunity, and outlined CRISPR screens resources that might facilitate the development and implementation of cancer immunotherapies in the clinic.
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Affiliation(s)
- Minghua Xiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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6
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Lin QXX, Rajagopalan D, Gamage AM, Tan LM, Venkatesh PN, Chan WOY, Kumar D, Agrawal R, Chen Y, Fong SW, Singh A, Sun LJ, Tan SY, Chai LYA, Somani J, Lee B, Renia L, Ng LFP, Ramanathan K, Wang LF, Young B, Lye D, Singhal A, Prabhakar S. Longitudinal single cell atlas identifies complex temporal relationship between type I interferon response and COVID-19 severity. Nat Commun 2024; 15:567. [PMID: 38238298 PMCID: PMC10796319 DOI: 10.1038/s41467-023-44524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
Due to the paucity of longitudinal molecular studies of COVID-19, particularly those covering the early stages of infection (Days 1-8 symptom onset), our understanding of host response over the disease course is limited. We perform longitudinal single cell RNA-seq on 286 blood samples from 108 age- and sex-matched COVID-19 patients, including 73 with early samples. We examine discrete cell subtypes and continuous cell states longitudinally, and we identify upregulation of type I IFN-stimulated genes (ISGs) as the predominant early signature of subsequent worsening of symptoms, which we validate in an independent cohort and corroborate by plasma markers. However, ISG expression is dynamic in progressors, spiking early and then rapidly receding to the level of severity-matched non-progressors. In contrast, cross-sectional analysis shows that ISG expression is deficient and IFN suppressors such as SOCS3 are upregulated in severe and critical COVID-19. We validate the latter in four independent cohorts, and SOCS3 inhibition reduces SARS-CoV-2 replication in vitro. In summary, we identify complexity in type I IFN response to COVID-19, as well as a potential avenue for host-directed therapy.
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Affiliation(s)
- Quy Xiao Xuan Lin
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Deepa Rajagopalan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Le Min Tan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Prasanna Nori Venkatesh
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Dilip Kumar
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
| | - Ragini Agrawal
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Yao Chen
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Louisa J Sun
- Alexandra Hospital, Singapore, 159964, Singapore
| | - Seow-Yen Tan
- Changi General Hospital, Singapore, 529889, Singapore
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Jyoti Somani
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore, 119228, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Laurent Renia
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore
| | - Kollengode Ramanathan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- National University Hospital, Singapore, 119074, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, 168753, Singapore
| | - Barnaby Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - David Lye
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- National Centre for Infectious diseases, Singapore, 308442, Singapore
- Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Amit Singhal
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore.
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), A*STAR, Singapore, 138648, Singapore.
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore.
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7
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Alduraibi FK, Tsokos GC. Lupus Nephritis Biomarkers: A Critical Review. Int J Mol Sci 2024; 25:805. [PMID: 38255879 PMCID: PMC10815779 DOI: 10.3390/ijms25020805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Lupus nephritis (LN), a major complication in individuals diagnosed with systemic lupus erythematosus, substantially increases morbidity and mortality. Despite marked improvements in the survival of patients with severe LN over the past 50 years, complete clinical remission after immunosuppressive therapy is achieved in only half of the patients. Therefore, timely detection of LN is vital for initiating prompt therapeutic interventions and improving patient outcomes. Biomarkers have emerged as valuable tools for LN detection and monitoring; however, the complex role of these biomarkers in LN pathogenesis remains unclear. Renal biopsy remains the gold standard for the identification of the histological phenotypes of LN and guides disease management. However, the molecular pathophysiology of specific renal lesions remains poorly understood. In this review, we provide a critical, up-to-date overview of the latest developments in the field of LN biomarkers.
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Affiliation(s)
- Fatima K. Alduraibi
- Department of Medicine, Division of Clinical Immunology and Rheumatology, Beth Israel Deaconess Medical Center, Harvard Teaching Hospital, Boston, MA 02215, USA
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, Division of Clinical Immunology and Rheumatology, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - George C. Tsokos
- Department of Medicine, Division of Clinical Immunology and Rheumatology, Beth Israel Deaconess Medical Center, Harvard Teaching Hospital, Boston, MA 02215, USA
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8
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Trujillo-Ochoa JL, Kazemian M, Afzali B. The role of transcription factors in shaping regulatory T cell identity. Nat Rev Immunol 2023; 23:842-856. [PMID: 37336954 PMCID: PMC10893967 DOI: 10.1038/s41577-023-00893-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
Forkhead box protein 3-expressing (FOXP3+) regulatory T cells (Treg cells) suppress conventional T cells and are essential for immunological tolerance. FOXP3, the master transcription factor of Treg cells, controls the expression of multiples genes to guide Treg cell differentiation and function. However, only a small fraction (<10%) of Treg cell-associated genes are directly bound by FOXP3, and FOXP3 alone is insufficient to fully specify the Treg cell programme, indicating a role for other accessory transcription factors operating upstream, downstream and/or concurrently with FOXP3 to direct Treg cell specification and specialized functions. Indeed, the heterogeneity of Treg cells can be at least partially attributed to differential expression of transcription factors that fine-tune their trafficking, survival and functional properties, some of which are niche-specific. In this Review, we discuss the emerging roles of accessory transcription factors in controlling Treg cell identity. We specifically focus on members of the basic helix-loop-helix family (AHR), basic leucine zipper family (BACH2, NFIL3 and BATF), CUT homeobox family (SATB1), zinc-finger domain family (BLIMP1, Ikaros and BCL-11B) and interferon regulatory factor family (IRF4), as well as lineage-defining transcription factors (T-bet, GATA3, RORγt and BCL-6). Understanding the imprinting of Treg cell identity and specialized function will be key to unravelling basic mechanisms of autoimmunity and identifying novel targets for drug development.
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Affiliation(s)
- Jorge L Trujillo-Ochoa
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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9
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Zhou W, Geng H, Huang Y, Shi S, Wang Z, Wang D. Mechanism of BLIMP1/TRIM66/COX2 in human decidua participates in parturition†. Biol Reprod 2023; 109:507-519. [PMID: 37515773 DOI: 10.1093/biolre/ioad081] [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: 02/17/2023] [Revised: 06/09/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
The mechanism underlying the initiation of parturition remains unclear. Cyclooxygenase 2 and prostaglandins in decidual membrane tissue play an important role in the "parturition cascade." With the advancement of gestation, the expression of the transcriptional suppressor B lymphocyte-induced maturation protein 1 in the decidual membrane gradually decreases. Through chromatin immunoprecipitation sequencing, we found that B lymphocyte-induced maturation protein 1 has a binding site in the distal intergenic of PTGS2(COX2). Tripartite motif-containing protein 66 is a chromatin-binding protein that usually performs transcriptional regulatory functions by "reading" histone modification sites in chromatin. In this study, tripartite motif-containing protein 66 exhibits the same trend of expression as B lymphocyte-induced maturation protein 1 in the decidua during gestation. Moreover, the co-immunoprecipitation assay revealed that tripartite motif-containing protein 66 combined with B lymphocyte-induced maturation protein 1. This finding indicated that tripartite motif-containing protein 66 formed a transcription complex with B lymphocyte-induced maturation protein 1, which coregulated the expression of COX2. In animal experiments, we injected si-Blimp1 adenoviruses (si-Blimp1), Blimp1 overexpression plasmid (Blimp1-OE), and Trim66 overexpression plasmid (Trim66-OE) through the tail vein of mice. The results showed that B lymphocyte-induced maturation protein 1 and tripartite motif-containing protein 66 affected the initiation of parturition in mice. Therefore, the present evidence suggests that B lymphocyte-induced maturation protein 1 and tripartite motif-containing protein 66 partially participate in the initiation of labor, which may provide a new perspective for exploring the mechanism of term labor.
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Affiliation(s)
- Wei Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huizhen Geng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yihong Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaole Shi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zilian Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongyu Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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10
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Lemaître QIB, Bartsch N, Kouzel IU, Busengdal H, Richards GS, Steinmetz PRH, Rentzsch F. NvPrdm14d-expressing neural progenitor cells contribute to non-ectodermal neurogenesis in Nematostella vectensis. Nat Commun 2023; 14:4854. [PMID: 37563174 PMCID: PMC10415408 DOI: 10.1038/s41467-023-39789-4] [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: 09/20/2022] [Accepted: 06/29/2023] [Indexed: 08/12/2023] Open
Abstract
Neurogenesis has been studied extensively in the ectoderm, from which most animals generate the majority of their neurons. Neurogenesis from non-ectodermal tissue is, in contrast, poorly understood. Here we use the cnidarian Nematostella vectensis as a model to provide new insights into the molecular regulation of non-ectodermal neurogenesis. We show that the transcription factor NvPrdm14d is expressed in a subpopulation of NvSoxB(2)-expressing endodermal progenitor cells and their NvPOU4-expressing progeny. Using a new transgenic reporter line, we show that NvPrdm14d-expressing cells give rise to neurons in the body wall and in close vicinity of the longitudinal retractor muscles. RNA-sequencing of NvPrdm14d::GFP-expressing cells and gene knockdown experiments provide candidate genes for the development and function of these neurons. Together, the identification of a population of endoderm-specific neural progenitor cells and of previously undescribed putative motoneurons in Nematostella provide new insights into the regulation of non-ectodermal neurogenesis.
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Affiliation(s)
- Quentin I B Lemaître
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Natascha Bartsch
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
- Department for Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Ian U Kouzel
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Henriette Busengdal
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | - Gemma Sian Richards
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway
| | | | - Fabian Rentzsch
- Michael Sars Centre, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
- Department for Biological Sciences, University of Bergen, Thormøhlensgate 55, 5006, Bergen, Norway.
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11
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de la Cruz-Ruiz P, Rodríguez-Palero MJ, Askjaer P, Artal-Sanz M. Tissue-specific chromatin-binding patterns of Caenorhabditis elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression. Genetics 2023; 224:iyad081. [PMID: 37119802 PMCID: PMC10324947 DOI: 10.1093/genetics/iyad081] [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: 03/08/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
Heterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs in Caenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them with heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with the methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements conversely with HPL-1, which exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a corepressive role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.
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Affiliation(s)
- Patricia de la Cruz-Ruiz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Peter Askjaer
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville 41013, Spain
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12
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Velazquez-Salinas L, Medina GN, Valdez F, Zarate S, Collinson S, Zhu JJ, Rodriguez LL. Exploring the Molecular Basis of Vesicular Stomatitis Virus Pathogenesis in Swine: Insights from Expression Profiling of Primary Macrophages Infected with M51R Mutant Virus. Pathogens 2023; 12:896. [PMID: 37513744 PMCID: PMC10384765 DOI: 10.3390/pathogens12070896] [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: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Vesicular stomatitis virus (VSV) is an emergent virus affecting livestock in the US. Previously, using a recombinant VSV carrying the M51R mutation in the matrix protein (rNJ0612NME6-M51R), we evaluated the pathogenesis of this virus in pigs. Our results indicated that rNJ0612NME6-M51R represented an attenuated phenotype in in-vivo and in ex-vivo in pig macrophages, resembling certain clinical features observed in field VSV isolates. In order to gain more insight into the molecular basis leading to the attenuation of rNJ0612NME6-M51R in pigs, we conducted a microarray analysis to assess the gene expression profiles of primary porcine macrophages infected with rNJ0612NME6-M51R compared to its parental virus (rNJ0612NME6). Our results showed an overall higher gene expression in macrophages infected with rNJ0612NME6-M51R. Specifically, we observed that the pathways related with immune cytokine signaling and interferon (IFN)-related responses (including activation, signaling, induction, and antiviral mechanisms) were the ones comprising most of the relevant genes identified during this study. Collectively, the results presented herein highlight the relevance of type I interferon during the pathogenesis of VSV in pigs. The information generated from this study may represent a framework for future studies intended to understand the molecular bases of the pathogenesis of field strains in livestock.
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Affiliation(s)
- Lauro Velazquez-Salinas
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Federico Valdez
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- Oak Ridge Institute for Science and Education (ORISE)-PIADC, Oak Ridge, TN 37831, USA
| | - Selene Zarate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de Mexico, Ciudad de Mexico 04510, Mexico
| | - Shannon Collinson
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- Oak Ridge Institute for Science and Education (ORISE)-PIADC, Oak Ridge, TN 37831, USA
| | - James J Zhu
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Luis L Rodriguez
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
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13
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Li Q, Wang W, Wu S, Li J, Dong M, Wang L, Song L. CgBlimp-1 inhibits granulocytes proliferation and interleukin production in the immune response of oyster Crassostrea gigas. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 142:104652. [PMID: 36736934 DOI: 10.1016/j.dci.2023.104652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
B lymphocyte-inducible maturation protein 1 (Blimp-1) is a SET domain and zinc fingers containing transcriptional repressor, which is necessary for regulating the development of many immune cell lineages and keeping immune homeostasis. In the present study, a Blimp-1 homologue (designated as CgBlimp-1) was identified from oyster Crassostrea gigas, which contained a conserved SET domain and five ZnF_C2H2 domains and shared high homology with Blimp-1 from other species. The mRNA transcripts of CgBlimp-1 were highly expressed in gill and hepatopancreas. CgBlimp-1 protein was detected to be specifically expressed in granulocytes. After V. splendidus stimulation, the mRNA expression level of CgBlimp-1 in haemocytes up-regulated significantly at 24, 48, and 96 h, which was 4.39-fold (p < 0.05), 7.68-fold (p < 0.01) and 2.65-fold (p < 0.05) of that in control group, respectively. When the expression of CgBlimp-1 was knocked-down in vivo by RNAi, the mRNA expressions of downstream transcription factor CgMyc-A (1.63-fold of that in control group, p < 0.05) and cell cycle related gene CgCDK2 (1.70-fold, p < 0.05) increased significantly at 24 h after V. splendidus stimulation. Concomitantly, the ratio of EdU+ haemocytes increased notably (p < 0.01) while the proportion of haemocytes in G0/G1 phase decreased dramatically (p < 0.001), compared to that in control group. More specifically, the proportion of granulocytes in total haemocytes increased apparently (p < 0.05) in CgBlimp-1-RNAi oysters, together with up-regulation (p < 0.05) of the ratio of EdU+ granulocytes and down-regulation (p < 0.001) of the proportion of granulocytes in G0/G1 phase. Furthermore, the mRNA expression levels of CgIL17-1, CgIL17-2 and CgIL17-4 in haemocytes increased significantly in CgBlimp-1-RNAi oysters, which was 1.71-fold (p < 0.05), 144.70-fold (p < 0.01) and 1.93-fold (p < 0.05) of that in control group, respectively. Aforementioned results suggested that CgBlimp-1 could reduce the proliferation of granulocytes by arresting cell cycle in G1/G0 phase and avoid over-expression of interleukin to maintain homeostasis in the immune response of oyster.
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Affiliation(s)
- Qing Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Shasha Wu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Jialuo Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Miren Dong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
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14
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Rossi M, Anerillas C, Idda ML, Munk R, Shin CH, Donega S, Tsitsipatis D, Herman AB, Martindale JL, Yang X, Piao Y, Mazan-Mamczarz K, Fan J, Ferrucci L, Johnson PF, De S, Abdelmohsen K, Gorospe M. Pleiotropic effects of BAFF on the senescence-associated secretome and growth arrest. eLife 2023; 12:e84238. [PMID: 37083495 PMCID: PMC10121226 DOI: 10.7554/elife.84238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/26/2023] [Indexed: 04/22/2023] Open
Abstract
Senescent cells release a variety of cytokines, proteases, and growth factors collectively known as the senescence-associated secretory phenotype (SASP). Sustained SASP contributes to a pattern of chronic inflammation associated with aging and implicated in many age-related diseases. Here, we investigated the expression and function of the immunomodulatory cytokine BAFF (B-cell activating factor; encoded by the TNFSF13B gene), a SASP protein, in multiple senescence models. We first characterized BAFF production across different senescence paradigms, including senescent human diploid fibroblasts (WI-38, IMR-90) and monocytic leukemia cells (THP-1), and tissues of mice induced to undergo senescence. We then identified IRF1 (interferon regulatory factor 1) as a transcription factor required for promoting TNFSF13B mRNA transcription in senescence. We discovered that suppressing BAFF production decreased the senescent phenotype of both fibroblasts and monocyte-like cells, reducing IL6 secretion and SA-β-Gal staining. Importantly, however, the influence of BAFF on the senescence program was cell type-specific: in monocytes, BAFF promoted the early activation of NF-κB and general SASP secretion, while in fibroblasts, BAFF contributed to the production and function of TP53 (p53). We propose that BAFF is elevated across senescence models and is a potential target for senotherapy.
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Affiliation(s)
- Martina Rossi
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Maria Laura Idda
- Institute for Genetic and Biomedical Research (IRGB), National Research CouncilSassaryItaly
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Chang Hoon Shin
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Stefano Donega
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
- Translational Gerontology Branch, NIA IRP, NIHBaltimoreUnited States
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Allison B Herman
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Jinshui Fan
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Luigi Ferrucci
- Translational Gerontology Branch, NIA IRP, NIHBaltimoreUnited States
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute IRPFrederickUnited States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of HealthBaltimoreUnited States
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15
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Massa C, Wang Y, Marr N, Seliger B. Interferons and Resistance Mechanisms in Tumors and Pathogen-Driven Diseases—Focus on the Major Histocompatibility Complex (MHC) Antigen Processing Pathway. Int J Mol Sci 2023; 24:ijms24076736. [PMID: 37047709 PMCID: PMC10095295 DOI: 10.3390/ijms24076736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 04/08/2023] Open
Abstract
Interferons (IFNs), divided into type I, type II, and type III IFNs represent proteins that are secreted from cells in response to various stimuli and provide important information for understanding the evolution, structure, and function of the immune system, as well as the signaling pathways of other cytokines and their receptors. They exert comparable, but also distinct physiologic and pathophysiologic activities accompanied by pleiotropic effects, such as the modulation of host responses against bacterial and viral infections, tumor surveillance, innate and adaptive immune responses. IFNs were the first cytokines used for the treatment of tumor patients including hairy leukemia, renal cell carcinoma, and melanoma. However, tumor cells often develop a transient or permanent resistance to IFNs, which has been linked to the escape of tumor cells and unresponsiveness to immunotherapies. In addition, loss-of-function mutations in IFN signaling components have been associated with susceptibility to infectious diseases, such as COVID-19 and mycobacterial infections. In this review, we summarize general features of the three IFN families and their function, the expression and activity of the different IFN signal transduction pathways, and their role in tumor immune evasion and pathogen clearance, with links to alterations in the major histocompatibility complex (MHC) class I and II antigen processing machinery (APM). In addition, we discuss insights regarding the clinical applications of IFNs alone or in combination with other therapeutic options including immunotherapies as well as strategies reversing the deficient IFN signaling. Therefore, this review provides an overview on the function and clinical relevance of the different IFN family members, with a specific focus on the MHC pathways in cancers and infections and their contribution to immune escape of tumors.
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Affiliation(s)
- Chiara Massa
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
| | - Yuan Wang
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
| | - Nico Marr
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
| | - Barbara Seliger
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany
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16
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da Costa LCO, Gardinassi LG, Veras FP, Milanezi C, Ramalho LNZ, Benevides L, Alves-Filho JC, da Silva JS, da Silva Souza C. Expression of B lymphocyte-induced maturation protein 1 (Blimp-1) in keratinocyte and cytokine signalling drives human Th17 response in psoriasis. Arch Dermatol Res 2023; 315:481-490. [PMID: 36042041 DOI: 10.1007/s00403-022-02379-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 06/30/2022] [Accepted: 08/01/2022] [Indexed: 11/02/2022]
Abstract
Transcriptional factor B lymphocyte-induced maturation protein 1 (Blimp-1) is pivotally implicated in T helper 17 (Th17) cell differentiation. This study investigated expression of the Blimp-1 protein, positive regulatory domain 1 (PRDM1), and cytokine genes in psoriasis (PsO). Affected (AS-PsO) and non-affected skin (nAS-PsO) samples were used to assess gene and protein expressions by reverse transcription-quantitative PCR (RT-qPCR), and immunostaining and confocal microscopy, respectively; the normalised public transcriptomic data permitted differential gene expression analyses. On RT-qPCR, PRDM1 and IL17A transcripts showed higher expression in AS-PsO than in nAS-PsO (n = 34) (p < 0.001; p < 0.0001, respectively). Confocal microscopy showed Blimp-1 protein expression in epidermal layer keratinocytes in AS-PsO, but not in nAS-PsO. Bioinformatic analysis of the transcriptomic dataset GSE13355 corroborated the increased PRDM1, signal transducer and activator of transcription 3 (STAT3), IL12B, TNF, IL17A, IL6, IL1B, IL22, and IL10 gene expression in AS-PsO, when compared to normal skin and nAS-PsO (p < 0.001). PRDM1 expression correlated positively (p < 0.0001) with that of IL17A (r = 0.7), IL1B (r = 0.67), IL12B (r = 0.6), IL6 (r = 0.59), IL22 (r = 0.53), IL23A (r = 0.47), IL21 (r = 0.47), IL27 (r = 0.34), IL23R (r = 0.32), S100 calcium binding protein A9 (r = 0.63), and lipocalin 2 (r = 0.50), and negatively with that of TGFB1 (r = - 0.28) and RORC (r = - 0.60). Blimp-1 may be critical in the pathogenesis of PsO dysregulation involving the Th17 inflammatory pathway. This knowledge may accelerate the development of new treatments.
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Affiliation(s)
- Lorena Carla Oliveira da Costa
- Dermatology Division, Department of Internal Medicine, Ribeirão Preto Medical School, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14048-900, Brazil
| | - Luiz Gustavo Gardinassi
- Department of Biosciences and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Flávio Protásio Veras
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cristiane Milanezi
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Luciana Benevides
- Fiocruz-Bi-Institutional Translational Medicine Plataform, Ribeirão Preto, São Paulo, Brazil
| | - José Carlos Alves-Filho
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Santana da Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Fiocruz-Bi-Institutional Translational Medicine Plataform, Ribeirão Preto, São Paulo, Brazil
| | - Cacilda da Silva Souza
- Dermatology Division, Department of Internal Medicine, Ribeirão Preto Medical School, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14048-900, Brazil.
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17
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Sarhan M, Miyagawa K, Ueda H. Domain analysis of Drosophila Blimp-1 reveals the importance of its repression function and instability in determining pupation timing. Genes Cells 2023; 28:338-347. [PMID: 36852536 DOI: 10.1111/gtc.13020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
The PRDM family transcription repressor Blimp-1 is present in almost all multicellular organisms and plays important roles in various developmental processes. This factor has several conserved motifs among different species, but the function of each motif is unclear. Drosophila Blimp-1 plays an important role in determining pupation timing by acting as an unstable transcriptional repressor of the βftz-f1 gene. Thus, Drosophila provides a good system for analyzing the molecular and biological functions of each region in Blimp-1. Various Blimp-1 mutants carrying deletions at the conserved motifs were induced under the control of the heat shock promoter in prepupae, and the expression patterns of βFTZ-F1 and Blimp-1 and pupation timing were observed. The results showed that the regions with strong and weak repressor functions exist within the proline-rich middle section of the factor and near the N-terminal conserved motif, respectively. Rapid degradation was supported by multiple regions that were mainly located in a large proline-rich region. Results revealed that pupation timing was affected by the repression ability and stability of Blimp-1. This suggests that both the repression function and instability of Blimp-1 are indispensable for the precise determination of pupation timing.
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Affiliation(s)
- Moustafa Sarhan
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koichi Miyagawa
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hitoshi Ueda
- The Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.,Department of Biology, Faculty of Science, Okayama University, Okayama, Japan
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18
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Bunker J, Bashir M, Bailey S, Boodram P, Perry A, Delaney R, Tsachaki M, Sprecher SG, Nelson E, Call GB, Rister J. Blimp-1/PRDM1 and Hr3/RORβ specify the blue-sensitive photoreceptor subtype in Drosophila by repressing the hippo pathway. Front Cell Dev Biol 2023; 11:1058961. [PMID: 36960411 PMCID: PMC10027706 DOI: 10.3389/fcell.2023.1058961] [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: 09/30/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
During terminal differentiation of the mammalian retina, transcription factors control binary cell fate decisions that generate functionally distinct subtypes of photoreceptor neurons. For instance, Otx2 and RORβ activate the expression of the transcriptional repressor Blimp-1/PRDM1 that represses bipolar interneuron fate and promotes rod photoreceptor fate. Moreover, Otx2 and Crx promote expression of the nuclear receptor Nrl that promotes rod photoreceptor fate and represses cone photoreceptor fate. Mutations in these four transcription factors cause severe eye diseases such as retinitis pigmentosa. Here, we show that a post-mitotic binary fate decision in Drosophila color photoreceptor subtype specification requires ecdysone signaling and involves orthologs of these transcription factors: Drosophila Blimp-1/PRDM1 and Hr3/RORβ promote blue-sensitive (Rh5) photoreceptor fate and repress green-sensitive (Rh6) photoreceptor fate through the transcriptional repression of warts/LATS, the nexus of the phylogenetically conserved Hippo tumor suppressor pathway. Moreover, we identify a novel interaction between Blimp-1 and warts, whereby Blimp-1 represses a warts intronic enhancer in blue-sensitive photoreceptors and thereby gives rise to specific expression of warts in green-sensitive photoreceptors. Together, these results reveal that conserved transcriptional regulators play key roles in terminal cell fate decisions in both the Drosophila and the mammalian retina, and the mechanistic insights further deepen our understanding of how Hippo pathway signaling is repurposed to control photoreceptor fates for Drosophila color vision.
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Affiliation(s)
- Joseph Bunker
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Mhamed Bashir
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Sydney Bailey
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Pamela Boodram
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- NYU Langone Medical Center, New York, NY, United States
| | - Alexis Perry
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Rory Delaney
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
| | - Maria Tsachaki
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Simon G. Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Erik Nelson
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, United States
| | - Gerald B. Call
- Department of Pharmacology, College of Graduate Studies, Midwestern University, Glendale, AZ, United States
| | - Jens Rister
- Department of Biology, Integrated Sciences Complex, University of Massachusetts Boston, Boston, MA, United States
- *Correspondence: Jens Rister,
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19
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Yavuz S, Pucholt P, Sandling JK, Bianchi M, Leonard D, Bolin K, Imgenberg-Kreuz J, Eloranta ML, Kozyrev SV, Lanata CM, Jönsen A, Bengtsson AA, Sjöwall C, Svenungsson E, Gunnarsson I, Rantapää-Dahlqvist S, Nititham J, Criswell LA, Lindblad-Toh K, Rönnblom L. Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease. Lupus Sci Med 2022; 9:e000752. [PMID: 36332927 PMCID: PMC9639142 DOI: 10.1136/lupus-2022-000752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Lupus nephritis (LN) is a common and severe manifestation of SLE. The genetic risk for nephritis and progression to end-stage renal disease (ESRD) in patients with LN remains unclear. Herein, we aimed to identify novel genetic associations with LN, focusing on subphenotypes and ESRD. METHODS We analysed genomic data on 958 patients with SLE (discovery cohort: LN=338) with targeted sequencing data from 1832 immunological pathway genes. We used an independent multiethnic cohort comprising 1226 patients with SLE (LN=603) as a replication dataset. Detailed functional annotation and functional epigenomic enrichment analyses were applied to predict functional effects of the candidate variants. RESULTS A genetic variant (rs56097910) within the MERTK gene was associated with ESRD in both cohorts, meta-analysis OR=5.4 (2.8 to 10.6); p=1.0×10-6. We observed decreased methylation levels in peripheral blood cells from SLE patients with ESRD, compared with patients without renal SLE (p=2.7×10-4), at one CpG site (cg16333401) in close vicinity to the transcription start site of MERTK and located in a DNAse hypersensitivity region in T and B cells. Rs56097910 is linked to altered MERTK expression in kidney tissue in public eQTL databases. Two loci were replicated for association with proliferative LN: PRDM1 (rs6924535, pmeta=1.6×10-5, OR=0.58) and APOA1BP (NAXE) (rs942960, pmeta=1.2×10-5, OR=2.64). CONCLUSION We identified a novel genetic risk locus, MERTK, associated with SLE-ESRD using the data from two large SLE cohorts. Through DNA methylation analysis and functional annotation, we showed that the risk could be mediated through regulation of gene expression. Our results suggest that variants in the MERTK gene are important for the risk of developing SLE-ESRD and suggest a role for PRDM1 and APOA1BP in proliferative LN.
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Affiliation(s)
- Sule Yavuz
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Bolin
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juliana Imgenberg-Kreuz
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sergey V Kozyrev
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Cristina M Lanata
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andreas Jönsen
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Lund, Sweden
- Rheumatology, Skåne University Hospital Lund, Lund, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Lund, Sweden
- Rheumatology, Skåne University Hospital Lund, Lund, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Östergötland, Sweden
| | - Elisabet Svenungsson
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Department of Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Department of Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Joanne Nititham
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lindsey A Criswell
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute, Cambridge, Massachusetts, USA
| | - Lars Rönnblom
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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20
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Manti PG, Darbellay F, Leleu M, Coughlan AY, Moret B, Cuennet J, Droux F, Stoudmann M, Mancini GF, Hautier A, Sordet-Dessimoz J, Vincent SD, Testa G, Cossu G, Barrandon Y. The Transcriptional Regulator Prdm1 Is Essential for the Early Development of the Sensory Whisker Follicle and Is Linked to the Beta-Catenin First Dermal Signal. Biomedicines 2022; 10:2647. [PMID: 36289911 PMCID: PMC9599752 DOI: 10.3390/biomedicines10102647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/18/2022] Open
Abstract
Prdm1 mutant mice are one of the rare mutant strains that do not develop whisker hair follicles while still displaying a pelage. Here, we show that Prdm1 is expressed at the earliest stage of whisker development in clusters of mesenchymal cells before placode formation. Its conditional knockout in the murine soma leads to the loss of expression of Bmp2, Shh, Bmp4, Krt17, Edar, and Gli1, though leaving the β-catenin-driven first dermal signal intact. Furthermore, we show that Prdm1 expressing cells not only act as a signaling center but also as a multipotent progenitor population contributing to the several lineages of the adult whisker. We confirm by genetic ablation experiments that the absence of macro vibrissae reverberates on the organization of nerve wiring in the mystacial pads and leads to the reorganization of the barrel cortex. We demonstrate that Lef1 acts upstream of Prdm1 and identify a primate-specific deletion of a Lef1 enhancer named Leaf. This loss may have been significant in the evolutionary process, leading to the progressive defunctionalization and disappearance of vibrissae in primates.
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Affiliation(s)
- Pierluigi G Manti
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Fabrice Darbellay
- Laboratory of Developmental Genomics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Marion Leleu
- BioInformatics Competence Center, UNIL-EPFL, 1015 Lausanne, Switzerland
| | - Aisling Y Coughlan
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Bernard Moret
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Julien Cuennet
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Frederic Droux
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Magali Stoudmann
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Gian-Filippo Mancini
- Histology Core Facility, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | - Agnès Hautier
- Histology Core Facility, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
| | | | - Stephane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester M139PL, UK
- Division of Neuroscience, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Yann Barrandon
- Laboratory of Stem Cell Dynamics, School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, 1015 Lausanne, Switzerland
- Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
- Department of Plastic, Reconstructive and Aesthetic Surgery, Singapore General Hospital, Singapore 169608, Singapore
- A*STAR Skin Research Labs, Singapore 138648, Singapore
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21
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Tang TF, Chan YT, Cheong HC, Cheok YY, Anuar NA, Looi CY, Gan GG, Wong WF. Regulatory network of BLIMP1, IRF4, and XBP1 triad in plasmacytic differentiation and multiple myeloma pathogenesis. Cell Immunol 2022; 380:104594. [PMID: 36081178 DOI: 10.1016/j.cellimm.2022.104594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
Antibody secreting plasma cell plays an indispensable role in humoral immunity. As activated B cell undergoes germinal center reaction and develops into plasma cell, it gradually loses B cell characteristics and embraces functional changes associated with immunoglobulins production. Differentiation of B cell into plasma cell involves drastic changes in cell structure, granularity, metabolism, gene expression and epigenetic regulation that couple with the mounting capacity for synthesis of a large quantity of antigen-specific antibodies. The interplay between three hallmark transcriptional regulators IRF4, BLIMP1, and XBP1, is critical for supporting the cellular reprograming activities during B to plasma cell transition. IRF4 promotes plasma cell generation by directing immunoglobulin class switching, proliferation and survival; BLIMP1 serves as a transcriptional repressor that extinguishes B cell features; whereas XBP1 controls unfolded protein response that relieves endoplasmic reticulum stress and permits antibody release during terminal differentiation. Intriguingly, high expression of IRF4, BLIMP1, and XBP1 molecules have been reported in myeloma cells derived from multiple myeloma patients, which negatively impact treatment outcome, prognosis, and relapse frequency. Despite the introduction of immunomodulatory drugs in recent years, multiple myeloma is still an incurable disease with poor survival rate. An in-depth review of IRF4, BLIMP1, and XBP1 triad molecules in plasma cell generation and multiple myeloma tumorigenesis may provide clues to the possibility of targeting these molecules in disease management.
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Affiliation(s)
- Ting Fang Tang
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yee Teng Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Heng Choon Cheong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yi Ying Cheok
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nur Adila Anuar
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chung Yeng Looi
- School of Bioscience, Taylor's University, 47500 Subang Jaya, Selangor, Malaysia
| | - Gin Gin Gan
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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22
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Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity. Cell Stem Cell 2022; 29:1197-1212.e8. [PMID: 35931030 PMCID: PMC9623845 DOI: 10.1016/j.stem.2022.07.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/31/2022] [Accepted: 07/13/2022] [Indexed: 01/02/2023]
Abstract
Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing sporadic Alzheimer's disease. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral APOE3 allele remains unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a lipid-accumulated state that renders microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia in response to neuronal conditioned media, we established that neuronal cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro-inflammatory signals. Through decreased uptake of extracellular fatty acids and lipoproteins, we identified that APOE4 microglia disrupts the coordinated activity of neuronal ensembles. These findings suggest that abnormal neuronal network-level disturbances observed in Alzheimer's disease patients harboring APOE4 may in part be triggered by impairment in lipid homeostasis in non-neuronal cells.
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23
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Nadeau S, Martins GA. Conserved and Unique Functions of Blimp1 in Immune Cells. Front Immunol 2022; 12:805260. [PMID: 35154079 PMCID: PMC8829541 DOI: 10.3389/fimmu.2021.805260] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022] Open
Abstract
B-lymphocyte-induced maturation protein-1 (Blimp1), is an evolutionarily conserved transcriptional regulator originally described as a repressor of gene transcription. Blimp1 crucially regulates embryonic development and terminal differentiation in numerous cell lineages, including immune cells. Initial investigations of Blimp1’s role in immunity established its non-redundant role in lymphocytic terminal effector differentiation and function. In B cells, Blimp1 drives plasmablast formation and antibody secretion, whereas in T cells, Blimp1 regulates functional differentiation, including cytokine gene expression. These studies established Blimp1 as an essential transcriptional regulator that promotes efficient and controlled adaptive immunity. Recent studies have also demonstrated important roles for Blimp1 in innate immune cells, specifically myeloid cells, and Blimp1 has been established as an intrinsic regulator of dendritic cell maturation and T cell priming. Emerging studies have determined both conserved and unique functions of Blimp1 in different immune cell subsets, including the unique direct activation of the igh gene transcription in B cells and a conserved antagonism with BCL6 in B cells, T cells, and myeloid cells. Moreover, polymorphisms associated with the gene encoding Blimp1 (PRDM1) have been linked to numerous chronic inflammatory conditions in humans. Blimp1 has been shown to regulate target gene expression by either competing with other transcription factors for binding to the target loci, and/or by recruiting various chromatin-modifying co-factors that promote suppressive chromatin structure, such as histone de-acetylases and methyl-transferases. Further, Blimp1 function has been shown to be essentially dose and context-dependent, which adds to Blimp1’s versatility as a regulator of gene expression. Here, we review Blimp1’s complex roles in immunity and highlight specific gaps in the understanding of the biology of this transcriptional regulator, with a major focus on aspects that could foster the description and understanding of novel pathways regulated by Blimp1 in the immune system.
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Affiliation(s)
- Samantha Nadeau
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute (IBIRI), Cedars-Sinai Medical Center (CSMC), Los Angeles, CA, United States.,Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center (CSMC), Los Angeles, CA, United States
| | - Gislâine A Martins
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute (IBIRI), Cedars-Sinai Medical Center (CSMC), Los Angeles, CA, United States.,Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center (CSMC), Los Angeles, CA, United States.,Department of Medicine, Gastroenterology Division, Cedars-Sinai Medical Center (CSMC), Los Angeles, CA, United States
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24
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Lee H, Huang DY, Chang HC, Lin CY, Ren WY, Dai YS, Lin WW. Blimp-1 Upregulation by Multiple Ligands via EGFR Transactivation Inhibits Cell Migration in Keratinocytes and Squamous Cell Carcinoma. Front Pharmacol 2022; 13:763678. [PMID: 35185556 PMCID: PMC8847214 DOI: 10.3389/fphar.2022.763678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
B lymphocyte-induced maturation protein-1 (Blimp-1) is a transcriptional repressor and plays a crucial role in the regulation of development and functions of various immune cells. Currently, there is limited understanding about the regulation of Blimp-1 expression and cellular functions in keratinocytes and cancer cells. Previously we demonstrated that EGF can upregulate Blimp-1 gene expression in keratinocytes, playing a negative role in regulation of cell migration and inflammation. Because it remains unclear if Blimp-1 can be regulated by other stimuli beyond EGF, here we further investigated multiple stimuli for their regulation of Blimp-1 expression in keratinocytes and squamous cell carcinoma (SCC). We found that PMA, TNF-α, LPS, polyIC, H2O2 and UVB can upregulate the protein and/or mRNA levels of Blimp-1 in HaCaT and SCC cells. Concomitant EGFR activation was observed by these stimuli, and EGFR inhibitor gefitinib and Syk inhibitor can block Blimp-1 gene expression caused by PMA. Reporter assay of Blimp-1 promoter activity further indicated the involvement of AP-1 in PMA-, TNF-α-, LPS- and EGF-elicited Blimp-1 mRNA expression. Confocal microscopic data indicated the nuclear loclization of Blimp-1, and such localization was not changed by stimuli. Moreover, Blimp-1 silencing enhanced SCC cell migration. Taken together, Blimp-1 can be transcriptionally upregulated by several stimuli in keratinocytes and SCC via EGFR transactivation and AP-1 pathway. These include growth factor PMA, cytokine TNF-α, TLR ligands (LPS and polyIC), and ROS insults (H2O2 and UVB). The function of Blimp-1 as a negative regulator of cell migration in SCC can provide a new therapeutic target in SCC.
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Affiliation(s)
- Hyemin Lee
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Duen-Yi Huang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hua-Ching Chang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Dermatology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chia-Yee Lin
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wan-Yu Ren
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yang-Shia Dai
- Department of Dermatology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wan-Wan Lin
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department and Graduate Institute of Pharmacology, National Defense Medical Center, Taipei, Taiwan.,Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
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25
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Dowling JW, Forero A. Beyond Good and Evil: Molecular Mechanisms of Type I and III IFN Functions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:247-256. [PMID: 35017214 DOI: 10.4049/jimmunol.2100707] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022]
Abstract
IFNs are comprised of three families of cytokines that confer protection against pathogen infection and uncontrolled cellular proliferation. The broad role IFNs play in innate and adaptive immune regulation has placed them under heavy scrutiny to position them as "friend" or "foe" across pathologies. Genetic lesions in genes involving IFN synthesis and signaling underscore the disparate outcomes of aberrant IFN signaling. Abrogation of the response leads to susceptibility to microbial infections whereas unabated IFN induction underlies a variety of inflammatory diseases and tumor immune evasion. Type I and III IFNs have overlapping roles in antiviral protection, yet the mechanisms by which they are induced and promote the expression of IFN-stimulated genes and inflammation can distinguish their biological functions. In this review, we examine the molecular factors that shape the shared and distinct roles of type I and III IFNs in immunity.
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Affiliation(s)
- Jack W Dowling
- Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, OH 43210; and.,Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH 43210
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26
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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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The Immunogenetics of Systemic Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:259-298. [DOI: 10.1007/978-3-030-92616-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Martinez-Ruíz GU, Morales-Sánchez A, Bhandoola A. Transcriptional and epigenetic regulation in thymic epithelial cells. Immunol Rev 2022; 305:43-58. [PMID: 34750841 PMCID: PMC8766885 DOI: 10.1111/imr.13034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/03/2023]
Abstract
The thymus is required for the development of both adaptive and innate-like T cell subsets. There is keen interest in manipulating thymic function for therapeutic purposes in circumstances of autoimmunity, immunodeficiency, and for purposes of immunotherapy. Within the thymus, thymic epithelial cells play essential roles in directing T cell development. Several transcription factors are known to be essential for thymic epithelial cell development and function, and a few transcription factors have been studied in considerable detail. However, the role of many other transcription factors is less well understood. Further, it is likely that roles exist for other transcription factors not yet known to be important in thymic epithelial cells. Recent progress in understanding of thymic epithelial cell heterogeneity has provided some new insight into transcriptional requirements in subtypes of thymic epithelial cells. However, it is unknown whether progenitors of thymic epithelial cells exist in the adult thymus, and consequently, developmental relationships linking putative precursors with differentiated cell types are poorly understood. While we do not presently possess a clear understanding of stage-specific requirements for transcription factors in thymic epithelial cells, new single-cell transcriptomic and epigenomic technologies should enable rapid progress in this field. Here, we review our current knowledge of transcription factors involved in the development, maintenance, and function of thymic epithelial cells, and the mechanisms by which they act.
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Affiliation(s)
- Gustavo Ulises Martinez-Ruíz
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Abigail Morales-Sánchez
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Genetic ablation of PRDM1 in antitumor T cells enhances therapeutic efficacy of adoptive immunotherapy. Blood 2021; 139:2156-2172. [PMID: 34861037 DOI: 10.1182/blood.2021012714] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/23/2021] [Indexed: 11/20/2022] Open
Abstract
Adoptive cancer immunotherapy can induce objective clinical efficacy in patients with advanced cancer; however, a sustained response is achieved in a minority of cases. The persistence of infused T cells is an essential determinant of a durable therapeutic response. Antitumor T cells undergo a genome-wide remodeling of the epigenetic architecture upon repeated antigen encounters, which inevitably induces progressive T-cell differentiation and the loss of longevity. In this study, we identified PR domain zinc finger protein 1 (PRDM1) i.e., Blimp-1, as a key epigenetic gene associated with terminal T-cell differentiation. The genetic knockout of PRDM1 by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) supported the maintenance of an early memory phenotype and polyfunctional cytokine secretion in repeatedly stimulated chimeric antigen receptor (CAR)-engineered T cells. PRDM1 disruption promoted the expansion of less differentiated memory CAR-T cells in vivo, which enhanced T-cell persistence and improved therapeutic efficacy in multiple tumor models. Mechanistically, PRDM1-ablated T cells displayed enhanced chromatin accessibility of the genes that regulate memory formation, thereby leading to the acquisition of gene expression profiles representative of early memory T cells. PRDM1 knockout also facilitated maintaining an early memory phenotype and cytokine polyfunctionality in T-cell receptor-engineered T cells as well as tumor-infiltrating lymphocytes. In other words, targeting PRDM1 enabled the generation of superior antitumor T cells, which is potentially applicable to a wide range of adoptive cancer immunotherapies.
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Jiang HS, Ghose P, Han HF, Wu YZ, Tsai YY, Lin HC, Tseng WC, Wu JC, Shaham S, Wu YC. BLMP-1 promotes developmental cell death in C. elegans by timely repression of ced-9 transcription. Development 2021; 148:dev193995. [PMID: 34541605 PMCID: PMC8572009 DOI: 10.1242/dev.193995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/14/2021] [Indexed: 11/20/2022]
Abstract
Programmed cell death (PCD) is a common cell fate in metazoan development. PCD effectors are extensively studied, but how they are temporally regulated is less understood. Here, we report a mechanism controlling tail-spike cell death onset during Caenorhabditis elegans development. We show that the zinc-finger transcription factor BLMP-1, which controls larval development timing, also regulates embryonic tail-spike cell death initiation. BLMP-1 functions upstream of CED-9 and in parallel to DRE-1, another CED-9 and tail-spike cell death regulator. BLMP-1 expression is detected in the tail-spike cell shortly after the cell is born, and blmp-1 mutations promote ced-9-dependent tail-spike cell survival. BLMP-1 binds ced-9 gene regulatory sequences, and inhibits ced-9 transcription just before cell-death onset. BLMP-1 and DRE-1 function together to regulate developmental timing, and their mammalian homologs regulate B-lymphocyte fate. Our results, therefore, identify roles for developmental timing genes in cell-death initiation, and suggest conservation of these functions.
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Affiliation(s)
- Hang-Shiang Jiang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Piya Ghose
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA
- Department of Biology, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Hsiao-Fen Han
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Yun-Zhe Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Ya-Yin Tsai
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Huang-Chin Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Wei-Chin Tseng
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
| | - Jui-Ching Wu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 100229, Taiwan
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Yi-Chun Wu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106216, Taiwan
- Department of Life Science, Center for Systems Biology, and Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106216, Taiwan
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 106216, Taiwan
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Molecular Pathogenesis and Immune Evasion of Vesicular Stomatitis New Jersey Virus Inferred from Genes Expression Changes in Infected Porcine Macrophages. Pathogens 2021; 10:pathogens10091134. [PMID: 34578166 PMCID: PMC8469936 DOI: 10.3390/pathogens10091134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/17/2022] Open
Abstract
The molecular mechanisms associated with the pathogenesis of vesicular stomatitis virus (VSV) in livestock remain poorly understood. Several studies have highlighted the relevant role of macrophages in controlling the systemic dissemination of VSV during infection in different animal models, including mice, cattle, and pigs. To gain more insight into the molecular mechanisms used by VSV to impair the immune response in macrophages, we used microarrays to determine the transcriptomic changes produced by VSV infection in primary cultures of porcine macrophages. The results indicated that VSV infection induced the massive expression of multiple anorexic, pyrogenic, proinflammatory, and immunosuppressive genes. Overall, the interferon (IFN) response appeared to be suppressed, leading to the absence of stimulation of interferon-stimulated genes (ISG). Interestingly, VSV infection promoted the expression of several genes known to downregulate the expression of IFNβ. This represents an alternate mechanism for VSV control of the IFN response, beyond the recognized mechanisms mediated by the matrix protein. Although there was no significant differential gene expression in macrophages infected with a highly virulent epidemic strain compared to a less virulent endemic strain, the endemic strain consistently induced higher expression of all upregulated cytokines and chemokines. Collectively, this study provides novel insights into VSV molecular pathogenesis and immune evasion that warrant further investigation.
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Mucosal ribosomal stress-induced PRDM1 promotes chemoresistance via stemness regulation. Commun Biol 2021; 4:543. [PMID: 33972671 PMCID: PMC8110964 DOI: 10.1038/s42003-021-02078-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
The majorities of colorectal cancer (CRC) cases are sporadic in origin and a large proportion of etiologies are associated with environmental stress responses. In response to external and internal stress, the ribosome stands sentinel and stress-driven ribosomal dysfunction triggers the cellular decision pathways via transcriptional reprogramming. In the present study, PR domain zinc finger protein (PRDM) 1, a master transcriptional regulator, was found to be closely associated with ribosomal actions in patients with CRC and the murine models. Stress-driven ribosomal dysfunction enhanced PRDM1 levels in intestinal cancer cells, which contributed to their survival and enhanced cancer cell stemness against cancer treatment. Mechanistically, PRDM1 facilitated clustering modulation of insulin-like growth factor (IGF) receptor-associated genes, which supported cancer cell growth and stemness-linked features. Ribosomal dysfunction-responsive PRDM1 facilitated signaling remodeling for the survival of tumor progenitors, providing compelling evidence for the progression of sporadic CRC.
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Li B, Li Y, Wu S, Yang Y, Fu S, Yin X, Tu X, Fang L, Guo Z, Ye J. Identification and functional characterization of CD154 in T cell-dependent immune response in Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2021; 111:102-110. [PMID: 33513438 DOI: 10.1016/j.fsi.2021.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
CD154, a member of the TNF superfamily, is a multifunctional molecule highly expressed in activated T cells, and plays important roles in T cell-dependent humoral immune response. In this study, CD154 of Nile tilapia (Oreochromis niloticus) was identified, and its functions in the T cell-dependent immune response were demonstrated. The open reading frame (ORF) of OnCD154 is 699 bp, encoding a protein of 232 amino acids with a 23 amino acid transmembrane region. Amino acid sequence of OnCD154 is highly homologous to that of other teleost fish, especially rainbow trout. Quantitative real-time PCR (qRT-PCR) demonstrated that mRNA of OnCD154 is highly expressed in immune organs, especially in spleen, thymus, gills, head kidney, etc. In addition, the anti-OnCD154 polyclonal antibody (anti-(r)OnCD154) was successfully prepared, and it can react with natural protein in head kidney leukocytes. Following two immunizations with keyhole limpet hemocyanin (KLH) in vivo, the significantly up-regulated expression level of OnCD154 mRNA appeared earlier (fifth day) and higher (42.9 folds) in the second challenge than the first on in head kidney. Further, after stimulation with KLH in vitro, the expressions of T cell-dependent immune response-related molecules (activated T cell specific surface molecules CD3ε and CD154) and B cell differentiation-related molecules (Blimp1 and sIgM) and CD40 were significantly up-regulated in head kidney leukocytes. Moreover, the up-regulated expressions of these molecules were blocked with the treatment of anti-(r)OnCD154 antibody. Taken together, these results indicate that OnCD154 might get involved in T cell-dependent immune response, and provide a new insight into the humoral immune response of teleost fish.
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Affiliation(s)
- Bingxi Li
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Yuan Li
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Siwei Wu
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Yanjian Yang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Shengli Fu
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Xiaoxue Yin
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Xiao Tu
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China
| | - Liang Fang
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China.
| | - Zheng Guo
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China.
| | - Jianmin Ye
- Institute of Modern Aquaculture Science and Engineering, School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong, 510631, PR China.
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Di Tullio F, Schwarz M, Zorgati H, Mzoughi S, Guccione E. The duality of PRDM proteins: epigenetic and structural perspectives. FEBS J 2021; 289:1256-1275. [PMID: 33774927 DOI: 10.1111/febs.15844] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/26/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
PRDF1 and RIZ1 homology domain containing (PRDMs) are a subfamily of Krüppel-like zinc finger proteins controlling key processes in metazoan development and in cancer. PRDMs exhibit unique dualities: (a) PR domain/ZNF arrays-their structure combines a SET-like domain known as a PR domain, typically found in methyltransferases, with a variable array of C2H2 zinc fingers (ZNF) characteristic of DNA-binding transcription factors; (b) transcriptional activators/repressors-their physiological function is context- and cell-dependent; mechanistically, some PRDMs have a PKMT activity and directly catalyze histone lysine methylation, while others are rather pseudomethyltransferases and act by recruiting transcriptional cofactors; (c) oncogenes/tumor suppressors-their pathological function depends on the specific PRDM isoform expressed during tumorigenesis. This duality is well known as the 'Yin and Yang' of PRDMs and involves a complex regulation of alternative splicing or alternative promoter usage, to generate full-length or PR-deficient isoforms with opposing functions in cancer. In conclusion, once their dualities are fully appreciated, PRDMs represent a promising class of targets in oncology by virtue of their widespread upregulation across multiple tumor types and their somatic dispensability, conferring a broad therapeutic window and limited toxic side effects. The recent discovery of a first-in-class compound able to inhibit PRDM9 activity has paved the way for the identification of further small molecular inhibitors able to counteract PRDM oncogenic activity.
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Affiliation(s)
- Federico Di Tullio
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan Schwarz
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Habiba Zorgati
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Mzoughi
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ernesto Guccione
- Department of Oncological Sciences and Pharmacological Sciences, Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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35
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Johnson JS, De Veaux N, Rives AW, Lahaye X, Lucas SY, Perot BP, Luka M, Garcia-Paredes V, Amon LM, Watters A, Abdessalem G, Aderem A, Manel N, Littman DR, Bonneau R, Ménager MM. A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. Cell Rep 2021; 30:914-931.e9. [PMID: 31968263 PMCID: PMC7039998 DOI: 10.1016/j.celrep.2019.12.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/25/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023] Open
Abstract
Transcriptional programming of the innate immune response is pivotal for host protection. However, the transcriptional mechanisms that link pathogen sensing with innate activation remain poorly under-stood. During HIV-1 infection, human dendritic cells (DCs) can detect the virus through an innate sensing pathway, leading to antiviral interferon and DC maturation. Here, we develop an iterative experimental and computational approach to map the HIV-1 innate response circuitry in monocyte-derived DCs (MDDCs). By integrating genome-wide chromatin accessibility with expression kinetics, we infer a gene regulatory network that links 542 transcription factors with 21,862 target genes. We observe that an interferon response is required, yet insufficient, to drive MDDC maturation and identify PRDM1 and RARA as essential regulators of the interferon response and MDDC maturation, respectively. Our work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting complexity and cooperativity in the regulatory circuit controlling the response to infection. Pathogen sensing leads to host transcriptional reprogramming to protect against infection. However, it is unclear how transcription factor activity is coordinated across the genome. Johnson et al. integrate chromatin accessibility and gene expression data to infer and validate a gene regulatory network that directs the innate immune response to HIV.
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Affiliation(s)
- Jarrod S Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Center for Infectious Disease Research, Seattle, WA 98109, USA.
| | - Nicholas De Veaux
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Alexander W Rives
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Xavier Lahaye
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Sasha Y Lucas
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Brieuc P Perot
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Marine Luka
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Victor Garcia-Paredes
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Lynn M Amon
- Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Aaron Watters
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA
| | - Ghaith Abdessalem
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Alan Aderem
- Center for Infectious Disease Research, Seattle, WA 98109, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Richard Bonneau
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA; Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Data Science, New York University, New York, NY 10011, USA
| | - Mickaël M Ménager
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, Imagine Institute, INSERM UMR 1163, ATIP-Avenir Team, Université de Paris, 24 Boulevard du Montparnasse, 75015 Paris, France; The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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36
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Diallo MS, Samri A, Charpentier C, Bertine M, Cheynier R, Thiébaut R, Matheron S, Collin F, Braibant M, Candotti D, Brun-Vézinet F, Autran B, Appay V, Autran B, Brun-Vezinet F, Chaghil N, Descamps D, Hosmalin A, Pancino G, Manel N, Marchand L, Pedroza-Martins L, Sàez-Cirion A, Vieillard V, Agut H, Clauvel JP, Costagliola D, Debré P, Theodorou I, Sicard D, Viard JP, Barin F, Vieillard V, Autran B. A Comparison of Cell Activation, Exhaustion, and Expression of HIV Coreceptors and Restriction Factors in HIV-1- and HIV-2-Infected Nonprogressors. AIDS Res Hum Retroviruses 2021; 37:214-223. [PMID: 33050708 DOI: 10.1089/aid.2020.0084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency viruses induce rare attenuated diseases due either to HIV-1 in the exceptional long-term nonprogressors (LTNPs) or to HIV-2 in West Africa. To better understand characteristics of these two disease types we performed a multiplex comparative analysis of cell activation, exhaustion, and expression of coreceptors and restriction factors in CD4 T cells susceptible to harbor those viruses. We analyzed by flow cytometry the expression of HLA-DR, PD1, CCR5, CXCR6, SAMHD1, Blimp-1, and TRIM5α on CD4 T cell subsets from 10 HIV-1+ LTNPs and 14 HIV-2+ (12 nonprogressors and 2 progressors) of the ANRS CO-15 and CO-5 cohorts, respectively, and 12 HIV- healthy donors (HD). The V3 loop of the HIV-1 envelope from 6 HIV-1+ LTNPs was sequenced to determine the CXCR6-binding capacity. Proportions of HLA-DR+ and PD1+ cells were higher in memory CD4 T subsets from HIV-1 LTNPs compared with HIV-2 and HD. Similar findings were observed for CCR5+ cells although limited to central-memory CD4 T cell (TCM) and follicular helper T cell subsets, whereas all major subsets from HIV-1 LTNPs contained less CXCR6+ cells compared with HIV-2. All six V3 loop sequences from HIV-1 LTNPs contained a proline at position 326. Proportions of SAMHD1+ cells were higher in all resting CD4 T subsets from HIV-1 LTNPs compared with the other groups, whereas Blimp-1+ and Trim5α+ cells did not differ. The CD4 T cell subsets from HIV-1 LTNPs differ from those of HIV-2-infected subjects by higher levels of activation, exhaustion, and SAMHD1 expression that can reflect the distinct patterns of host/virus relationships.
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Affiliation(s)
- Mariama Sadjo Diallo
- Inserm 1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Sorbonne Université, Paris, France
| | - Assia Samri
- Inserm 1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Sorbonne Université, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137, Inserm, Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Virologie, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mélanie Bertine
- IAME, UMR 1137, Inserm, Université Paris Diderot, Sorbonne Paris Cité, Laboratoire de Virologie, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Rémi Cheynier
- Institut Cochin, Inserm, U1016, CNRS, UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Rodolphe Thiébaut
- Inserm U1219 Bordeaux Population Health, INRIA SISTM, University of Bordeaux, Bordeaux, France
| | - Sophie Matheron
- Inserm, IAME, UMR 1137, University of Paris Diderot, Sorbonne Paris Cité, Assistance Publique -Hôpitaux de Paris, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, HUPNVS, Paris, France
| | - Fidéline Collin
- Inserm, IAME, UMR 1137, University of Paris Diderot, Sorbonne Paris Cité, Assistance Publique -Hôpitaux de Paris, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, HUPNVS, Paris, France
| | - Martine Braibant
- Université François-Rabelais, Inserm U1259 & CHRU de Tours, Tours, France
| | | | | | - Brigitte Autran
- Inserm 1135, Centre d'Immunologie et des Maladies Infectieuses, Cimi-Paris, Sorbonne Université, Paris, France
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Saitou M. Mammalian Germ Cell Development: From Mechanism to In Vitro Reconstitution. Stem Cell Reports 2021; 16:669-680. [PMID: 33577794 PMCID: PMC8072030 DOI: 10.1016/j.stemcr.2021.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
The germ cell lineage gives rise to totipotency and perpetuates and diversifies genetic as well as epigenetic information. Specifically, germ cells undergo epigenetic reprogramming/programming, replicate genetic information with high fidelity, and create genetic diversity through meiotic recombination. Driven by advances in our understanding of the mechanisms underlying germ cell development and stem cell/reproductive technologies, research over the past 2 decades has culminated in the in vitro reconstitution of mammalian germ cell development: mouse pluripotent stem cells (PSCs) can now be induced into primordial germ cell-like cells (PGCLCs) and then differentiated into fully functional oocytes and spermatogonia, and human PSCs can be induced into PGCLCs and into early oocytes and prospermatogonia with epigenetic reprogramming. Here, I provide my perspective on the key investigations that have led to the in vitro reconstitution of mammalian germ cell development, which will be instrumental in exploring salient themes in germ cell biology and, with further refinements/extensions, in developing innovative medical applications.
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Affiliation(s)
- Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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Li Y, Gao J, Kamran M, Harmacek L, Danhorn T, Leach SM, O'Connor BP, Hagman JR, Huang H. GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers. Nat Commun 2021; 12:494. [PMID: 33479210 PMCID: PMC7820599 DOI: 10.1038/s41467-020-20766-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors. However, it is unclear whether these lineage-determining factors regulate chromatin accessibility at mast cell enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation. We find that the number and densities of GATA2- but not MITF-bound sites at the super-enhancers are several folds higher than that at the typical enhancers. Our studies reveal that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation by binding to super-enhancer regions with dense GATA2 binding sites available at key mast cell genes.
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Affiliation(s)
- Yapeng Li
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Junfeng Gao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Mohammad Kamran
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Laura Harmacek
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Thomas Danhorn
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Sonia M Leach
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Brian P O'Connor
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA.
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Emerging Roles of PRDM Factors in Stem Cells and Neuronal System: Cofactor Dependent Regulation of PRDM3/16 and FOG1/2 (Novel PRDM Factors). Cells 2020; 9:cells9122603. [PMID: 33291744 PMCID: PMC7761934 DOI: 10.3390/cells9122603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) (PR) homologous domain containing (PRDM) transcription factors are expressed in neuronal and stem cell systems, and they exert multiple functions in a spatiotemporal manner. Therefore, it is believed that PRDM factors cooperate with a number of protein partners to regulate a critical set of genes required for maintenance of stem cell self-renewal and differentiation through genetic and epigenetic mechanisms. In this review, we summarize recent findings about the expression of PRDM factors and function in stem cell and neuronal systems with a focus on cofactor-dependent regulation of PRDM3/16 and FOG1/2. We put special attention on summarizing the effects of the PRDM proteins interaction with chromatin modulators (NuRD complex and CtBPs) on the stem cell characteristic and neuronal differentiation. Although PRDM factors are known to possess intrinsic enzyme activity, our literature analysis suggests that cofactor-dependent regulation of PRDM3/16 and FOG1/2 is also one of the important mechanisms to orchestrate bidirectional target gene regulation. Therefore, determining stem cell and neuronal-specific cofactors will help better understanding of PRDM3/16 and FOG1/2-controlled stem cell maintenance and neuronal differentiation. Finally, we discuss the clinical aspect of these PRDM factors in different diseases including cancer. Overall, this review will help further sharpen our knowledge of the function of the PRDM3/16 and FOG1/2 with hopes to open new research fields related to these factors in stem cell biology and neuroscience.
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Lycium barbarum Polysaccharides Promote Maturity of Murine Dendritic Cells through Toll-Like Receptor 4-Erk1/2-Blimp1 Signaling Pathway. J Immunol Res 2020; 2020:1751793. [PMID: 33344654 PMCID: PMC7725586 DOI: 10.1155/2020/1751793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/11/2020] [Accepted: 10/30/2020] [Indexed: 12/04/2022] Open
Abstract
In previous studies, Lycium barbarum polysaccharides (LBP), a traditional Chinese medicine, can promote immature dendritic cells (DCs) to mature. However, the molecular mechanisms by which LBP works are not yet elucidated. Here, we found that LBP can induce DCs maturation, which is mainly characterized by the upregulation of MHCII and costimulatory molecules (CD80, CD86), and increase the production of IL-6 and IL-4. Furthermore, we found that LBP could increase the mRNA and protein expression of TLR4, p38, Erk1/2, JNK, and Blimp1 signal molecules. More interestingly, after blocking by Toll-like receptor 4 inhibitor, Resatorvid (TAK 242), the mRNA and protein expression of TLR4, Erk1/2, and Blimp1 was significantly decreased while the expression of p38 and JNK has not changed. Then, we found that after blocking by p38 inhibitor (SB203580), Erk inhibitor (PD98059), and JNK inhibitor (SP603580) separately, Blimp1 protein expression was significantly reduced; after downregulating Blimp1 by Blimp1-siRNA, the production of IL-6 was reduced. In conclusion, our results indicate that LBP can induce maturation of DCs through the TLR4-Erk1/2-Blimp1 signal pathway instead of the JNK/p38-Blimp1 pathway. Our findings may provide a novel evidence for understanding the molecular mechanisms of LBP on activating murine DCs.
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41
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Perdiguero P, Goméz-Esparza MC, Martín D, Bird S, Soleto I, Morel E, Díaz-Rosales P, Tafalla C. Insights Into the Evolution of the prdm1/Blimp1 Gene Family in Teleost Fish. Front Immunol 2020; 11:596975. [PMID: 33193451 PMCID: PMC7662092 DOI: 10.3389/fimmu.2020.596975] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/08/2020] [Indexed: 12/27/2022] Open
Abstract
In mammals, Blimp1 (B lymphocyte-induced maturation protein 1) encoded by the prdm1 gene and its homolog Hobit (homolog of Blimp1 in T cells) encoded by znf683, represent key transcriptional factors that control the development and differentiation of both B and T cells. Despite their essential role in the regulation of acquired immunity, this gene family has been largely unexplored in teleosts to date. Until now, one prdm1 gene has been identified in most teleost species, whereas a znf683 homolog has not yet been reported in any of these species. Focusing our analysis on rainbow trout (Oncorhynchus mykiss), an in silico identification and characterization of prdm1-like genes has been undertaken, confirming that prdm1 and znf683 evolved from a common ancestor gene, acquiring three gene copies after the teleost-specific whole genome duplication event (WGD) and six genes after the salmonid-specific WGD. Additional transcriptional studies to study how each of these genes are regulated in homeostasis, in response to a viral infection or in B cells in different differentiation stages, provide novel insights as to how this gene family evolved and how their encoded products might be implicated in the lymphocyte differentiation process in teleosts.
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Affiliation(s)
| | | | - Diana Martín
- Animal Health Research Center (CISA-INIA), Madrid, Spain
| | - Steve Bird
- Biomedical Unit, School of Science, University of Waikato, Hamilton, New Zealand
| | - Irene Soleto
- Animal Health Research Center (CISA-INIA), Madrid, Spain
| | - Esther Morel
- Animal Health Research Center (CISA-INIA), Madrid, Spain
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42
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Differential epigenetic regulation between the alternative promoters, PRDM1α and PRDM1β, of the tumour suppressor gene PRDM1 in human multiple myeloma cells. Sci Rep 2020; 10:15899. [PMID: 32985591 PMCID: PMC7522722 DOI: 10.1038/s41598-020-72946-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 09/07/2020] [Indexed: 12/23/2022] Open
Abstract
Multiple myeloma (MM) is a B-cell neoplasm that is characterized by the accumulation of malignant plasma cells in the bone marrow. The transcription factor PRDM1 is a master regulator of plasma cell development and is considered to be an oncosuppressor in several lymphoid neoplasms. The PRDM1β isoform is an alternative promoter of the PRDM1 gene that may interfere with the normal role of the PRDM1α isoform. To explain the induction of the PRDM1β isoform in MM and to offer potential therapeutic strategies to modulate its expression, we characterized the cis regulatory elements and epigenetic status of its promoter. We observed unexpected patterns of hypermethylation and hypomethylation at the PRDM1α and PRDM1β promoters, respectively, and prominent H3K4me1 and H3K9me2 enrichment at the PRDM1β promoter in non-expressing cell lines compared to PRDM1β-expressing cell lines. After treatment with drugs that inhibit DNA methylation, we were able to modify the activity of the PRDM1β promoter but not that of the PRDM1α promoter. Epigenetic drugs may offer the ability to control the expression of the PRDM1α/PRDM1β promoters as components of novel therapeutic approaches.
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43
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Ulmert I, Henriques-Oliveira L, Pereira CF, Lahl K. Mononuclear phagocyte regulation by the transcription factor Blimp-1 in health and disease. Immunology 2020; 161:303-313. [PMID: 32799350 PMCID: PMC7692253 DOI: 10.1111/imm.13249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 02/04/2023] Open
Abstract
B lymphocyte‐induced maturation protein‐1 (Blimp‐1), the transcription factor encoded by the gene Prdm1, plays a number of crucial roles in the adaptive immune system, which result in the maintenance of key effector functions of B‐ and T‐cells. Emerging clinical data, as well as mechanistic evidence from mouse studies, have additionally identified critical functions of Blimp‐1 in the maintenance of immune homeostasis by the mononuclear phagocyte (MNP) system. Blimp‐1 regulation of gene expression affects various aspects of MNP biology, including developmental programmes such as fate decisions of monocytes entering peripheral tissue, and functional programmes such as activation, antigen presentation and secretion of soluble inflammatory mediators. The highly tissue‐, subset‐ and state‐specific regulation of Blimp‐1 expression in MNPs suggests that Blimp‐1 is a dynamic regulator of immune activation, integrating environmental cues to fine‐tune the function of innate cells. In this review, we will discuss the current knowledge regarding Blimp‐1 regulation and function in macrophages and dendritic cells.
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Affiliation(s)
- Isabel Ulmert
- Division of Biopharma, Institute for Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | | | - Carlos-Filipe Pereira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Katharina Lahl
- Division of Biopharma, Institute for Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark.,Immunology Section, Lund University, Lund, Sweden
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44
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Lee K, Jang SH, Tian H, Kim SJ. NonO Is a Novel Co-factor of PRDM1 and Regulates Inflammatory Response in Monocyte Derived-Dendritic Cells. Front Immunol 2020; 11:1436. [PMID: 32765503 PMCID: PMC7378894 DOI: 10.3389/fimmu.2020.01436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/03/2020] [Indexed: 12/21/2022] Open
Abstract
Proper expression of the transcription factor, Positive regulatory domain 1 (PRDM1), is required for maintaining homeostasis of human monocyte derived-dendritic cells (MO-DCs). The molecular mechanisms and gene targets of PRDM1 in B and T lymphocytes have been identified. However, the function of PRDM1 in dendritic cells (DCs) remains unclear. We investigate co-regulators of PRDM1 in MO-DCs identified by mass spectrometry (MS) and co-immunoprecipitation (Co-IP). Notably, non-POU domain-containing octamer-binding protein (NonO) was found to be a PRDM1 binding protein in the nucleus of MO-DCs. NonO is recruited to the PRDM1 binding site in the promoter region of IL-6. Knockdown of NonO expression by siRNA lessened suppression of IL-6 promoter activity by PRMD1 following LPS stimulation. While NonO binding to PRDM1 was observed in human myeloma cell lines, an effect of NonO on IL-6 expression was not observed. Thus, loss of NonO interrupted the inhibitory effect of PRDM1 on IL-6 expression in MO-DCs, but not plasma cells. Moreover, MO-DCs with low expression of PRDM1 or NonO induce an increased number of IL-21-producing TFH-like cells in vitro. These data suggest that low level of PRDM1 and NonO lead to enhanced activation of MO-DCs and the regulation of MO-DC function by PRDM1 is mediated through cell lineage-specific mechanisms.
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Affiliation(s)
- Kyungwoo Lee
- Institute of Molecular Medicine, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Su Hwa Jang
- Institute of Molecular Medicine, The Feinstein Institute for Medical Research, Manhasset, NY, United States.,Department of Biomedical Science, Graduate School of Biomedical Sciences and Engineering, Hanyang University, Seoul, South Korea
| | - Hong Tian
- Institute of Molecular Medicine, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Sun Jung Kim
- Institute of Molecular Medicine, The Feinstein Institute for Medical Research, Manhasset, NY, United States
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45
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Schwanke H, Stempel M, Brinkmann MM. Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression. Viruses 2020; 12:E733. [PMID: 32645843 PMCID: PMC7411613 DOI: 10.3390/v12070733] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
The type I interferon (IFN) response is a principal component of our immune system that allows to counter a viral attack immediately upon viral entry into host cells. Upon engagement of aberrantly localised nucleic acids, germline-encoded pattern recognition receptors convey their find via a signalling cascade to prompt kinase-mediated activation of a specific set of five transcription factors. Within the nucleus, the coordinated interaction of these dimeric transcription factors with coactivators and the basal RNA transcription machinery is required to access the gene encoding the type I IFN IFNβ (IFNB1). Virus-induced release of IFNβ then induces the antiviral state of the system and mediates further mechanisms for defence. Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. In this review, we will revisit the steps enabling the trans-activating potential of IRF3 after its activation and the subsequent assembly of the multi-protein complex at the IFNβ enhancer that controls gene expression. Further, we will inspect the regulatory mechanisms of these steps imposed by the host cell and present the manifold strategies viruses have evolved to intervene with IFNβ transcription downstream of IRF3 activation in order to secure establishment of a productive infection.
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Affiliation(s)
- Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Stempel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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46
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Rivera-Serrano EE, Gizzi AS, Arnold JJ, Grove TL, Almo SC, Cameron CE. Viperin Reveals Its True Function. Annu Rev Virol 2020; 7:421-446. [PMID: 32603630 DOI: 10.1146/annurev-virology-011720-095930] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Most cells respond to viral infections by activating innate immune pathways that lead to the induction of antiviral restriction factors. One such factor, viperin, was discovered almost two decades ago based on its induction during viral infection. Since then, viperin has been shown to possess activity against numerous viruses via multiple proposed mechanisms. Most recently, however, viperin was demonstrated to catalyze the conversion of cytidine triphosphate (CTP) to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP), a previously unknown ribonucleotide. Incorporation of ddhCTP causes premature termination of RNA synthesis by the RNA-dependent RNA polymerase of some viruses. To date, production of ddhCTP by viperin represents the only activity of viperin that links its enzymatic activity directly to an antiviral mechanism in human cells. This review examines the multiple antiviral mechanisms and biological functions attributed to viperin.
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Affiliation(s)
- Efraín E Rivera-Serrano
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , .,Department of Pharmacology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; ,
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; ,
| | - Craig E Cameron
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
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47
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Altered Transcription Factor Binding and Gene Bivalency in Islets of Intrauterine Growth Retarded Rats. Cells 2020; 9:cells9061435. [PMID: 32527043 PMCID: PMC7348746 DOI: 10.3390/cells9061435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Intrauterine growth retardation (IUGR), which induces epigenetic modifications and permanent changes in gene expression, has been associated with the development of type 2 diabetes. Using a rat model of IUGR, we performed ChIP-Seq to identify and map genome-wide histone modifications and gene dysregulation in islets from 2- and 10-week rats. IUGR induced significant changes in the enrichment of H3K4me3, H3K27me3, and H3K27Ac marks in both 2-wk and 10-wk islets, which were correlated with expression changes of multiple genes critical for islet function in IUGR islets. ChIP-Seq analysis showed that IUGR-induced histone mark changes were enriched at critical transcription factor binding motifs, such as C/EBPs, Ets1, Bcl6, Thrb, Ebf1, Sox9, and Mitf. These transcription factors were also identified as top upstream regulators in our previously published transcriptome study. In addition, our ChIP-seq data revealed more than 1000 potential bivalent genes as identified by enrichment of both H3K4me3 and H3K27me3. The poised state of many potential bivalent genes was altered by IUGR, particularly Acod1, Fgf21, Serpina11, Cdh16, Lrrc27, and Lrrc66, key islet genes. Collectively, our findings suggest alterations of histone modification in key transcription factors and genes that may contribute to long-term gene dysregulation and an abnormal islet phenotype in IUGR rats.
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The transcriptional repressor Blimp1/PRDM1 regulates the maternal decidual response in mice. Nat Commun 2020; 11:2782. [PMID: 32493987 PMCID: PMC7270082 DOI: 10.1038/s41467-020-16603-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
The transcriptional repressor Blimp1 controls cell fate decisions in the developing embryo and adult tissues. Here we describe Blimp1 expression and functional requirements within maternal uterine tissues during pregnancy. Expression is robustly up-regulated at early post-implantation stages in the primary decidual zone (PDZ) surrounding the embryo. Conditional inactivation results in defective formation of the PDZ barrier and abnormal trophectoderm invasion. RNA-Seq analysis demonstrates down-regulated expression of genes involved in cell adhesion and markers of decidualisation. In contrast, genes controlling immune responses including IFNγ are up-regulated. ChIP-Seq experiments identify candidate targets unique to the decidua as well as those shared across diverse cell types including a highly conserved peak at the Csf-1 gene promoter. Interestingly Blimp1 inactivation results in up-regulated Csf1 expression and macrophage recruitment into maternal decidual tissues. These results identify Blimp1 as a critical regulator of tissue remodelling and maternal tolerance during early stages of pregnancy.
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49
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Fong HT, Hagen T, Inoue T. LDB1 and the SWI/SNF complex participate in both transcriptional activation and repression by Caenorhabditis elegans BLIMP1/PRDM1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194577. [PMID: 32417234 DOI: 10.1016/j.bbagrm.2020.194577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/05/2023]
Abstract
Transcription factors of the BLIMP1/PRDM1 family are important regulators of development. BLIMP1/PRDM1 can both activate and repress gene expression, however, the mechanism of activation is not well understood. Therefore, we looked for factors involved in gene activation by C. elegans BLMP-1, the ortholog of BLIMP1/PRDM1. BLMP-1 activates the expression of bed-3, a gene involved in vulval development. By screening nuclear proteins that function in vulval development, we identified two proteins (LDB-1 and HAM-3) required for BLMP-1 dependent bed-3 expression. LDB-1 is the sole C. elegans member of the LIM Binding Protein (LDB) family, whereas HAM-3 is an accessory subunit of the SWI/SNF complex (ortholog of human SMARCD3/BAF60C). A core SWI/SNF subunit SWSN-1 (ortholog of human SMARCC1/BAF155) is also involved. We found that LDB-1 and HAM-3 bind to BLMP-1, suggesting that BLMP-1 recruits LDB-1 and the SWI/SNF complex to activate bed-3 expression. Interestingly, LDB-1 and HAM-3 are involved in both transcriptional activation and repression. In particular, BLMP-1, LDB-1 and HAM-3 co-regulate a set of hypodermal genes including bed-3 (activated), col-124 (activated) and lin-29 (repressed). On the other hand, LDB-1 and HAM-3 are not required for activation or repression of some genes regulated by BLMP-1 (e.g. T09D3.8, nas-10). We also found that human LDB1, SMARCD3/BAF60C and SMARCC1/BAF155 all physically interact with human BLIMP1/PRDM1 in vitro and are closely associated with BLIMP1/PRDM1 in vivo. Taken together, these results identify LDB1 and SWI/SNF as likely conserved cofactors of BLIMP1/PRDM1, which participate in activation and repression of a subset of BLIMP1/PRDM1-regulated genes.
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Affiliation(s)
- Hei Tung Fong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Thilo Hagen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
| | - Takao Inoue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.
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50
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Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
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