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Taylor CH, Friberg IM, Jackson JA, Arriero E, Begon M, Wanelik KM, Paterson S, Bradley JE. Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent. Mol Ecol 2023; 32:1197-1210. [PMID: 36478482 DOI: 10.1111/mec.16819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/07/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Apicomplexans are a protozoan phylum of obligate parasites which may be highly virulent during acute infections, but may also persist as chronic infections which appear to have little fitness cost. Babesia microti is an apicomplexan haemoparasite that, in immunocompromised individuals, can cause severe, potentially fatal disease. However, in its natural host, wild field voles (Microtus agrestis), it exhibits chronic infections that have no detectable impact on survival or female fecundity. How is damage minimized, and what is the impact on the host's immune state and health? We examine the differences in immune state (here represented by expression of immune-related genes in multiple tissues) associated with several common chronic infections in a population of wild field voles. While some infections show little impact on immune state, we find strong associations between immune state and B. microti. These include indications of clearance of infected erythrocytes (increased macrophage activity in the spleen) and activity likely associated with minimizing damage from the infection (anti-inflammatory and antioxidant activity in the blood). By analysing gene expression from the same individuals at multiple time points, we show that the observed changes are a response to infection, rather than a risk factor. Our results point towards continual investment to minimize the damage caused by the infection. Thus, we shed light on how wild animals can tolerate some chronic infections, but emphasize that this tolerance does not come without a cost.
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Affiliation(s)
| | - Ida M Friberg
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Elena Arriero
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Mike Begon
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Klara M Wanelik
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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Yoshinaga M, Han K, Morgens DW, Horii T, Kobayashi R, Tsuruyama T, Hia F, Yasukura S, Kajiya A, Cai T, Cruz PHC, Vandenbon A, Suzuki Y, Kawahara Y, Hatada I, Bassik MC, Takeuchi O. The N 6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity. Nat Commun 2022; 13:6435. [PMID: 36307435 PMCID: PMC9616860 DOI: 10.1038/s41467-022-34078-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/12/2022] [Indexed: 02/07/2023] Open
Abstract
During erythroid differentiation, the maintenance of genome integrity is key for the success of multiple rounds of cell division. However, molecular mechanisms coordinating the expression of DNA repair machinery in erythroid progenitors are poorly understood. Here, we discover that an RNA N6-methyladenosine (m6A) methyltransferase, METTL16, plays an essential role in proper erythropoiesis by safeguarding genome integrity via the control of DNA-repair-related genes. METTL16-deficient erythroblasts exhibit defective differentiation capacity, DNA damage and activation of the apoptotic program. Mechanistically, METTL16 controls m6A deposition at the structured motifs in DNA-repair-related transcripts including Brca2 and Fancm mRNAs, thereby upregulating their expression. Furthermore, a pairwise CRISPRi screen revealed that the MTR4-nuclear RNA exosome complex is involved in the regulation of METTL16 substrate mRNAs in erythroblasts. Collectively, our study uncovers that METTL16 and the MTR4-nuclear RNA exosome act as essential regulatory machinery to maintain genome integrity and erythropoiesis.
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Affiliation(s)
- Masanori Yoshinaga
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Kyuho Han
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - David W. Morgens
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Takuro Horii
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Ryosuke Kobayashi
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Tatsuaki Tsuruyama
- grid.258799.80000 0004 0372 2033Department of Drug and Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Fabian Hia
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Shota Yasukura
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Asako Kajiya
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Ting Cai
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Pedro H. C. Cruz
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Alexis Vandenbon
- grid.258799.80000 0004 0372 2033Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XLaboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yukio Kawahara
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Izuho Hatada
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan ,grid.256642.10000 0000 9269 4097Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Gunma, 371-8512 Japan
| | - Michael C. Bassik
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Osamu Takeuchi
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
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3
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Bai H, He Y, Ding Y, Chu Q, Lian L, Heifetz EM, Yang N, Cheng HH, Zhang H, Chen J, Song J. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genet 2020; 21:77. [PMID: 32677890 PMCID: PMC7364486 DOI: 10.1186/s12863-020-00884-w] [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: 07/29/2019] [Accepted: 07/05/2020] [Indexed: 11/13/2022] Open
Abstract
Background Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. Results In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study. Conclusions Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.
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Affiliation(s)
- Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, 225009, China.,Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanghua He
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Yi Ding
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Qin Chu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ling Lian
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Eliyahu M Heifetz
- Faculty of Health Sciences, Jerusalem College of Technology, 9116001, Jerusalem, Israel
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hans H Cheng
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Huanmin Zhang
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Jilan Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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Li Z, Chen J, Li P, Li XY, Lu L, Li S. Functional characterization of dark sleeper (Odontobutis obscura) IRF3 in IFN regulation. FISH & SHELLFISH IMMUNOLOGY 2019; 89:411-419. [PMID: 30978449 DOI: 10.1016/j.fsi.2019.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/29/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
The dark sleeper, Odontobutis obscura (O. obscura), is a commercially important species of freshwater sleeper native to East Asia. However, its molecular biology system is unexplored, including the interferon (IFN) signaling pathway, which is crucial to the antiviral response. In this study, we characterised the IFN regulation pattern of dark sleeper interferon regulatory factor 3 (OdIRF3), supplementing evidence of the conservation of this classical pathway in fish. First, the open reading frame (ORF) of OdIRF3 was cloned from the liver tissue by Rapid amplification of cDNA ends (RACE). Amino acid sequence analysis suggested that OdIRF3 is homologous with other fish IRF3 and that the N-terminal DNA-binding domain (DBD) and the C-terminal IRF-association domain (IAD) are conserved. Then, the cellular distribution demonstrated that OdIRF3 is located in the cytoplasm region and transfers into the nuclear region under stimulation. For the function identification, OdIRF3 activated several types of IFN promoters and induced downstream interferon stimulated genes (ISGs) expression. Finally, the overexpression of OdIRF3 significantly decreased viral proliferation. Taken together, these data systematically characterised the sequence, cellular location, and function in IFN expression of OdIRF3, shedding light on the molecular biology mechanism of the dark sleeper.
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Affiliation(s)
- Zhuocong Li
- University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Longfeng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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Li S, Lu LF, Li ZC, Zhang C, Zhou XY, Zhou Y, Zhang YA. Zebrafish MVP Recruits and Degrades TBK1 To Suppress IFN Production. THE JOURNAL OF IMMUNOLOGY 2018; 202:559-566. [PMID: 30530482 DOI: 10.4049/jimmunol.1801325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 11/19/2022]
Abstract
IFN production is crucial for hosts to defend against viral infection, yet it must be tightly controlled to maintain immune homeostasis. TANK-binding kinase 1 (TBK1) is a pivotal kinase in the IFN induction signaling pathway, but it is negatively regulated by multiple molecules to avoid the excessive expression of IFN in mammals. However, the identified TBK1 suppressors and the mechanisms are rare in fish. In this study, we show that zebrafish major vault protein (MVP) recruits and degrades TBK1 in a lysosome-dependent manner to inhibit IFN production. Through viral infection, polyinosinic:polycytidylic acid and RIG-I-like receptor factor stimulation upregulated IFN expression, but overexpression of MVP significantly subverted these inductions. On the protein level, MVP interacted with TBK1, and interestingly, MVP recruited TBK1 from a uniformly distributed state in the cytoplasm to an aggregated state. Finally, MVP mediated the lysosome-dependent degradation of TBK1 and decreased the IFN response and IFN-stimulated genes expression. Our findings reveal that zebrafish MVP is a negative regulator of IFN production by restricting the activation of TBK1, supplying evidence of the balanced mechanisms of IFN expression in lower vertebrates.
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Affiliation(s)
- Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266071 Qingdao, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Zhuo-Cong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China.,University of Chinese Academy of Sciences, 100049 Beijing, China; and
| | - Can Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China.,University of Chinese Academy of Sciences, 100049 Beijing, China; and
| | - Xiao-Yu Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China.,University of Chinese Academy of Sciences, 100049 Beijing, China; and
| | - Yu Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China.,University of Chinese Academy of Sciences, 100049 Beijing, China; and
| | - Yong-An Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China; .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266071 Qingdao, China.,State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, 43007 Wuhan, China
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6
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Elias HK, Bryder D, Park CY. Molecular mechanisms underlying lineage bias in aging hematopoiesis. Semin Hematol 2017; 54:4-11. [DOI: 10.1053/j.seminhematol.2016.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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7
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Li S, Lu LF, Wang ZX, Chen DD, Zhang YA. Fish IRF6 is a positive regulator of IFN expression and involved in both of the MyD88 and TBK1 pathways. FISH & SHELLFISH IMMUNOLOGY 2016; 57:262-268. [PMID: 27577537 DOI: 10.1016/j.fsi.2016.08.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 06/06/2023]
Abstract
Interferon (IFN) regulatory factors (IRF) are the crucial transcription factors for IFN expression, leading host cell response to viral infection. In mammals, only IRF6 is unaffected by IFN expression in the IRF family; however, in fish, a lower vertebrate, whether IRF6 is related to IFN regulation is unclear. In this study, we identified that zebrafish IRF6 was a positive regulator of IFN transcription and could be phosphorylated by both MyD88 and TBK1. First, the transcript level of cellular irf6 was upregulated by treatment with poly I:C (a mimic of viral RNAs), indicating IRF6 might be involved in the process of host cell response to viruses. Overexpression of IRF6 could upregulate IFN promoter activity significantly, meaning IRF6 is a positive regulator of IFN transcription. Subsequently, at the protein regulation level and in the interaction relationship, IRF6 was phosphorylated by and associated with both MyD88 and TBK1. In addition, overexpression of IRF6 activated the transcription of isg15, rig-i and mavs of host cells; meanwhile, the transcripts of p, m and n genes of SVCV were significantly declined in IRF6-overexpressing cells. Taken together, our data demonstrate that fish IRF6 is distinguished from the homolog of mammals by being a positive regulator of IFN transcription and phosphorylated by MyD88 and TBK1, suggesting that differences in the IRF6 regulation pattern exist between lower and higher vertebrates.
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Affiliation(s)
- Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao-Xi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan-Dan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong-An Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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8
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Gu M, Lin G, Lai Q, Zhong B, Liu Y, Mi Y, Chen H, Wang B, Fan L, Hu C. Ctenopharyngodon idella IRF2 plays an antagonistic role to IRF1 in transcriptional regulation of IFN and ISG genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 49:103-112. [PMID: 25463511 DOI: 10.1016/j.dci.2014.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
Interferon Regulatory Factors (IRFs) make up a family of transcription factors involved in transcriptional regulation of type I IFN and IFN-stimulated genes (ISG) in cells. In the present study, an IRF2 gene (termed CiIRF2, JX628585) was cloned and characterized from grass carp (Ctenopharyngodon idella). The full-length cDNA of CiIRF2 is 1809 bp in length, with the largest open reading frame (ORF) of 981 bp encoding a putative protein of 326 amino acids. CiIRF2 contains a conserved DNA-binding domain (DBD) in N-terminal and a non-conserved C-terminal region. Protein sequence analysis revealed that CiIRF2 shares significant homology to the known IRF2 counterparts. Phylogenetic reconstruction confirmed its closer evolutionary relationship with other fish counterparts, especially with zebra fish IRF2. CiIRF2 was ubiquitously expressed at low level in all tested grass carp tissues and significantly up-regulated except in brain following poly I:C 6-12 h post stimulation. In order to understand fish innate immune and resistance to virus diseases, recombinant CiIRF2 with His-tag was over-expressed in BL21 Escherichia coli, and the expressed protein was purified by affinity chromatography with Ni-NTA His-Bind Resin. Promoter sequences of grass carp type I IFN gene (CiIFN) and two ISG genes (CiPKR and CiPKZ) were amplified and cloned. In vitro, gel mobility shift assays were employed to analyze the interaction of CiIRF2 protein with promoters of CiIFN, CiPKR and CiPKZ respectively. The results showed that CiIRF2 bound to these promoters with high affinity by means of its DBD. Afterwards, recombinant plasmids of pGL3-CiIFN, pGL3-CiPKR and pGL3-CiPKZ were constructed and transiently co-transfected with pcDNA3.1-CiIRF2 or pcDNA3.1-CiIRF1 respectively into C. idella kidney (CIK) cells. Dual-luciferase reporter assays demonstrated that CiIRF2 down-regulates the transcription activity of CiIFN, CiPKR and CiPKZ genes in CIK cells. To further understand the function of fish IRF2, expression plasmids (pcDNA3.1-IRF2 and pcDNA3.1-IRF1) were transiently co-transfected with pGL3-IFN or pGL3-CiPKZ into CIK cells, respectively. The results revealed that CiIRF2 plays an antagonistic role to CiIRF1 in transcriptional regulation of IFN and ISG genes.
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Affiliation(s)
- Meihui Gu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Gang Lin
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Qinan Lai
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Bin Zhong
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yong Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yichuan Mi
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Huarong Chen
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Binhua Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Lihua Fan
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
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9
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Mizutani T, Neugebauer N, Putz EM, Moritz N, Simma O, Zebedin-Brandl E, Gotthardt D, Warsch W, Eckelhart E, Kantner HP, Kalinke U, Lienenklaus S, Weiss S, Strobl B, Müller M, Sexl V, Stoiber D. Conditional IFNAR1 ablation reveals distinct requirements of Type I IFN signaling for NK cell maturation and tumor surveillance. Oncoimmunology 2014; 1:1027-1037. [PMID: 23170251 PMCID: PMC3494617 DOI: 10.4161/onci.21284] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mice with an impaired Type I interferon (IFN) signaling (IFNAR1- and IFNβ-deficient mice) display an increased susceptibility toward v-ABL-induced B-cell leukemia/lymphoma. The enhanced leukemogenesis in the absence of an intact Type I IFN signaling is caused by alterations within the tumor environment. Deletion of Ifnar1 in tumor cells (as obtained in Ifnar1f/f CD19-Cre mice) failed to impact on disease latency or type. In line with this observation, the initial transformation and proliferative capacity of tumor cells were unaltered irrespective of whether the cells expressed IFNAR1 or not. v-ABL-induced leukemogenesis is mainly subjected to natural killer (NK) cell-mediated tumor surveillance. Thus, we concentrated on NK cell functions in IFNAR1 deficient animals. Ifnar1-/- NK cells displayed maturation defects as well as an impaired cytolytic activity. When we deleted Ifnar1 selectively in mature NK cells (by crossing Ncr1-iCre mice to Ifnar1f/f animals), maturation was not altered. However, NK cells derived from Ifnar1f/f Ncr1-iCre mice showed a significant cytolytic defect in vitro against the hematopoietic cell lines YAC-1 and RMA-S, but not against the melanoma cell line B16F10. Interestingly, this defect was not related to an in vivo phenotype as v-ABL-induced leukemogenesis was unaltered in Ifnar1f/f Ncr1-iCre compared with Ifnar1f/f control mice. Moreover, the ability of Ifnar1f/f Ncr1-iCre NK cells to kill B16F10 melanoma cells was unaltered, both in vitro and in vivo. Our data reveal that despite the necessity for Type I IFN in NK cell maturation the expression of IFNAR1 on mature murine NK cells is not required for efficient tumor surveillance.
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10
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Li S, Lu LF, Feng H, Wu N, Chen DD, Zhang YB, Gui JF, Nie P, Zhang YA. IFN regulatory factor 10 is a negative regulator of the IFN responses in fish. THE JOURNAL OF IMMUNOLOGY 2014; 193:1100-9. [PMID: 24958903 DOI: 10.4049/jimmunol.1400253] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
IFN regulatory factor (IRF) 10 belongs to the IRF family and exists exclusively in birds and fish. Most IRFs have been identified as critical regulators in the IFN responses in both fish and mammals; however, the role of IRF10 is unclear. In this study, we identified IRF10 in zebrafish (Danio rerio) and found that it serves as a negative regulator to balance the innate antiviral immune responses. Zebrafish IRF10 (DrIRF10) was induced by intracellular polyinosinic:polycytidylic acid in ZF4 (zebrafish embryo fibroblast-like) cells. DrIRF10 inhibited the activation of zebrafish IFN1 (DrIFN1) and DrIFN3 promoters in epithelioma papulosum cyprinid cells in the presence or absence of polyinosinic:polycytidylic acid stimulation through direct interaction with the IFN promoters, and this inhibition was also shown to block IFN signaling. Overexpression of DrIRF10 was able to abolish the induction of DrIFN1 and DrIFN3 mediated by the retinoic acid-inducible gene I-like receptors. In addition, functional domain analysis of DrIRF10 showed that either the DNA binding domain or the IRF association domain is sufficient for its inhibitory activity for IFN signaling. Lastly, overexpression of DrIRF10 decreased the transcription level of several IFN-stimulated genes, resulting in the susceptibility of host cells to spring viremia of carp virus infection. Collectively, these data suggest that DrIRF10 inhibits the expression of DrIFN1 and DrIFN3 to avoid an excessive immune response, a unique regulation mechanism of the IFN responses in lower vertebrates.
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Affiliation(s)
- Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Nan Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dan-Dan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yi-Bing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yong-An Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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11
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Greenfest-Allen E, Malik J, Palis J, Stoeckert CJ. Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis. BMC SYSTEMS BIOLOGY 2013; 7:38. [PMID: 23675896 PMCID: PMC3668222 DOI: 10.1186/1752-0509-7-38] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/30/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hematopoietic ontogeny is characterized by overlapping waves of primitive, fetal definitive, and adult definitive erythroid lineages. Our aim is to identify differences in the transcriptional control of these distinct erythroid cell maturation pathways by inferring and analyzing gene-interaction networks from lineage-specific expression datasets. Inferred networks are strongly connected and do not fit a scale-free model, making it difficult to identify essential regulators using the hub-essentiality standard. RESULTS We employed a semi-supervised machine learning approach to integrate measures of network topology with expression data to score gene essentiality. The algorithm was trained and tested on the adult and fetal definitive erythroid lineages. When applied to the primitive erythroid lineage, 144 high scoring transcription factors were found to be differentially expressed between the primitive and adult definitive erythroid lineages, including all expressed STAT-family members. Differential responses of primitive and definitive erythroblasts to a Stat3 inhibitor and IFNγ in vitro supported the results of the computational analysis. Further investigation of the original expression data revealed a striking signature of Stat1-related genes in the adult definitive erythroid network. Among the potential pathways known to utilize Stat1, interferon (IFN) signaling-related genes were expressed almost exclusively within the adult definitive erythroid network. CONCLUSIONS In vitro results support the computational prediction that differential regulation and downstream effectors of STAT signaling are key factors that distinguish the transcriptional control of primitive and definitive erythroid cell maturation.
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Affiliation(s)
- Emily Greenfest-Allen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey Malik
- Center for Pediatric Biomedical Research, Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - James Palis
- Center for Pediatric Biomedical Research, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Christian J Stoeckert
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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12
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Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell 2012; 23:796-811. [PMID: 23041383 DOI: 10.1016/j.devcel.2012.09.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 07/05/2012] [Accepted: 09/06/2012] [Indexed: 12/13/2022]
Abstract
Gene-distal enhancers are critical for tissue-specific gene expression, but their genomic determinants within a specific lineage at different stages of development are unknown. Here we profile chromatin state maps, transcription factor occupancy, and gene expression profiles during human erythroid development at fetal and adult stages. Comparative analyses of human erythropoiesis identify developmental stage-specific enhancers as primary determinants of stage-specific gene expression programs. We find that erythroid master regulators GATA1 and TAL1 act cooperatively within active enhancers but confer little predictive value for stage specificity. Instead, a set of stage-specific coregulators collaborates with master regulators and contributes to differential gene expression. We further identify and validate IRF2, IRF6, and MYB as effectors of an adult-stage expression program. Thus, the combinatorial assembly of lineage-specific master regulators and transcriptional coregulators within developmental stage-specific enhancers determines gene expression programs and temporal regulation of transcriptional networks in a mammalian genome.
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Affiliation(s)
- Jian Xu
- Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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13
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Zhou Q, Lu G, Liu A, Kohno T. Extraskeletal myxoid chondrosarcoma in the lung: asymptomatic lung mass with severe anemia. Diagn Pathol 2012; 7:112. [PMID: 22925697 PMCID: PMC3487864 DOI: 10.1186/1746-1596-7-112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 08/13/2012] [Indexed: 12/14/2022] Open
Abstract
Extraskeletal myxoid chondrosarcoma (EMC) is a rare soft-tissue sarcoma, which primarily occurs deep in the extremities, especially in skeletal muscle, or tendon. EMC of the pleura has been described, however, no case of primary EMC arising from lung has been previously reported. We describe herein, a 51-year-old Asian female initially manifested with signs of severe anemia who presented with a lung mass unrelated to pleura that was morphologically typical EMC, with strong immunoreactivity for vimentin and NSE. Two weeks after resection, the anemia was cured. The patient continued with follow-up, without sign of abnormality 32 months after operation.
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Affiliation(s)
- Qianjun Zhou
- Department of General thoracic surgery, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, PR China.
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14
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Chronic IFN-γ production in mice induces anemia by reducing erythrocyte life span and inhibiting erythropoiesis through an IRF-1/PU.1 axis. Blood 2011; 118:2578-88. [DOI: 10.1182/blood-2010-10-315218] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Anemia of chronic disease is a complication accompanying many inflammatory diseases. The proinflammatory cytokine IFN-γ has been implicated in this form of anemia, but the underlying mechanism remains unclear. Here we describe a novel mouse model for anemia of chronic disease, in which enhanced CD27-mediated costimulation strongly increases the formation of IFN-γ–producing effector T cells, leading to a progressive anemia. We demonstrate that the anemia in these mice is fully dependent on IFN-γ and that this cytokine reduces both the life span and the formation of red blood cells. Molecular analysis revealed that IFN-γ induces expression of the transcription factors of interferon regulatory factor-1 (IRF-1) and PU.1 in both murine and human erythroid precursors. We found that, on IFN-γ stimulation, IRF-1 binds to the promoter of SPI.1 (PU.1) and induces PU.1 expression, leading to inhibition of erythropoiesis. Notably, down-regulation of either IRF-1 or PU.1 expression is sufficient to overcome IFN-γ–induced inhibition of erythropoiesis. These findings reveal a molecular mechanism by which chronic exposure to IFN-γ induces anemia.
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15
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Gan T, Jude CD, Zaffuto K, Ernst P. Developmentally induced Mll1 loss reveals defects in postnatal haematopoiesis. Leukemia 2010; 24:1732-41. [PMID: 20724987 PMCID: PMC2954260 DOI: 10.1038/leu.2010.171] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Mixed Lineage Leukemia (MLL) gene is disrupted by chromosomal translocations in acute leukemia, producing a fusion oncogene with altered properties relative to the wild-type gene. Murine loss-of-function studies have demonstrated an essential role for Mll in developing the haematopoietic system, yet studies using different conditional knockout models have yielded conflicting results regarding the requirement for Mll during adult steady-state haematopoiesis. Here, we employ a loxP-flanked Mll allele (MllF) and a developmentally-regulated, haematopoietic-specific VavCre transgene to re-assess the consequences of Mll loss in the haematopoietic lineage, without the need for inducers of Cre recombinase. We show that VavCre;Mll mutants exhibit phenotypically normal fetal haematopoiesis, but rarely survive past 3 weeks of age. Surviving animals are anemic, thrombocytopenic and exhibit a significant reduction in bone marrow haematopoietic stem/progenitor populations, consistent with our previous findings using the inducible Mx1Cre transgene. Furthermore, the analysis of VavCre mutants revealed additional defects in B-lymphopoiesis that could not be assessed using Mx1Cre-mediated Mll deletion. Collectively, these data support the conclusion that Mll plays an essential role in sustaining postnatal haematopoiesis.
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Affiliation(s)
- T Gan
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755, USA
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16
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Savitsky D, Tamura T, Yanai H, Taniguchi T. Regulation of immunity and oncogenesis by the IRF transcription factor family. Cancer Immunol Immunother 2010; 59:489-510. [PMID: 20049431 PMCID: PMC11030943 DOI: 10.1007/s00262-009-0804-6] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 12/01/2009] [Indexed: 02/06/2023]
Abstract
Nine interferon regulatory factors (IRFs) compose a family of transcription factors in mammals. Although this family was originally identified in the context of the type I interferon system, subsequent studies have revealed much broader functions performed by IRF members in host defense. In this review, we provide an update on the current knowledge of their roles in immune responses, immune cell development, and regulation of oncogenesis.
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Affiliation(s)
- David Savitsky
- Department of Immunology, Faculty of Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tomohiko Tamura
- Department of Immunology, Faculty of Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Hideyuki Yanai
- Department of Immunology, Faculty of Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tadatsugu Taniguchi
- Department of Immunology, Faculty of Medicine, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
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17
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Battistini A. Interferon regulatory factors in hematopoietic cell differentiation and immune regulation. J Interferon Cytokine Res 2010; 29:765-80. [PMID: 19929577 DOI: 10.1089/jir.2009.0030] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Members of the interferon regulatory factor (IRF) family are transcription factors implicated in the regulation of a variety of biological processes. Originally identified as intracellular mediators of the induction and biological activities of interferons, their central role in host resistance to pathogens has recently been confirmed by the recognition of their involvement in the regulation of gene expression in responses triggered by Toll-like receptors and other pattern recognition receptors (PRRs). Their function in regulating the development as well as the activity of hematopoietic cells puts them at the interface between innate and adaptive immune responses. IRFs also regulate cell growth and apoptosis in several cell types, thereby affecting susceptibility to and the progression of cancer. In this review the role of some members of the family more deeply involved in the differentiation of hematopoietic cells and in immune regulation is addressed, with a specific focus on T cells and dendritic cells.
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Affiliation(s)
- Angela Battistini
- Molecular Pathogenesis Unit, Department of Infectious, Parasitic, and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy.
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18
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Wada M, Marusawa H, Yamada R, Nasu A, Osaki Y, Kudo M, Nabeshima M, Fukuda Y, Chiba T, Matsuda F. Association of genetic polymorphisms with interferon-induced haematologic adverse effects in chronic hepatitis C patients. J Viral Hepat 2009; 16:388-96. [PMID: 19200137 DOI: 10.1111/j.1365-2893.2009.01095.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Interferon (IFN)-based combination therapy with ribavirin has become the gold standard for the treatment of chronic hepatitis C virus infection. Haematologic toxicities, such as neutropenia, thrombocytopenia, and anaemia, however, frequently cause poor treatment tolerance, resulting in poor therapeutic efficacy. The aim of this study was to identify host genetic polymorphisms associated with the efficacy or haematologic toxicity of IFN-based combination therapy in chronic hepatitis C patients. We performed comprehensive single nucleotide polymorphism detection in all exonic regions of the 12 genes involved in the IFN signalling pathway in 32 healthy Japanese volunteers. Of 167 identified polymorphisms, 35 were genotyped and tested for an association with the efficacy or toxicity of IFN plus ribavirin therapy in 240 chronic hepatitis C patients. Multiple logistic regression analysis revealed that low viral load, viral genotypes 2 and 3, and a lower degree of liver fibrosis, but none of the genetic polymorphisms, were significantly associated with a sustained virologic response. In contrast to efficacy, multiple linear regression analyses demonstrated that two polymorphisms (IFNAR1 10848-A/G and STAT2 4757-G/T) were significantly associated with IFN-induced neutropenia (P = 0.013 and P = 0.011, respectively). Thrombocytopenia was associated with the IRF7 789-G/A (P = 0.031). In conclusion, genetic polymorphisms in IFN signalling pathway-related genes were associated with IFN-induced neutropenia and thrombocytopenia in chronic hepatitis C patients. In contrast to toxicity, the efficacy of IFN-based therapy was largely dependent on viral factors and degree of liver fibrosis.
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Affiliation(s)
- M Wada
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
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19
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Sato T, Onai N, Yoshihara H, Arai F, Suda T, Ohteki T. Interferon regulatory factor-2 protects quiescent hematopoietic stem cells from type I interferon–dependent exhaustion. Nat Med 2009; 15:696-700. [DOI: 10.1038/nm.1973] [Citation(s) in RCA: 315] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 04/23/2009] [Indexed: 01/05/2023]
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