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Korsten P, Tampe B. A Transcriptome Array-Based Approach Links Proteinuria and Distinct Molecular Signatures to Intrarenal Expression of Type I Interferon IFNA5 in Lupus Nephritis. Int J Mol Sci 2023; 24:10636. [PMID: 37445814 DOI: 10.3390/ijms241310636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
In systemic lupus erythematosus (SLE), the relevance of non-hematopoietic sources of type I interferon in human autoimmunity has recently been recognized. Particularly, type I interferon production precedes autoimmunity in early skin lesions related to SLE. However, the relevance of intrarenal type I interferon expression has not been shown in lupus nephritis. From transcriptome array datasets, median-centered log2 mRNA expression levels of IFNα (IFNA1, IFNA2, IFNA4, IFNA5, IFNA6, IFNA7, IFNA8, IFNA10, IFNA13, IFNA14, IFNA16, IFNA17, and IFNA21), IFNω (IFNW1), and IFNβ (IFNB1) in lupus nephritis were extracted specifically from microdissected tubulointerstitial (n = 32) and glomerular compartments (n = 32). We found an association between proteinuria and tubulointerstitial expression of type I interferon IFNA5 (p = 0.0142), while all others were not significantly associated. By contrast, no such correlation was observed between proteinuria and any type I interferon expression in the glomerular compartment in lupus nephritis. Interestingly, there was no difference between female and male patients (p = 0.8237) and no association between type I interferon IFNA5 expression and kidney function or lupus nephritis progression. Finally, we identified distinct molecular signatures involved in transcriptional regulation (GLI protein-regulated transcription, IRF7 activation, and HSF1-dependent transactivation) and receptor signaling (BMP signaling and GPCR ligand binding) in association with tubulointerstitial expression of type I interferon IFNA5 in the kidney. In summary, this transcriptome array-based approach links proteinuria to the tubulointerstitial expression of type I interferon IFNA5 in lupus nephritis. Because type I interferon receptor subunit I antagonism has recently been investigated in active SLE, the current study further emphasizes the role of type I interferons in lupus nephritis and might also be of relevance for mechanistic studies.
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Affiliation(s)
- Peter Korsten
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Björn Tampe
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, 37075 Göttingen, Germany
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2
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Miersch S, Kuruganti S, Walter MR, Sidhu SS. A panel of synthetic antibodies that selectively recognize and antagonize members of the interferon alpha family. Protein Eng Des Sel 2017; 30:697-704. [PMID: 28981904 PMCID: PMC5914384 DOI: 10.1093/protein/gzx048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/25/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
The 12 distinct subtypes that comprise the interferon alpha (IFNα) family of cytokines possess anti-viral, anti-proliferative and immunomodulatory activities. They are implicated in the etiology and progression of many diseases, and also used as therapeutic agents for viral and oncologic disorders. However, a deeper understanding of their role in disease is limited by a lack of tools to evaluate single subtypes at the protein level. Antibodies that selectively inhibit single IFNα subtypes could enable interrogation of each protein in biological samples and could be used for characterization and treatment of disease. Using phage-displayed synthetic antibody libraries, we have conducted selections against 12 human IFNα subtypes to explore our ability to obtain fine-specificity antibodies that recognize and antagonize the biological signals induced by a single IFNα subtype. For the first time, we have isolated antibodies that specifically recognize individual IFNα subtypes (IFNα2a/b, IFNα6, IFNα8b and IFNα16) with high affinity that antagonize signaling. Our results show that highly specific antibodies capable of distinguishing between closely related cytokines can be isolated from synthetic libraries and can be used to characterize cytokine abundance and function.
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Affiliation(s)
- S Miersch
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
| | - S Kuruganti
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M R Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - S S Sidhu
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
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Elaldi N, Yilmaz M, Bagci B, Yelkovan I, Bagci G, Gozel MG, Engin A, Bakir M, Dokmetas I. Relationship between IFNA1, IFNA5, IFNA10, and IFNA17 gene polymorphisms and Crimean-Congo hemorrhagic fever prognosis in a Turkish population range. J Med Virol 2016; 88:1159-67. [PMID: 26694082 DOI: 10.1002/jmv.24456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2015] [Indexed: 11/11/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a fatal emerging acute viral infection. Not much is known regarding the pathogenic mechanisms and the reasons behind severe or mild disease courses in CCHF. IFN-alpha (IFNA) is one of the essential cytokines in the immune system. Existence of single nucleotide gene polymorphisms (SNPs) in cytokines can cause susceptibility or resistance to viral agents and different clinical courses. Hence, the relationship between SNPs in genes encoding cytokines (IFNA1 -1823G/A (rs1332190), IFNA5 -2529T/A (rs758236), IFNA10 Cys20stop (rs10119910), and IFNA17 Ile184Arg (rs9298814) SNPs and disease susceptibility were investigated. The associations between SNPs and CCHF prognosis were also studied. Total 150 patients with CCHF and 170 healthy individuals were enrolled. Genotyping was performed by PCR-RFLP methods. The frequency of IFNA1 -1823 (rs1332190) GG genotype was significantly higher in control subjects than CCHF patients (20% vs. 8%; P = 0.01). For IFNA17 Ile184Arg (rs9298814) polymorphism, CCHF patients having TG genotype had a higher frequency than the control subjects (38% vs. 32.4%; P = 0.039). The distribution of TT + TG genotype frequencies was also significantly higher in CCHF group than the controls (97.3% vs. 91.8%; P = 0.049). Genotype and allele frequencies for IFNA subtypes between fatal and survivors were the same (P > 0.05). Genotype and allele frequencies between severe and mild/moderate CCHF patients were also the same (P > 0.05). The results show that IFNA1 rs1332190 and IFNA17 rs9298814 SNPs may play an important role in CCHF susceptibility. Determining the existence of other connections for IFNA SNPs and CCHF severity and fatality requires further investigations.
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Affiliation(s)
- Nazif Elaldi
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Meral Yilmaz
- Cumhuriyet University Medical Faculty Research Center (CUTFAM), Cumhuriyet University, Sivas, Turkey
| | - Binnur Bagci
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Cumhuriyet University, Sivas, Turkey.,Advanced Technology Research and Development Research and Application Center, Cumhuriyet University, Sivas, Turkey
| | - Izzet Yelkovan
- Department of Medical Biology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Gokhan Bagci
- Department of Biochemistry, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Mustafa Gokhan Gozel
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Aynur Engin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Mehmet Bakir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Cumhuriyet University, Sivas, Turkey
| | - Ilyas Dokmetas
- Department of Infectious Diseases and Clinical Microbiology, Sisli Etfal Training and Research Hospital, Istanbul, Turkey
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Kimkong I, Tangkijvanich P, Hirankarn N. Association of interferon-alpha gene polymorphisms with chronic hepatitis B virus infection. Int J Immunogenet 2013; 40:476-81. [PMID: 23566196 DOI: 10.1111/iji.12055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/30/2013] [Accepted: 03/10/2013] [Indexed: 12/15/2022]
Abstract
In this study, the association between the risk of chronic hepatitis B virus infection and the polymorphisms within promoter regions of IFN-α1 and five genes was explored. This association study was performed on 180 Thai patients with chronic HBV infection [hepatocellular carcinoma (HCC) = 65 and non-HCC = 115], 173 individuals with self-limited HBV infection and 140 healthy controls. Our results showed that the A allele of -1823G/A SNP within IFNA1 gene was significantly associated with an increased risk of chronic HBV infection as compared to healthy individuals and self-limited HBV group [OR (95% CI) = 2.20 (1.51-3.19), P = 0.000014 and OR (95% CI) = 1.61 (1.12-2.33), P = 0.0073, respectively]. The effect of A allele was similar to autosomal recessive in which the presence of AA genotype when compared to GG and GA conferred the OR of 2.79 (95% CI = 1.72-4.52, P = 0.0000085). By multifactor dimensionality reduction analysis, we found the interaction between IFNA5 (-2529) and IFNA1 (-1823) genes that gave the risk to chronic HBV infection, with the OR (95% CI) of the high-risk to low-risk group was 2.79 (1.77-4.40), P < 0.0001. However, further study in functional significance is required.
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Affiliation(s)
- I Kimkong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
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Lenci RE, Bevier M, Brandt A, Bermejo JL, Sucker A, Moll I, Planelles D, Requena C, Nagore E, Hemminki K, Schadendorf D, Kumar R. Influence of genetic variants in type I interferon genes on melanoma survival and therapy. PLoS One 2012; 7:e50692. [PMID: 23209811 PMCID: PMC3507747 DOI: 10.1371/journal.pone.0050692] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 10/23/2012] [Indexed: 01/19/2023] Open
Abstract
Melanoma is an immunogenic tumor; however, the efficacy of immune-therapy shows large inter-individual variation with possible influence of background genetic variation. In this study we report the influence of genetic polymorphisms in the type I interferon gene cluster on chromosome 9p22 on melanoma survival. We genotyped 625 melanoma patients recruited in an oncology center in Germany for 44 polymorphisms located on chromosome 9p22 that were informative for 299 polymorphisms and spanned 15 type I interferon genes. Our results showed associations between time to metastasis/survival and two linked (r2 = 0.76) polymorphisms, rs10964859 (C>G) and rs10964862 (C>A). The rs10964859 polymorphism was located at 3′UTR and rs10964862 was 9.40 Kb towards 5′UTR of IFNW1 gene. The carriers of the variant alleles of the rs10964859 and rs10964862 polymorphisms were associated with a reduced disease-free survival. The validation of data in an independent group of 710 patients from Spain showed that the direction of the effect was similar. Stratification based on therapy showed that the adverse effect on metastasis development was statistically significant in the patients from Spain who did not receive any treatment and were homozygous for variant allele of rs10964862 (HR = 2.52, 95% CI 1.07–5.90; P = 0.03). Patients homozygous for rs10964859 (HR = 2.01, 95% CI 1.17–3.44; P = 0.01) and rs10964862 (HR 1.84, 95%CI 1.03–3.27, P = 0.04) were associated to increased risk of death following metastasis. GTCGACAA haplotype, found in 8.8% of the patients, was associated with an increased risk of death (HR 1.94, 95%CI 1.16–3.26, P = 0.01). In conclusion, our results identified genetic variants in interferon genes that influence melanoma progression and survival with modulation of effect due to treatment status.
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Affiliation(s)
- Romina Elizabeth Lenci
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Melanie Bevier
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Andreas Brandt
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Iris Moll
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Dolores Planelles
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
- * E-mail:
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Hillyer P, Mane VP, Schramm LM, Puig M, Verthelyi D, Chen A, Zhao Z, Navarro MB, Kirschman KD, Bykadi S, Jubin RG, Rabin RL. Expression profiles of human interferon-alpha and interferon-lambda subtypes are ligand- and cell-dependent. Immunol Cell Biol 2012; 90:774-83. [PMID: 22249201 PMCID: PMC3442264 DOI: 10.1038/icb.2011.109] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 10/18/2011] [Accepted: 11/20/2011] [Indexed: 01/03/2023]
Abstract
Recent genome-wide association studies suggest distinct roles for 12 human interferon-alpha (IFN-α) and 3 IFN-λ subtypes that may be elucidated by defining the expression patterns of these sets of genes. To overcome the impediment of high homology among each of the sets, we designed a quantitative real-time PCR assay that incorporates the use of molecular beacon and locked nucleic acid (LNA) probes, and in some instances, LNA oligonucleotide inhibitors. We then measured IFN subtype expression by human peripheral blood mononuclear cells and by purified monocytes, myeloid dendritic cells (mDC), plasmacytoid dendritic cells (pDC), and monocyte-derived macrophages (MDM), and -dendritic cells (MDDC) in response to poly I:C, lipopolysaccharide (LPS), imiquimod and CpG oligonucleotides. We found that in response to poly I:C and LPS, monocytes, MDM and MDDC express a subtype pattern restricted primarily to IFN-β and IFN-λ1. In addition, while CpG elicited expression of all type I IFN subtypes by pDC, imiquimod did not. Furthermore, MDM and mDC highly express IFN-λ, and the subtypes of IFN-λ are expressed hierarchically in the order IFN-λ1 followed by IFN-λ2, and then IFN-λ3. These data support a model of coordinated cell- and ligand-specific expression of types I and III IFN. Defining IFN subtype expression profiles in a variety of contexts may elucidate specific roles for IFN subtypes as protective, therapeutic or pathogenic mediators.
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Affiliation(s)
- Philippa Hillyer
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Viraj P Mane
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
- These authors contributed equally to this work
- Current address: Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD, USA
| | - Lynnsie M Schramm
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Montserrat Puig
- Center for Drugs Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Daniela Verthelyi
- Center for Drugs Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Aaron Chen
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Zeng Zhao
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Maria B Navarro
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Kevin D Kirschman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | - Srikant Bykadi
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
| | | | - Ronald L Rabin
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, USA
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Schramm LM, Kirschman KD, Heuer M, Chen AA, Verthelyi D, Puig M, Rabin RL. High-throughput quantitative real-time polymerase chain reaction array for absolute and relative quantification of rhesus macaque types I, II, and III interferon and their subtypes. J Interferon Cytokine Res 2012; 32:407-15. [PMID: 22817480 DOI: 10.1089/jir.2012.0015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rhesus macaques provide a valuable research and preclinical model for cancer and infectious diseases, as nonhuman primates share immune pathways with humans. Interferons (IFNs) are key cytokines in both innate and adaptive immunity, so a detailed analysis of gene expression in peripheral blood and tissues may shed insight into immune responses. Macaques have 18 IFN genes, of which 14 encode for 13 distinct IFN-α subtypes, and one for IFN-β. Here, we developed a high-throughput array to evaluate each of the IFN-α subtypes, as well as IFN-β, IFN-γ and 2 subtypes of IFN-λ. With this array, expression of each IFN species may be quantified as relative to a reference (housekeeping) gene (ΔCq) or fitted to its own 4-point standard curve for absolute quantification (copy number per mass unit RNA). After validating the assay with IFN complementary DNA, we determined the IFN expression profile of peripheral blood mononuclear cells from 3 rhesus macaques in response to TLR agonists, and demonstrated that the profiles are consistent among animals. Furthermore, because the IFN expression profiles differ depending on the TLR stimuli, they suggest different biological functions for many of the IFN species measured, including individual subtypes of IFN-α.
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Affiliation(s)
- Lynnsie M Schramm
- Division of Bacterial, Parasite and Allergenic Products, Office of Vaccine Research and Regulation, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bldg 29, Rm 203A, 9000 Rockville Pike, Bethesda, MD 20892, USA
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Puig M, Tosh KW, Schramm LM, Grajkowska LT, Kirschman KD, Tami C, Beren J, Rabin RL, Verthelyi D. TLR9 and TLR7 agonists mediate distinct type I IFN responses in humans and nonhuman primates in vitro and in vivo. J Leukoc Biol 2011; 91:147-58. [DOI: 10.1189/jlb.0711371] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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Delgado-Vega AM, Alarcón-Riquelme ME, Kozyrev SV. Genetic associations in type I interferon related pathways with autoimmunity. Arthritis Res Ther 2010; 12 Suppl 1:S2. [PMID: 20392289 PMCID: PMC2991775 DOI: 10.1186/ar2883] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Type I interferons play an outstanding role in innate and adaptive immunity by enhancing functions of dendritic cells, inducing differentiation of monocytes, promoting immunoglobulin class switching in B cells and stimulating effector functions of T cells. The increased production of IFNα/β by plasmacytoid dendritic cells could be responsible for not only efficient antiviral defence, but it also may be a pathological factor in the development of various autoimmune disorders. The first evidence of a genetic link between type I interferons and autoimmune diseases was the observation that elevated IFNα activity is frequently detected in the sera of patients with systemic lupus erythematosus, and that this trait shows high heritability and familial aggregation in their first-degree healthy relatives. To date, a number of genes involved in interferon signalling have been associated with various autoimmune diseases. Patients with systemic lupus erythematosus, Sjögren's syndrome, dermatomyositis, psoriasis, and a fraction of patients with rheumatoid arthritis display a specific expression pattern of interferon-dependent genes in their leukocytes, termed the interferon signature. Here, in an attempt to understand the role of type I interferons in the pathogenesis of autoimmunity, we review the recent advances in the genetics of autoimmune diseases focusing on the association of genes involved in type I interferon pathways.
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Affiliation(s)
- Angélica M Delgado-Vega
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, Uppsala, Sweden
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