1
|
Ghodke-Puranik Y, Olferiev M, Crow MK. Systemic lupus erythematosus genetics: insights into pathogenesis and implications for therapy. Nat Rev Rheumatol 2024; 20:635-648. [PMID: 39232240 DOI: 10.1038/s41584-024-01152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prime example of how the interplay between genetic and environmental factors can trigger systemic autoimmunity, particularly in young women. Although clinical disease can take years to manifest, risk is established by the unique genetic makeup of an individual. Genome-wide association studies have identified almost 200 SLE-associated risk loci, yet unravelling the functional effect of these loci remains a challenge. New analytic tools have enabled researchers to delve deeper, leveraging DNA sequencing and cell-specific and immune pathway analysis to elucidate the immunopathogenic mechanisms. Both common genetic variants and rare non-synonymous mutations can interact to increase SLE risk. Notably, variants strongly associated with SLE are often located in genome super-enhancers that regulate MHC class II gene expression. Additionally, the 3D conformations of DNA and RNA contribute to genome regulation and innate immune system activation. Improved therapies for SLE are urgently needed and current and future knowledge from genetic and genomic research should provide new tools to facilitate patient diagnosis, enhance the identification of therapeutic targets and optimize testing of agents.
Collapse
Affiliation(s)
- Yogita Ghodke-Puranik
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA
| | - Mikhail Olferiev
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA
| | - Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery and Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
2
|
Nln I, Shum J, Ghodke-Puranik Y, Tipon R, Triese D, Amin S, Makol A, Osborn T, Chowdhary V, Thanarajasingam U, Muskardin TLW, Oke V, Gunnarsson I, Zickert A, Zervou MI, Boumpas DT, Svenungsson E, Goulielmos GN, Niewold TB. Regional European genetic ancestry predicts type I interferon level and risk of severe viral infection. QJM 2024; 117:581-588. [PMID: 38530799 PMCID: PMC11389909 DOI: 10.1093/qjmed/hcae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Viral infection outcomes vary widely between individuals, ranging from mild symptoms to severe organ failure and death, and it is clear that host genetic factors play a role in this variability. Type I interferon (IFN) is a critical anti-viral cytokine, and we have previously noted differences in type I IFN levels between world populations. METHODS In this study, we investigate the interrelationship between regional European genetic ancestry, type I IFN levels and severe viral infection outcomes. RESULTS In cohorts of European ancestry lupus patients living in Europe, we noted higher IFN in the Northwestern populations as compared to Southeastern populations. In an independent cohort of European ancestry lupus patients from the USA with varying proportional regional European genetic admixture, we observed the same Northwest vs. Southeast European ancestry IFN gradient. We developed a model to predict type I IFN level based on regional European ancestry (Area under the curve (AUC) = 0.73, P = 6.1e-6). Examining large databases containing serious viral outcomes data, we found that lower predicted IFN in the corresponding European country was significantly correlated with increased viral infection fatality rate, including Coronavirus Disease 2019 (COVID-19), viral hepatitis and HIV [correlation coefficients: -0.79 (P = 4e-2), -0.94 (P = 6e-3) and -0.96 (P = 8e-2), respectively]. CONCLUSIONS This association between predicted type I IFN level and viral outcome severity suggests a potential causal relationship, as greater intrinsic type I IFN is beneficial in host defense against viruses. Genetic testing could provide insight into individual and population level risk of fatality due to viruses prior to infection, across a wide range of viral pathogens.
Collapse
Affiliation(s)
- I Nln
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - J Shum
- Department of Medicine, MarinHealth Medical Center, Kentfield, CA, USA
| | - Y Ghodke-Puranik
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - R Tipon
- The New York Stem Cell Foundation, New York, NY, USA
| | - D Triese
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - S Amin
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - A Makol
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - T Osborn
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - V Chowdhary
- Division of Rheumatology, Yale University, New Haven, CT, USA
| | | | - T L W Muskardin
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| | - V Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - I Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - A Zickert
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - M I Zervou
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - D T Boumpas
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - E Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - G N Goulielmos
- Laboratory of Molecular Medicine and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - T B Niewold
- Division of Rheumatology, Department of Medicine, Hospital for Special Surgery, New York, NY, USA
| |
Collapse
|
3
|
Liu J, Wei B, Zhang Y, You Y, Zhi Y. Association between PRKG1 gene and gene-environment interactions with pediatric asthma. J Asthma 2024; 61:754-761. [PMID: 38193459 DOI: 10.1080/02770903.2024.2303763] [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: 10/04/2023] [Accepted: 01/07/2024] [Indexed: 01/10/2024]
Abstract
OBJECTIVE To investigate the relationship between single nucleotide polymorphisms (SNPs) of cGMP-dependent protein kinase I (PRKG1) gene and gene-environment interactions with bronchial asthma in children. METHODS 109 asthma patients and 158 healthy controls from the General Hospital of Northern Theater Command were enrolled, based case-control study. The iMLDR® multiple SNP typing technique was applied to detect the genotypes of rs7903366, rs7081864, rs7070958 and rs7897633 in PRKG1 gene. The percentage of eosinophils (EOS%) in peripheral blood and serum immunoglobulin E (IgE) in the case group were also measured. Gene-environment interactions were examined using the generalized multi-factor dimensionality reduction (GMDR) method. RESULTS There were polymorphisms in four SNPs of PRKG1 gene in the case and control groups. The genotype and allele frequencies distribution of rs7897633 demonstrated statistical significance (p < 0.05). There were no statistically significant differences in EOS% and IgE among genotypes at the four SNPs of PRKG1 gene (p > 0.05). The haplotypes CAGA and TGAC presented significant association with asthma risk (p < 0.05). The four-factor model indicated a potential gene-environment interaction in rs7897633, allergen exposure, residence, and environmental tobacco smoke (ETS) exposure (p < 0.05). CONCLUSIONS The rs7897633 in PRKG1 gene was associated with susceptibility to childhood asthma, and C allele is a protective factor. The haplotype CAGA had a protective effect against asthma risk and TGAC was linked to the high risk of developing asthma. Moreover, the interaction of rs7897633, allergen exposure, residence, and ETS exposure conferred susceptibility to childhood asthma.
Collapse
Affiliation(s)
- Jun Liu
- Department of Neonatology, General Hospital of Northern Theater Command, Shenyang, P.R. China
- Post-graduate College, China Medical University, Shenyang, P.R. China
| | - Bing Wei
- Department of Neonatology, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Yuxuan Zhang
- Department of Neonatology, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Yuan You
- Department of Neonatology, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Yanjie Zhi
- Department of Neonatology, General Hospital of Northern Theater Command, Shenyang, P.R. China
| |
Collapse
|
4
|
Drougkas K, Skarlis C, Mavragani C. Type I Interferons in Systemic Autoimmune Rheumatic Diseases: Pathogenesis, Clinical Features and Treatment Options. Mediterr J Rheumatol 2024; 35:365-380. [PMID: 39193187 PMCID: PMC11345602 DOI: 10.31138/mjr.270324.tis] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 08/29/2024] Open
Abstract
Type I interferon (IFN) pathway dysregulation plays a crucial role in the pathogenesis of several systemic autoimmune rheumatic diseases (SARDs), including systemic lupus erythematosus (SLE), Sjögren's disease (SjD), systemic sclerosis (SSc), dermatomyositis (DM) and rheumatoid arthritis (RA). Genetic and epigenetic alterations have been involved in dysregulated type I IFN responses in systemic autoimmune disorders. Aberrant type I IFN production and secretion have been associated with distinct clinical phenotypes, disease activity, and severity as well as differentiated treatment responses among SARDs. In this review, we provide an overview of the role of type I IFNs in systemic autoimmune diseases including SLE, RA, SjD, SSc, and DM focusing on pathophysiological, clinical, and therapeutical aspects.
Collapse
Affiliation(s)
- Konstantinos Drougkas
- Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Charalampos Skarlis
- Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Clio Mavragani
- Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Joint Academic Rheumatology Program, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
5
|
Niewold TB, Aksentijevich I, Gorevic PD, Gibson G, Yao Q. Genetically transitional disease: conceptual understanding and applicability to rheumatic disease. Nat Rev Rheumatol 2024; 20:301-310. [PMID: 38418715 DOI: 10.1038/s41584-024-01086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
In genomic medicine, the concept of genetically transitional disease (GTD) refers to cases in which gene mutation is necessary but not sufficient to cause disease. In this Perspective, we apply this novel concept to rheumatic diseases, which have been linked to hundreds of genetic variants via association studies. These variants are in the 'grey zone' between monogenic variants with large effect sizes and common susceptibility alleles with small effect sizes. Among genes associated with rare autoinflammatory diseases, many low-frequency and/or low-penetrance variants are known to increase susceptibility to systemic inflammation. In autoimmune diseases, hundreds of HLA and non-HLA genetic variants have been revealed to be modest- to moderate-risk alleles. These diseases can be reclassified as GTDs. The same concept could apply to many other human diseases. GTD could improve the reporting of genetic testing results, diagnostic yields, genetic counselling and selection of therapy, as well as facilitating research using a novel approach to human genetic diseases.
Collapse
Affiliation(s)
- Timothy B Niewold
- Department of Rheumatology, Hospital for Special Surgery, New York, NY, USA
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Gorevic
- Division of Rheumatology, Allergy and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Qingping Yao
- Division of Rheumatology, Allergy and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA.
| |
Collapse
|
6
|
Wang CM, Jan Wu YJ, Zheng JW, Huang LY, Tan KP, Chen JY. T cell expressions of aberrant gene signatures and Co-inhibitory receptors (Co-IRs) as predictors of renal damage and lupus disease activity. J Biomed Sci 2024; 31:41. [PMID: 38650001 PMCID: PMC11034032 DOI: 10.1186/s12929-024-01024-7] [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: 10/04/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is distinguished by an extensive range of clinical heterogeneity with unpredictable disease flares and organ damage. This research investigates the potential of aberrant signatures on T cell genes, soluble Co-IRs/ligands, and Co-IRs expression on T cells as biomarkers for lupus disease parameters. METHODS Comparative transcriptome profiling analysis of non-renal and end-stage renal disease (ESRD) phenotypes of SLE was performed using CD4 + and CD8 + cDNA microarrays of sorted T cells. Comparing the expression of Co-IRs on T cells and serum soluble mediators among healthy and SLE phenotypes. RESULTS SLE patients with ESRD were downregulated CD38, PLEK, interferon-γ, CX3CR1, FGFBP2, and SLCO4C1 transcripts on CD4 + and CD8 + T cells simultaneously and NKG7, FCRL6, GZMB/H, FcγRIII, ITGAM, Fas ligand, TBX21, LYN, granulysin, CCL4L1, CMKLR1, HLA-DRβ, KIR2DL3, and KLRD1 in CD8 T cells. Pathway enrichment and PPI network analyses revealed that the overwhelming majority of Differentially Expressed Genes (DEGs) have been affiliated with novel cytotoxic, antigen presentation, and chemokine-cell migration signature pathways. CD8 + GZMK + T cells that are varied in nature, including CD161 + Mucosal-associated invariant T (MAIT) cells and CD161- aged-associated T (Taa) cells and CD161-GZMK + GZMB + T cells might account for a higher level of GZMK in CD8 + T cells associated with ESRD. SLE patients have higher TIGIT + , PD1 + , and lower CD127 + cell percentages on CD4 + T cells, higher TIM3 + , TIGIT + , HLA-DR + cell frequency, and lower MFI expression of CD127, CD160 in CD8 T cells. Co-IRs expression in T cells was correlated with soluble PD-1, PDL-2, and TIM3 levels, as well as SLE disease activity, clinical phenotypes, and immune-therapy responses. CONCLUSION The signature of dysfunctional pathways defines a distinct immunity pattern in LN ESRD patients. Expression levels of Co-IRs in peripheral blood T cells and serum levels of soluble PD1/PDL-2/TIM3 can serve as biomarkers for evaluating clinical parameters and therapeutic responses.
Collapse
Affiliation(s)
- Chin-Man Wang
- Department of Rehabilitation, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, No. 5, Fu-Shin St. Kwei-Shan, Taoyuan, Republic of China
| | - Yeong-Jian Jan Wu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Jian-Wen Zheng
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Li Yu Huang
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Keng Poo Tan
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China
| | - Ji-Yih Chen
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan, No. 5, Fu-Shin St. Kwei-Shan, Republic of China.
| |
Collapse
|
7
|
Sun X, Liu Z, Li Z, Zeng Z, Peng W, Zhu J, Zhao J, Zhu C, Zeng C, Stearrett N, Crandall KA, Bachali P, Grammer AC, Lipsky PE. Abnormalities in intron retention characterize patients with systemic lupus erythematosus. Sci Rep 2023; 13:5141. [PMID: 36991079 PMCID: PMC10060252 DOI: 10.1038/s41598-023-31890-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Regulation of intron retention (IR), a form of alternative splicing, is a newly recognized checkpoint in gene expression. Since there are numerous abnormalities in gene expression in the prototypic autoimmune disease systemic lupus erythematosus (SLE), we sought to determine whether IR was intact in patients with this disease. We, therefore, studied global gene expression and IR patterns of lymphocytes in SLE patients. We analyzed RNA-seq data from peripheral blood T cell samples from 14 patients suffering from systemic lupus erythematosus (SLE) and 4 healthy controls and a second, independent data set of RNA-seq data from B cells from16 SLE patients and 4 healthy controls. We identified intron retention levels from 26,372 well annotated genes as well as differential gene expression and tested for differences between cases and controls using unbiased hierarchical clustering and principal component analysis. We followed with gene-disease enrichment analysis and gene-ontology enrichment analysis. Finally, we then tested for significant differences in intron retention between cases and controls both globally and with respect to specific genes. Overall decreased IR was found in T cells from one cohort and B cells from another cohort of patients with SLE and was associated with increased expression of numerous genes, including those encoding spliceosome components. Different introns within the same gene displayed both up- and down-regulated retention profiles indicating a complex regulatory mechanism. These results indicate that decreased IR in immune cells is characteristic of patients with active SLE and may contribute to the abnormal expression of specific genes in this autoimmune disease.
Collapse
Affiliation(s)
- Xiaoqian Sun
- Computer Science Department, George Washington University, Washington, DC, 20052, USA
| | - Zhichao Liu
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Zongzhu Li
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Zhouhao Zeng
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Weiqun Peng
- Physics Department, George Washington University, Washington, DC, 20052, USA
| | - Jun Zhu
- Mokobio Biotechnology R&D Center, 1445 Research Blvd, Suite 150, Rockville, MD, 20850, USA
| | - Joel Zhao
- Walt Whitman High School, Bethesda, MD, 20817, USA
| | | | - Chen Zeng
- Physics Department, George Washington University, Washington, DC, 20052, USA.
| | - Nathaniel Stearrett
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
| | - Prathyusha Bachali
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- RILITE Research Institute and AMPEL BioSolutions, 250 W Main St, Ste 300, Charlottesville, VA, 22902, USA.
| |
Collapse
|
8
|
Innate and adaptive immune abnormalities underlying autoimmune diseases: the genetic connections. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-021-2187-3. [PMID: 36738430 PMCID: PMC9898710 DOI: 10.1007/s11427-021-2187-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
With the exception of an extremely small number of cases caused by single gene mutations, most autoimmune diseases result from the complex interplay between environmental and genetic factors. In a nutshell, etiology of the common autoimmune disorders is unknown in spite of progress elucidating certain effector cells and molecules responsible for pathologies associated with inflammatory and tissue damage. In recent years, population genetics approaches have greatly enriched our knowledge regarding genetic susceptibility of autoimmunity, providing us with a window of opportunities to comprehensively re-examine autoimmunity-associated genes and possible pathways. In this review, we aim to discuss etiology and pathogenesis of common autoimmune disorders from the perspective of human genetics. An overview of the genetic basis of autoimmunity is followed by 3 chapters detailing susceptibility genes involved in innate immunity, adaptive immunity and inflammatory cell death processes respectively. With such attempts, we hope to expand the scope of thinking and bring attention to lesser appreciated molecules and pathways as important contributors of autoimmunity beyond the 'usual suspects' of a limited subset of validated therapeutic targets.
Collapse
|
9
|
Germline genetic variation and predicting immune checkpoint inhibitor induced toxicity. NPJ Genom Med 2022; 7:73. [PMID: 36564402 PMCID: PMC9789157 DOI: 10.1038/s41525-022-00345-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionised the treatment of various cancer types. ICIs reinstate T-cell function to elicit an anti-cancer immune response. The resulting immune response can however have off-target effects which manifest as autoimmune type serious immune-related adverse events (irAE) in ~10-55% of patients treated. It is currently challenging to predict both who will experience irAEs and to what severity. Identification of patients at high risk of serious irAE would revolutionise patient care. While the pathogenesis driving irAE development is still unclear, host genetic factors are proposed to be key determinants of these events. This review presents current evidence supporting the role of the host genome in determining risk of irAE. We summarise the spectrum and timing of irAEs following treatment with ICIs and describe currently reported germline genetic variation associated with expression of immuno-modulatory factors within the cancer immunity cycle, development of autoimmune disease and irAE occurrence. We propose that germline genetic determinants of host immune function and autoimmune diseases could also explain risk of irAE development. We also endorse genome-wide association studies of patients being treated with ICIs to identify genetic variants that can be used in polygenic risk scores to predict risk of irAE.
Collapse
|
10
|
Villalvazo P, Carriazo S, Rojas-Rivera J, Ramos AM, Ortiz A, Perez-Gomez MV. Gain-of-function TLR7 and loss-of-function A20 gene variants identify a novel pathway for Mendelian lupus and lupus nephritis. Clin Kidney J 2022; 15:1973-1980. [PMID: 36324999 PMCID: PMC9613427 DOI: 10.1093/ckj/sfac152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 11/25/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic and inflammatory autoimmune disease of unknown origin that may cause kidney disease, i.e. lupus nephritis (LN). Within a wider trend towards an expanding field of genetic causes of kidney disease, two recent reports have emphasized the role of Mendelian autoimmune disorders in causing LN both in children and in young adults. Loss-of-function (LOF) variants of tumor necrosis factor alpha-induced protein 3 (TNFAIP3) and gain of function (GOF) variants of Toll-like receptor 7 (TLR7) cause SLE and LN, respectively. Interestingly, both genes regulate the same signaling route, as A20, the protein encoded by TNFAIP3, inhibits nuclear factor ĸB (NF-ĸB) activation while TLR7 promoted NF-ĸB activation. Moreover, TNFAIP3 and TLR7 variants are relatively frequent, potentially contributing to polygenic risk for LN. Finally, they both may be expressed by kidney cells, potentially contributing to the severity of kidney injury in persons who have already developed autoimmunity. The fact that both genes regulate the same pathway may lead to novel therapeutic approaches targeting the shared molecular pathway.
Collapse
Affiliation(s)
- Priscila Villalvazo
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sol Carriazo
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS2040, Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jorge Rojas-Rivera
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS2040, Madrid, Spain
| | - Adrián M Ramos
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS2040,Madrid, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS2040,Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria Vanessa Perez-Gomez
- Department of Nephrology and Hypertension, Instituto de Investigación Sanitaria, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
- RICORS2040,Madrid, Spain
- Departamento de Medicina, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
11
|
García-Sancha N, Corchado-Cobos R, Gómez-Vecino A, Jiménez-Navas A, Pérez-Baena MJ, Blanco-Gómez A, Holgado-Madruga M, Mao JH, Cañueto J, Castillo-Lluva S, Mendiburu-Eliçabe M, Pérez-Losada J. Evolutionary Origins of Metabolic Reprogramming in Cancer. Int J Mol Sci 2022; 23:ijms232012063. [PMID: 36292921 PMCID: PMC9603151 DOI: 10.3390/ijms232012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.
Collapse
Affiliation(s)
- Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Cañueto
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007 Salamanca, Spain
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
| |
Collapse
|
12
|
Nln I, Fernandez-Ruiz R, Muskardin TLW, Paredes JL, Blazer AD, Tuminello S, Attur M, Iturrate E, Petrilli CM, Abramson SB, Chakravarti A, Niewold TB. Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19. Transl Res 2022; 244:47-55. [PMID: 35114420 PMCID: PMC8802623 DOI: 10.1016/j.trsl.2022.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR = 29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in antiviral immunity.
Collapse
Affiliation(s)
- Ilona Nln
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | | | - Jacqueline L Paredes
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Ashira D Blazer
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York
| | - Stephanie Tuminello
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, New York
| | - Mukundan Attur
- Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Eduardo Iturrate
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | | | - Steven B Abramson
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, New York
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, New York.
| |
Collapse
|
13
|
Ellena JF, Tang TX, Shanaiah N, Capelluto DGS. Backbone 1H, 15N, and 13C resonance assignments of the Phafin2 pleckstrin homology domain. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:27-30. [PMID: 34739631 PMCID: PMC9068824 DOI: 10.1007/s12104-021-10054-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/27/2021] [Indexed: 05/27/2023]
Abstract
Phafin2 is a peripheral protein that triggers cellular signaling from endosomal and lysosomal compartments. The specific subcellular localization of Phafin2 is mediated by the presence of a tandem of phosphatidylinositol 3-phosphate (PtdIns3P)-binding domains, the pleckstrin homology (PH) and the Fab-1, YOTB, Vac1, and EEA1 (FYVE) domains. The requirement for both domains for binding to PtdIns3P still remains unclear. To understand the molecular interactions of the Phafin2 PH domain in detail, we report its nearly complete 1H, 15N, and 13C backbone resonance assignments.
Collapse
Affiliation(s)
- Jeffrey F Ellena
- Biomolecular Magnetic Resonance Facility, University of Virginia, Charlottesville, VA, 22904, USA
| | - Tuo-Xian Tang
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA.
| |
Collapse
|
14
|
Fernandez-Ruiz R, Niewold TB. Type I Interferons in Autoimmunity. J Invest Dermatol 2022; 142:793-803. [PMID: 35016780 PMCID: PMC8860872 DOI: 10.1016/j.jid.2021.11.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/30/2022]
Abstract
Dysregulated IFN-1 responses play crucial roles in the development of multiple forms of autoimmunity. Many patients with lupus, systemic sclerosis, Sjogren's syndrome, and dermatomyositis demonstrate enhanced IFN-1 signaling. IFN-1 excess is associated with disease severity and autoantibodies and could potentially predict response to newer therapies targeting IFN-1 pathways. In this review, we provide an overview of the signaling pathway and immune functions of IFN-1s in health and disease. We also review the systemic autoimmune diseases classically associated with IFN-1 upregulation and current therapeutic strategies targeting the IFN-1 system.
Collapse
Affiliation(s)
- Ruth Fernandez-Ruiz
- Division of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Timothy B Niewold
- Judith & Stewart Colton Center for Autoimmunity, Department of Medicine Research, NYU Grossman School of Medicine, New York, New York, USA.
| |
Collapse
|
15
|
Nln I, Fernandez-Ruiz R, Wampler Muskardin TL, Paredes JL, Blazer AD, Tuminello S, Attur M, Iturrate E, Petrilli CM, Abramson SB, Chakravarti A, Niewold TB. Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.01.21265766. [PMID: 34751274 PMCID: PMC8575145 DOI: 10.1101/2021.11.01.21265766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Type I interferon (IFN) is critical in our defense against viral infections. Increased type I IFN pathway activation is a genetic risk factor for systemic lupus erythematosus (SLE), and a number of common risk alleles contribute to the high IFN trait. We hypothesized that these common gain-of-function IFN pathway alleles may be associated with protection from mortality in acute COVID-19. We studied patients admitted with acute COVID-19 (756 European-American and 398 African-American ancestry). Ancestral backgrounds were analyzed separately, and mortality after acute COVID-19 was the primary outcome. In European-American ancestry, we found that a haplotype of interferon regulatory factor 5 (IRF5) and alleles of protein kinase cGMP-dependent 1 (PRKG1) were associated with mortality from COVID-19. Interestingly, these were much stronger risk factors in younger patients (OR=29.2 for PRKG1 in ages 45-54). Variants in the IRF7 and IRF8 genes were associated with mortality from COVID-19 in African-American subjects, and these genetic effects were more pronounced in older subjects. Combining genetic information with blood biomarker data such as C-reactive protein, troponin, and D-dimer resulted in significantly improved predictive capacity, and in both ancestral backgrounds the risk genotypes were most relevant in those with positive biomarkers (OR for death between 14 and 111 in high risk genetic/biomarker groups). This study confirms the critical role of the IFN pathway in defense against COVID-19 and viral infections, and supports the idea that some common SLE risk alleles exert protective effects in anti-viral immunity. BACKGROUND We find that a number of IFN pathway lupus risk alleles significantly impact mortality following COVID-19 infection. These data support the idea that type I IFN pathway risk alleles for autoimmune disease may persist in high frequency in modern human populations due to a benefit in our defense against viral infections. TRANSLATIONAL SIGNIFICANCE We develop multivariate prediction models which combine genetics and known biomarkers of severity to result in greatly improved prediction of mortality in acute COVID-19. The specific associated alleles provide some clues about key points in our defense against COVID-19.
Collapse
Affiliation(s)
- Ilona Nln
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | | | | | - Ashira D Blazer
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| | - Stephanie Tuminello
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY
| | - Mukundan Attur
- Divison of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | - Eduardo Iturrate
- Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | | | - Steven B Abramson
- Department of Medicine, NYU Grossman School of Medicine, New York, NY
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, New York, NY
| |
Collapse
|
16
|
Nikopensius T, Niibo P, Haller T, Jagomägi T, Voog-Oras Ü, Tõnisson N, Metspalu A, Saag M, Pruunsild C. Association analysis of juvenile idiopathic arthritis genetic susceptibility factors in Estonian patients. Clin Rheumatol 2021; 40:4157-4165. [PMID: 34101054 PMCID: PMC8463396 DOI: 10.1007/s10067-021-05756-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Background Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition of childhood. Genetic association studies have revealed several JIA susceptibility loci with the strongest effect size observed in the human leukocyte antigen (HLA) region. Genome-wide association studies have augmented the number of JIA-associated loci, particularly for non-HLA genes. The aim of this study was to identify new associations at non-HLA loci predisposing to the risk of JIA development in Estonian patients. Methods We performed genome-wide association analyses in an entire JIA case–control sample (All-JIA) and in a case–control sample for oligoarticular JIA, the most prevalent JIA subtype. The entire cohort was genotyped using the Illumina HumanOmniExpress BeadChip arrays. After imputation, 16,583,468 variants were analyzed in 263 cases and 6956 controls. Results We demonstrated nominal evidence of association for 12 novel non-HLA loci not previously implicated in JIA predisposition. We replicated known JIA associations in CLEC16A and VCTN1 regions in the oligoarticular JIA sample. The strongest associations in the All-JIA analysis were identified at PRKG1 (P = 2,54 × 10−6), LTBP1 (P = 9,45 × 10−6), and ELMO1 (P = 1,05 × 10−5). In the oligoarticular JIA analysis, the strongest associations were identified at NFIA (P = 5,05 × 10−6), LTBP1 (P = 9,95 × 10−6), MX1 (P = 1,65 × 10−5), and CD200R1 (P = 2,59 × 10−5). Conclusion This study increases the number of known JIA risk loci and provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. The reported loci are involved in molecular pathways of immunological relevance and likely represent genomic regions that confer susceptibility to JIA in Estonian patients.
Key Points • Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease with heterogeneous presentation and genetic predisposition. • Present genome-wide association study for Estonian JIA patients is first of its kind in Northern and Northeastern Europe. • The results of the present study increase the knowledge about JIA risk loci replicating some previously described associations, so adding weight to their relevance and describing novel loci. • The study provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. |
Supplementary Information The online version contains supplementary material available at 10.1007/s10067-021-05756-x.
Collapse
Affiliation(s)
- Tiit Nikopensius
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.
| | - Priit Niibo
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Toomas Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Triin Jagomägi
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Ülle Voog-Oras
- Institute of Dentistry, University of Tartu, Tartu, Estonia.,Stomatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Neeme Tõnisson
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Mare Saag
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Chris Pruunsild
- Children's Clinic, Tartu University Hospital, Tartu, Estonia.,Children's Clinic, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
17
|
Chasset F, Dayer JM, Chizzolini C. Type I Interferons in Systemic Autoimmune Diseases: Distinguishing Between Afferent and Efferent Functions for Precision Medicine and Individualized Treatment. Front Pharmacol 2021; 12:633821. [PMID: 33986670 PMCID: PMC8112244 DOI: 10.3389/fphar.2021.633821] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
A sustained increase in type I interferon (IFN-I) may accompany clinical manifestations and disease activity in systemic autoimmune diseases (SADs). Despite the very frequent presence of IFN-I in SADs, clinical manifestations are extremely varied between and within SADs. The present short review will address the following key questions associated with high IFN-I in SADs in the perspective of precision medicine. 1) What are the mechanisms leading to high IFN-I? 2) What are the predisposing conditions favoring high IFN-I production? 3) What is the role of IFN-I in the development of distinct clinical manifestations within SADs? 4) Would therapeutic strategies targeting IFN-I be helpful in controlling or even preventing SADs? In answering these questions, we will underlie areas of incertitude and the intertwined role of autoantibodies, immune complexes, and neutrophils.
Collapse
Affiliation(s)
- François Chasset
- Department of Dermatology and Allergology, Faculty of Medicine, AP-HP, Tenon Hospital, Sorbonne University, Paris, France
| | - Jean-Michel Dayer
- Emeritus Professor of Medicine, School of Medicine, Geneva University, Geneva, Switzerland
| | - Carlo Chizzolini
- Department of Pathology and Immunology, School of Medicine, Geneva University, Geneva, Switzerland
| |
Collapse
|
18
|
Postal M, Vivaldo JF, Fernandez-Ruiz R, Paredes JL, Appenzeller S, Niewold TB. Type I interferon in the pathogenesis of systemic lupus erythematosus. Curr Opin Immunol 2020; 67:87-94. [PMID: 33246136 PMCID: PMC8054829 DOI: 10.1016/j.coi.2020.10.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 02/08/2023]
Abstract
Type I interferon (IFN) is a primary pathogenic factor in systemic lupus erythematosus (SLE). Gain-of-function genetic variants in the type I IFN pathway have been associated with risk of disease. Common polygenic as well as rare monogenic influences on type I IFN have been demonstrated, supporting a complex genetic basis for high IFN in many SLE patients. Both SLE-associated autoantibodies and high type I IFN can be observed in the pre-disease state. Patients with SLE and evidence of high type I IFN have more active disease and a greater propensity to nephritis and other severe manifestations. Despite the well-established association between type I IFN and SLE, the specific triggers of type I IFN production, the mechanisms by which IFNs help perpetuate the cycle of autoreactive cells and autoantibody production are not completely clear. This review provides an updated overview of type I IFN in SLE pathogenesis, clinical manifestations, and current therapeutic strategies targeting this pathway.
Collapse
Affiliation(s)
- Mariana Postal
- Autoimmunity Lab, School of Medical Science, State University of Campinas, Campinas, SP, Brazil
| | - Jessica F Vivaldo
- Autoimmunity Lab, School of Medical Science, State University of Campinas, Campinas, SP, Brazil; Graduate Program of Child and Adolescent Health, School of Medical Science, State University of Campinas, Campinas, SP, Brazil
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Jacqueline L Paredes
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Simone Appenzeller
- Autoimmunity Lab, School of Medical Science, State University of Campinas, Campinas, SP, Brazil; Rheumatology Unit, Department of Medicine, School of Medical Science, State University of Campinas, Campinas, SP, Brazil
| | - Timothy B Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
19
|
Paredes JL, Niewold TB. Type I interferon antagonists in clinical development for lupus. Expert Opin Investig Drugs 2020; 29:1025-1041. [PMID: 32700979 PMCID: PMC7924012 DOI: 10.1080/13543784.2020.1797677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a severe chronic and incurable autoimmune disease. Treatment includes glucocorticoids and immunosuppressants which typically result in partial responses, and hence there is a great need for new therapies. The type I interferon (IFN) pathway is activated in more than 50% of SLE patients, and it is strongly implicated as a pathogenic factor in SLE. AREAS COVERED We searched the literature using 'SLE and interferon antagonists' as search terms. This identified a number of therapeutics that have entered clinical development targeting type I IFN in SLE. These include monoclonal antibodies against type I IFN cytokines and a kinoid vaccination strategy to induce anti-IFN antibodies. EXPERT OPINION Type I IFN antagonists have had some success, but many molecules have not progressed to phase III. These varied results are likely attributed to the multiple concurrent cytokine abnormalities present in SLE, the imprecise nature of the IFN signature as a readout for type I IFN and difficulties with clinical trials such as background medication use and diffuse composite disease activity measures. Despite these challenges, it seems likely that a type I IFN antagonist will come to clinical utility for SLE given the large unmet need and the recent phase III success with anifrolumab.
Collapse
Affiliation(s)
- Jacqueline L Paredes
- Colton Center for Autoimmunity, New York University School of Medicine , New York, NY, USA
| | - Timothy B Niewold
- Colton Center for Autoimmunity, New York University School of Medicine , New York, NY, USA
| |
Collapse
|
20
|
Wu L, Shi PL, Tao SS, Tao JH, Wu GC. Decreased sleep quality in patients with systemic lupus erythematosus: a meta-analysis. Clin Rheumatol 2020; 40:913-922. [PMID: 32748069 DOI: 10.1007/s10067-020-05300-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To obtain a reliable estimation on the sleep quality in patients with systemic lupus erythematosus (SLE) and identify the main sleep problems, a meta-analysis was performed. METHODS Up to March 21, 2020, PubMed, EMBASE, and Cochrane Library were searched; quality evaluation were conducted with Newcastle-Ottawa Scale; statistical analyses were performed by stata14.0 software; results were expressed by weighted mean difference or standardized mean difference (WMD/SMD) and 95% confidence interval (CI). RESULTS Eighteen case-control studies were included in meta-analysis, 1086 SLE patients and 2866 controls were collected. The score of sleep quality in the case group was higher than that in the control group (SMD = 1.03, 95% CI: 0.80-1.27), and so was the Pittsburgh Sleep Quality Index (PSQI) (WMD = 3.45, 95% CI: 2.49-4.42). The first three complaints of sleep problems in PSQI were daytime dysfunction (WMD = 0.64, 95% CI: 0.36-0.92), subjective sleep quality (WMD = 0.62, 95% CI: 0.40-0.84), and habitual sleep efficiency (WMD = 0.54, 95% CI: 0.37-0.72). Subgroup analyses showed that the score of sleep quality in SLE patients were higher than controls among different regions, races, and disease duration. The sleep quality score of SLE patients with fibromyalgia (FM) was higher than that in general control, but no significant difference as compared with SLE patients without FM. CONCLUSIONS Our meta-analysis indicates that the sleep quality of SLE patients is worse than that of the general population; thus, more attention should be paid to the sleep status among this disease. Key Points •The sleep quality of SLE patients is worse than that of the general population. •Region, race, and disease duration are correlated with sleep quality in SLE patients.
Collapse
Affiliation(s)
- Li Wu
- School of Nursing, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Pei-Li Shi
- School of Nursing, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Sha-Sha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jin-Hui Tao
- Department of Rheumatology & Immunology, Anhui Provincial Hospital, Hefei, Anhui, China
| | - Guo-Cui Wu
- School of Nursing, Anhui Medical University, Hefei, 230032, Anhui, China.
| |
Collapse
|
21
|
Wampler Muskardin TL, Fan W, Jin Z, Jensen MA, Dorschner JM, Ghodke-Puranik Y, Dicke B, Vsetecka D, Wright K, Mason T, Persellin S, Michet CJ, Davis JM, Matteson E, Niewold TB. Distinct Single Cell Gene Expression in Peripheral Blood Monocytes Correlates With Tumor Necrosis Factor Inhibitor Treatment Response Groups Defined by Type I Interferon in Rheumatoid Arthritis. Front Immunol 2020; 11:1384. [PMID: 32765497 PMCID: PMC7378891 DOI: 10.3389/fimmu.2020.01384] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/29/2020] [Indexed: 01/14/2023] Open
Abstract
Previously, we demonstrated in test and validation cohorts that type I IFN (T1IFN) activity can predict non-response to tumor necrosis factor inhibitors (TNFi) in rheumatoid arthritis (RA). In this study, we examine the biology of non-classical and classical monocytes from RA patients defined by their pre-biologic treatment T1IFN activity. We compared single cell gene expression in purified classical (CL, n = 342) and non-classical (NC, n = 359) monocytes. In our previous work, RA patients who had either high IFNβ/α activity (>1.3) or undetectable T1IFN were likely to have EULAR non-response to TNFi. In this study comparisons were made among patients grouped according to their pre-biologic treatment T1IFN activity as clinically relevant: “T1IFN undetectable (T1IFN ND) or IFNβ/α >1.3” (n = 9) and “T1IFN detectable but IFNβ/α ≤ 1.3” (n = 6). In addition, comparisons were made among patients grouped according to their T1IFN activity itself: “T1IFN ND,” “T1IFN detected and IFNβ/α ≤ 1.3,” and “IFNβ/α >1.3.” Major differences in gene expression were apparent in principal component and unsupervised cluster analyses. CL monocytes from the T1IFN ND or IFNβ/α >1.3 group were unlikely to express JAK1 and IFI27 (p < 0.0001 and p 0.0005, respectively). In NC monocytes from the same group, expression of IFNAR1, IRF1, TNFA, TLR4 (p ≤ 0.0001 for each) and others was enriched. Interestingly, JAK1 expression was absent in CL and NC monocytes from nine patients. This pattern most strongly associated with the IFNβ/α>1.3 group. Differences in gene expression in monocytes among the groups suggest differential IFN pathway activation in RA patients who are either likely to respond or to have no response to TNFi. Additional transcripts enriched in NC cells of those in the T1IFN ND and IFNβ/α >1.3 groups included MYD88, CD86, IRF1, and IL8. This work could suggest key pathways active in biologically defined groups of patients, and potential therapeutic strategies for those patients unlikely to respond to TNFi.
Collapse
Affiliation(s)
- Theresa L Wampler Muskardin
- Department of Medicine, Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, United States.,Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Wei Fan
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongbo Jin
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Mark A Jensen
- Department of Medicine, Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, United States.,Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Jessica M Dorschner
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Yogita Ghodke-Puranik
- Department of Medicine, Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, United States.,Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Betty Dicke
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Danielle Vsetecka
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Kerry Wright
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Thomas Mason
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Scott Persellin
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Clement J Michet
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - John M Davis
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric Matteson
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Timothy B Niewold
- Department of Medicine, Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, United States
| |
Collapse
|
22
|
A Case with Purine Nucleoside Phosphorylase Deficiency Suffering from Late-Onset Systemic Lupus Erythematosus and Lymphoma. J Clin Immunol 2020; 40:833-839. [DOI: 10.1007/s10875-020-00800-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 11/25/2022]
|
23
|
Abstract
Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are two common autoimmune rheumatic diseases that vary in severity, clinical presentation, and disease course between individuals. Molecular and genetic studies of both diseases have identified candidate genes and molecular pathways that are linked to various disease outcomes and treatment responses. Currently, patients can be grouped into molecular subsets in each disease, and these molecular categories should enable precision medicine approaches to be applied in rheumatic diseases. In this article, we will review key lessons learned about disease heterogeneity and molecular characterization in rheumatology, which we hope will lead to personalized therapeutic strategies.
Collapse
Affiliation(s)
| | - Jaqueline L. Paredes
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Simone Appenzeller
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas, Campinas, Brazil
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
24
|
The C-terminal acidic motif of Phafin2 inhibits PH domain binding to phosphatidylinositol 3-phosphate. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183230. [PMID: 32126233 DOI: 10.1016/j.bbamem.2020.183230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Changes in membrane curvature are required to control the function of subcellular compartments; malfunctions of such processes are associated with a wide range of human diseases. Membrane remodeling often depends upon the presence of phosphoinositides, which recruit protein effectors for a variety of cellular functions. Phafin2 is a phosphatidylinositol 3-phosphate (PtdIns3P)-binding effector involved in endosomal and lysosomal membrane-associated signaling. Both the Phafin2 PH and the FYVE domains bind PtdIns3P, although their redundant function in the protein is unclear. Through a combination of lipid-binding assays, we found that, unlike the FYVE domain, recognition of the PH domain to PtdIns3P requires a lipid bilayer. Using site-directed mutagenesis and truncation constructs, we discovered that the Phafin2 FYVE domain is constitutive for PtdIns3P binding, whereas PH domain binding to PtdIns3P is autoinhibited by a conserved C-terminal acidic motif. These findings suggest that binding of the Phafin2 PH domain to PtdIns3P in membrane compartments occurs through a highly regulated mechanism. Potential mechanisms are discussed throughout this report.
Collapse
|
25
|
Interferons ( IFN-A/-B/-G) Genetic Variants in Patients with Mixed Connective Tissue Disease (MCTD). J Clin Med 2019; 8:jcm8122046. [PMID: 31766529 PMCID: PMC6947393 DOI: 10.3390/jcm8122046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/06/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022] Open
Abstract
Mixed connective tissue disease (MCTD) is a rare complex autoimmune disease in which autoantigens are recognized by endosomal TLRs. Their activation induces a higher secretion of the type I interferons, IFN-γ and the up-regulation of the INF-inducible genes. The present study aimed to investigate whether SNPs that are located in the IFN-A, IFN-B, and IFN-G genes are associated with MCTD. 145 MCTD patients and 281 healthy subjects were examined for IFN-A, IFN-B, and IFN-G genetic variants by TaqMan SNP genotyping assay. ELISA determined IFN-α/-β/-γ serum levels. Among the seven tested SNPs, four polymorphisms: IFN-A rs10757212, IFN-A rs3758236, IFN-G rs2069705, IFN-G rs2069718, as well as INF-G rs1861493A/rs2069705A/rs2069718G haplotype were significantly associated with a predisposition for MCTD. Raynaud's phenomenon, erosive arthritis, swollen hands and fingers, and sclerodactyly were significantly more frequently observed in MCTD patients with IFN-G rs2069718 G allele than in patients with IFN-G rs2069718 A allele. We also found that anti-U1-A autoantibodies most frequently occurred in MCTD patients with rs2069718 GA genotype, while the IFN-G rs2069705 AG and rs2069718 GA genotypes might be a marker of anti-Ro60 presence in MCTD patients. Our results indicate that IFN-G genetic variants may be potential genetic biomarkers for MCTD susceptibility and severity.
Collapse
|
26
|
Kwon YC, Chun S, Kim K, Mak A. Update on the Genetics of Systemic Lupus Erythematosus: Genome-Wide Association Studies and Beyond. Cells 2019; 8:cells8101180. [PMID: 31575058 PMCID: PMC6829439 DOI: 10.3390/cells8101180] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of complex etiology that primarily affects women of childbearing age. The development of SLE is attributed to the breach of immunological tolerance and the interaction between SLE-susceptibility genes and various environmental factors, resulting in the production of pathogenic autoantibodies. Working in concert with the innate and adaptive arms of the immune system, lupus-related autoantibodies mediate immune-complex deposition in various tissues and organs, leading to acute and chronic inflammation and consequent end-organ damage. Over the past two decades or so, the impact of genetic susceptibility on the development of SLE has been well demonstrated in a number of large-scale genetic association studies which have uncovered a large fraction of genetic heritability of SLE by recognizing about a hundred SLE-susceptibility loci. Integration of genetic variant data with various omics data such as transcriptomic and epigenomic data potentially provides a unique opportunity to further understand the roles of SLE risk variants in regulating the molecular phenotypes by various disease-relevant cell types and in shaping the immune systems with high inter-individual variances in disease susceptibility. In this review, the catalogue of SLE susceptibility loci will be updated, and biological signatures implicated by the SLE-risk variants will be critically discussed. It is optimistically hoped that identification of SLE risk variants will enable the prognostic and therapeutic biomarker armamentarium of SLE to be strengthened, a major leap towards precision medicine in the management of the condition.
Collapse
Affiliation(s)
- Young-Chang Kwon
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222–1 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea;
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| | - Anselm Mak
- Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| |
Collapse
|
27
|
Nasonov EL, Avdeeva AS. IMMUNOINFLAMMATORY RHEUMATIC DISEASES ASSOCIATED WITH TYPE I INTERFERON: NEW EVIDENCE. ACTA ACUST UNITED AC 2019. [DOI: 10.14412/1995-4484-2019-452-461] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Immunoinflammatory rheumatic diseases (IIRDs) are a large group of pathological conditions with impaired immunological tolerance to autogenous tissues, leading to inflammation and irreversible organ damage. The review discusses current ideas on the role of type I interferons in the immunopathogenesis of IIRDs, primarily systemic lupus erythematosus, and new possibilities for personalized therapy.
Collapse
Affiliation(s)
- E. L. Nasonov
- V.A. Nasonova Research Institute of Rheumatology;
I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | | |
Collapse
|
28
|
Thanarajasingam U, Muppirala AN, Jensen MA, Ghodke-Puranik Y, Dorschner JM, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold TB. Type I Interferon Predicts an Alternate Immune System Phenotype in Systemic Lupus Erythematosus. ACR Open Rheumatol 2019; 1:499-506. [PMID: 31777831 PMCID: PMC6858011 DOI: 10.1002/acr2.11073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Objective Type I interferon (IFN) is important to systemic lupus erythematosus (SLE) pathogenesis, but it is not clear how chronic elevations in IFN alter immune function. We compared cytokine responses after whole blood stimulation with Toll‐like receptor (TLR) agonists in high‐ and low‐IFN SLE patient subgroups. Methods SLE patients and nonautoimmune controls were recruited, and SLE patients were categorized as either high or low IFN. Whole blood was dispensed into tubes coated with lipopolysaccharide (LPS), oligonucleotides with cytosine‐guanine repeats, Resiquimod, IFN‐α, and IFN‐α + LPS. Cytokine production in patient sera and after whole blood TLR stimulation was measured by multiplex assay, and type I IFN was assessed using a functional assay. Results Circulating plasmacytoid dendritic cell numbers were specifically reduced in high‐IFN SLE patients and not in low‐IFN SLE patients. In serum, we observed that the correlations between cytokines in serum differed to a much greater degree between the high‐ and low‐IFN groups (P < 0.0001) than the absolute cytokine levels differed between these same groups. In stimulated conditions, the high‐IFN patients had less cytokine production in response to TLR ligation than the low‐IFN SLE patients. LPS produced the most diverse response, and a number of interactions between type I IFN and LPS were observed. Conclusion We find striking differences in resting and stimulated cytokine patterns in high‐ vs. low‐IFN SLE patients, which supports the biological importance of these patient subsets. These data could inform personalized treatment approaches and the pathogenesis of SLE flare following infection.
Collapse
|
29
|
An update on the role of type I interferons in systemic lupus erythematosus and Sjögren's syndrome. Curr Opin Rheumatol 2019; 30:471-481. [PMID: 29889694 DOI: 10.1097/bor.0000000000000524] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) share several clinical and laboratory features, including an overexpression of type I interferon (IFN) regulated genes. The genetic background to this IFN signature and the role of the type I IFN system in the disease process have been partly clarified. Here, we summarize the latest information concerning the type I IFN system in both diseases. RECENT FINDINGS A number of gene variants in the type I IFN signalling pathways associate with an increased risk for both SLE and pSS in several ethnicities. The function of some risk gene variants has been elucidated, as well as the importance of epigenetic changes in type I IFN regulated genes. MicroRNA-451 and miR-302d have been shown to target IFN regulatory factor 8 and 9, suggesting that noncoding RNAs can control the IFN system. A prominent type I IFN activation is related to several disease manifestations, and in SLE to a more severe disease phenotype. Phase II studies in SLE suggest beneficial effects of blocking the type I IFN receptor. SUMMARY The activated type I IFN system in SLE and pSS has a strong genetic component, is important in the disease etiopathogenesis and can be targeted.
Collapse
|
30
|
Matana A, Popović M, Boutin T, Torlak V, Brdar D, Gunjača I, Kolčić I, Boraska Perica V, Punda A, Polašek O, Hayward C, Barbalić M, Zemunik T. Genome-wide meta-analysis identifies novel gender specific loci associated with thyroid antibodies level in Croatians. Genomics 2019; 111:737-743. [DOI: 10.1016/j.ygeno.2018.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 11/16/2022]
|
31
|
Abstract
A state of relative immunosuppression exists in normal pregnancy. In this issue of JEM, Hong et al. (https://doi.org/10.1084/jem.20190185) perform blood immunomonitoring in pregnancy, in both healthy women and women with lupus, and observe early and sustained transcriptional modulation of lupus-related pathways in both groups. When signatures of inflammation did not normalize in lupus, risk of pregnancy complications was increased.
Collapse
Affiliation(s)
- Timothy B Niewold
- Departments of Medicine and Pathology, Colton Center for Autoimmunity, New York University School of Medicine, New York, NY
| | - Shilpi Mehta-Lee
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, New York University School of Medicine, New York, NY
| |
Collapse
|
32
|
de Sousa MJR, Ribeiro R, Syngelaki A, Nicolaides KH. First trimester combined screening in patients with systemic lupus erythematosus: impact of pre-analytical variables on risk assessment. Clin Rheumatol 2019; 38:1251-1255. [PMID: 30919147 DOI: 10.1007/s10067-019-04525-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/18/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND Prenatal diagnosis of fetal trisomy 21 and other chromosomal abnormalities is based on invasive tests, such as amniocentesis and chorionic villus sampling, which are carried out in women identified through screening as being at high risk for these abnormalities. The most widely used method of screening is the first-trimester combined test which utilizes maternal age, and measurements of fetal nuchal translucency thickness (NT) and maternal serum pregnancy-associated plasma protein-A (PAPP-A) and free β-human chorionic gonadotropin (hCG). OBJECTIVES To assess the influence of SLE on the levels of NT, PAPP-A, and β-hCG and whether any alterations in such levels may increase the rate of false positives and the subsequent number of invasive tests. METHOD This was a prospective first-trimester screening study for trisomies 21, 18, and 13 by a combination of maternal age, fetal nuchal translucency thickness, and serum PAPP-A and β-hCG at King's College Hospital, London, between March 2006 and February 2011. The study population included 47 cases with maternal SLE and 45,493 without SLE. The results of biomarkers in the SLE and non-SLE groups were compared. RESULTS In the SLE group, compared to the non-SLE group, there were no significant differences in median maternal age, fetal NT, or serum PAPP-A MoM, but serum free β-hCG MoM was increased (1.402, IQR 0.872-2.290 vs 0.994, IQR 0.676-1.508). CONCLUSION In first trimester screening for trisomies, the measured value of free ß-hCG should be adjusted for maternal SLE to avoid false positive results and overuse of invasive tests.
Collapse
Affiliation(s)
- Maria José Rego de Sousa
- Autoimmunity Unit, Centro de Medicina Laboratorial Germano de Sousa, R. Cupertino de Miranda, 1600-513, Lisbon, Portugal.
| | - Rita Ribeiro
- Autoimmunity Unit, Centro de Medicina Laboratorial Germano de Sousa, R. Cupertino de Miranda, 1600-513, Lisbon, Portugal
| | - Argyro Syngelaki
- Harris Birthright Research Center of Fetal Medicine, King's College Hospital, London, UK
| | - Kypros H Nicolaides
- Harris Birthright Research Center of Fetal Medicine, King's College Hospital, London, UK
| |
Collapse
|
33
|
Martínez-Bueno M, Alarcón-Riquelme ME. Exploring Impact of Rare Variation in Systemic Lupus Erythematosus by a Genome Wide Imputation Approach. Front Immunol 2019; 10:258. [PMID: 30863397 PMCID: PMC6399402 DOI: 10.3389/fimmu.2019.00258] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/29/2019] [Indexed: 01/31/2023] Open
Abstract
The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. Genome-wide association studies are therefore, underpowered to detect rare variation. We have used a combined approach of genome-wide-based imputation with a highly stringent sequence kernel association (SKAT) test and a case-control burden test. We identified 98 candidate genes containing rare variation that in aggregate show association with SLE many of which have recognized immunological function, but also function and expression related to relevant tissues such as the joints, skin, blood or central nervous system. In addition we also find that there is a significant enrichment of genes annotated for disease-causing mutations in the OMIM database, suggesting that in complex diseases such as SLE, such mutations may be involved in subtle or combined phenotypes or could accelerate specific organ abnormalities found in the disease. We here provide an important resource of candidate genes for SLE.
Collapse
Affiliation(s)
- Manuel Martínez-Bueno
- Department of Medical Genomics, GENYO, Center for Genomics and Oncological Research Pfizer, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- Unit of Chronic Inflammation, Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
34
|
Ghodke-Puranik Y, Imgruet M, Dorschner JM, Shrestha P, McCoy K, Kelly JA, Marion M, Guthridge JM, Langefeld CD, Harley JB, James JA, Sivils KL, Niewold TB. Novel genetic associations with interferon in systemic lupus erythematosus identified by replication and fine-mapping of trait-stratified genome-wide screen. Cytokine 2019; 132:154631. [PMID: 30685201 DOI: 10.1016/j.cyto.2018.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND/PURPOSE High serum interferon alpha (IFN-α) is an important heritable phenotype in systemic lupus erythematosus (SLE) which is involved in primary disease pathogenesis. High vs. low levels of IFN-α are associated with disease severity and account for some of the biological heterogeneity between SLE patients. The aim of the study was to replicate and fine-map previously detected genetic associations with serum IFN-α in SLE. METHODS We previously undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci identified in this screen were selected for follow up in a large independent cohort of 1370 SLE patients (703 European-ancestry, 432 African ancestry, and 235 Amerindian ancestry). Each ancestral background was analyzed separately, and ancestry-informative markers were used to control for ancestry and admixture. RESULTS We find a rare haplotype spanning the promoter region of EFNA5 that is strongly associated with serum IFN-α in both African-American and European-American SLE patients (OR = 3.0, p = 3.7 × 10-6). We also find SNPs in the PPM1H, PTPRM, and NRGN regions associated with IFN-α levels in European-American, Amerindian, and African-American SLE patients respectively. Many of these associations are within regulatory regions of the gene, suggesting an impact on transcription. CONCLUSION This study demonstrates the power of molecular sub-phenotypes to reveal genetic factors involved in complex autoimmune disease. The distinct associations observed in different ancestral backgrounds emphasize the heterogeneity of molecular pathogenesis in SLE.
Collapse
Affiliation(s)
- Yogita Ghodke-Puranik
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Molly Imgruet
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Kaci McCoy
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer A Kelly
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Miranda Marion
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Joel M Guthridge
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine and Cincinnati VA Medical Center, Cincinnati, OH, USA
| | - Judith A James
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kathy L Sivils
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Timothy B Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
35
|
Comprehensive assessment of the association between genes on JAK-STAT pathway (IFIH1, TYK2, IL-10) and systemic lupus erythematosus: a meta-analysis. Arch Dermatol Res 2018; 310:711-728. [DOI: 10.1007/s00403-018-1858-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 08/19/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022]
|
36
|
Detecting Rare Mutations with Heterogeneous Effects Using a Family-Based Genetic Random Field Method. Genetics 2018; 210:463-476. [PMID: 30104420 DOI: 10.1534/genetics.118.301266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/29/2018] [Indexed: 01/19/2023] Open
Abstract
The genetic etiology of many complex diseases is highly heterogeneous. A complex disease can be caused by multiple mutations within the same gene or mutations in multiple genes at various genomic loci. Although these disease-susceptibility mutations can be collectively common in the population, they are often individually rare or even private to certain families. Family-based studies are powerful for detecting rare variants enriched in families, which is an important feature for sequencing studies due to the heterogeneous nature of rare variants. In addition, family designs can provide robust protection against population stratification. Nevertheless, statistical methods for analyzing family-based sequencing data are underdeveloped, especially those accounting for heterogeneous etiology of complex diseases. In this article, we introduce a random field framework for detecting gene-phenotype associations in family-based sequencing studies, referred to as family-based genetic random field (FGRF). Similar to existing family-based association tests, FGRF could utilize within-family and between-family information separately or jointly to test an association. We demonstrate that FGRF has comparable statistical power with existing methods when there is no genetic heterogeneity, but can improve statistical power when there is genetic heterogeneity across families. The proposed method also shares the same advantages with the conventional family-based association tests (e.g., being robust to population stratification). Finally, we applied the proposed method to a sequencing data from the Minnesota Twin Family Study, and revealed several genes, including SAMD14, potentially associated with alcohol dependence.
Collapse
|
37
|
The genetics and molecular pathogenesis of systemic lupus erythematosus (SLE) in populations of different ancestry. Gene 2018; 668:59-72. [DOI: 10.1016/j.gene.2018.05.041] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/13/2018] [Indexed: 01/21/2023]
|
38
|
Abstract
The type I interferon pathway has been implicated in the pathogenesis of a number of rheumatic diseases, including systemic lupus erythematosus, Sjögren syndrome, myositis, systemic sclerosis, and rheumatoid arthritis. In normal immune responses, type I interferons have a critical role in the defence against viruses, yet in many rheumatic diseases, large subgroups of patients demonstrate persistent activation of the type I interferon pathway. Genetic variations in type I interferon-related genes are risk factors for some rheumatic diseases, and can explain some of the heterogeneity in type I interferon responses seen between patients within a given disease. Inappropriate activation of the immune response via Toll-like receptors and other nucleic acid sensors also contributes to the dysregulation of the type I interferon pathway in a number of rheumatic diseases. Theoretically, differences in type I interferon activity between patients might predict response to immune-based therapies, as has been demonstrated for rheumatoid arthritis. A number of type I interferon and type I interferon pathway blocking therapies are currently in clinical trials, the results of which are promising thus far. This Review provides an overview of the many ways in which the type I interferon system affects rheumatic diseases.
Collapse
Affiliation(s)
- Theresa L. Wampler Muskardin
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine and Pediatrics, New York University School of Medicine, New York, NY, USA
| |
Collapse
|
39
|
Zhao Q, Deng N, Chen S, Cui Y, Du X, Gu Z. Systemic lupus erythematosus is associated with negatively variable impacts on domains of sleep disturbances: a systematic review and meta-analysis. PSYCHOL HEALTH MED 2018; 23:685-697. [PMID: 29488396 DOI: 10.1080/13548506.2018.1442011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sleep disturbances are common in systemic lupus erythematosus (SLE), but the features of sleep disturbances are not well understood. The aim of this study was to identify the impact of SLE on specific sleep quality domains and to determine its prevalence and associations. We performed a systematic review and meta-analysis to compare the sleep outcomes of individuals with SLE and healthy controls. PubMed, MEDLINE, EMBASE, Cochrane Library, Web of Science CNKI, VIP, CNKI and Wanfang database were searched to find the published literatures (from these databases established to May 2017). Studies were screened according to inclusion and exclusion criteria and the qualities of included studies were evaluated. The data was analyzed using Revman5.3 software. Score of the Pittsburgh Sleep Quality Index (PSQI) scoring system was used as the outcome measurement, and mean differences (MD) with 95% confidence intervals (CI) were calculated. Five studies were included, including 350 SLE and 1396 healthy controls. A total of 5 studies including 827 patients were eligible for inclusion in the systematic review and meta-analysis. In this meta-analysis, each domain of the PSQI score: subjective sleep quality (MD, .58; 95% CI, .26, .89), sleep latency(MD, .47; 95% CI, .21, .73), sleep duration (MD, .36; 95% CI, .13, .58), habitual sleep efficiency (MD, .58; 95% CI, .32, .84),sleep disorders (MD, .56; 95% CI, .34, .77), use of sleep medication (MD, .56; 95% CI, .33, .80), daytime dysfunction (MD, .57; 95% CI, .11, 1.04) and the global score (MD, 3.59; 95% CI, 1.37, 5.80) were higher in SLE women than healthy controls. Furthermore, subjective sleep quality and habitual sleep efficiency were most severely affected especially. It demonstrated that targeted interventions should be done to improve their sleep quality. Early recognition and appropriate intervention are essential to reduce the negative impact of sleep disturbances on the patient's sleep quality and outcome of their disease.
Collapse
Affiliation(s)
- Qian Zhao
- a School of Nursing , Nantong University , Nantong , China.,b Department of Nursing , The Affiliated Hospital of Nantong University , Nantong , China
| | - Nan Deng
- a School of Nursing , Nantong University , Nantong , China
| | - Shengnan Chen
- a School of Nursing , Nantong University , Nantong , China
| | - Yafei Cui
- a School of Nursing , Nantong University , Nantong , China
| | - Xian Du
- a School of Nursing , Nantong University , Nantong , China
| | - Zhifeng Gu
- b Department of Nursing , The Affiliated Hospital of Nantong University , Nantong , China
| |
Collapse
|
40
|
|
41
|
Ghodke-Puranik Y, Dorschner JM, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Eliopoulos E, Zervou MI, Goulielmos GN, Jensen MA, Niewold TB. Lupus-Associated Functional Polymorphism in PNP Causes Cell Cycle Abnormalities and Interferon Pathway Activation in Human Immune Cells. Arthritis Rheumatol 2017; 69:2328-2337. [PMID: 28859258 DOI: 10.1002/art.40304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 08/25/2017] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is frequently characterized by activation of the type I interferon (IFN) pathway. We previously observed that a missense single-nucleotide polymorphism (rs1049564) in the purine nucleoside phosphorylase (PNP) gene was associated with high levels of IFN in SLE. PNP is a key enzyme involved in purine metabolism. In this study, we performed functional follow-up of this polymorphism in human cells. METHODS Type I IFN was measured in patient sera, using a reporter cell assay. Structural modeling of the PNP variant was performed using PyMOL software. PNP messenger RNA (mRNA) and protein levels and type I IFN-induced gene expression were measured in lymphoblastoid cell lines with known PNP rs1049564 genotypes. The cell cycle was assayed using flow cytometry. RESULTS Structural modeling indicated no major disruption in folding related to rs1049564. We observed that homozygous rs1049564 TT lymphoblastoid cells had decreased PNP mRNA expression and protein levels, and that cells with the TT genotype had reduced PNP enzymatic activity even when the amount of PNP was controlled. Cells with the TT genotype had a 2-fold increase in S-phase block as compared with cells with the homozygous CC phenotype. The S-phase block could be pharmacologically reversed with hypoxanthine and adenosine, supporting the notion that relative PNP deficiency is the cause of the S-phase block. Type I IFN-induced transcripts were increased in a dose-response manner related to the rs1049564 T allele, at both baseline and after type I IFN stimulation. CONCLUSION The PNP rs1049564 T allele is a loss-of-function variant that induces S-phase block and IFN pathway activation in lymphocytes. The S-phase block could be rescued in our in vitro experiments, suggesting the potential for personalized treatment.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Mark A Jensen
- New York University School of Medicine, New York, New York
| | | |
Collapse
|
42
|
Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle. Animal 2017; 12:205-214. [PMID: 28701235 DOI: 10.1017/s1751731117001562] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers. The environment was defined as contemporary group means of tick counts, since they seemed to be the most appropriate entities to describe the environmental gradient in beef cattle. A total of 4363 animals having tick counts (n=10 673) originated from 197 sires and 3966 dams were used. Genotypes were acquired on 3591 of these cattle. From top 1% SNPs (410) having the greatest effects in each environment, 75 were consistently relevant in all environments, which indicated SNP by environment interaction. The outliers/significant SNPs were mapped on chromosomes 1, 2, 5, 6, 7, 9, 11, 13, 14, 15, 16, 18, 21, 23, 24, 26 and 28, and potential candidate genes were detected across environments. The presence of SNP by environment interaction for tick resistance indicates that genetic expression of resistance depends upon tick burden. Markers with major portion of genetic variance explained across environments appeared to be close to genes with different direct or indirect functions related to immune system, inflammatory process and mechanisms of tissue destruction/repair, such as energy metabolism and cell differentiation.
Collapse
|
43
|
Hoffman RW, Merrill JT, Alarcón-Riquelme MME, Petri M, Dow ER, Nantz E, Nisenbaum LK, Schroeder KM, Komocsar WJ, Perumal NB, Linnik MD, Airey DC, Liu Y, Rocha GV, Higgs RE. Gene Expression and Pharmacodynamic Changes in 1,760 Systemic Lupus Erythematosus Patients From Two Phase III Trials of BAFF Blockade With Tabalumab. Arthritis Rheumatol 2017; 69:643-654. [PMID: 27723281 PMCID: PMC6585752 DOI: 10.1002/art.39950] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022]
Abstract
Objective To characterize baseline gene expression and pharmacodynamically induced changes in whole blood gene expression in 1,760 systemic lupus erythematosus (SLE) patients from 2 phase III, 52‐week, randomized, placebo‐controlled, double‐blind studies in which patients were treated with the BAFF‐blocking IgG4 monoclonal antibody tabalumab. Methods Patient samples were obtained from SLE patients from the ILLUMINATE‐1 and ILLUMINATE‐2 studies, and control samples were obtained from healthy donors. Blood was collected in Tempus tubes at baseline, week 16, and week 52. RNA was analyzed using Affymetrix Human Transcriptome Array 2.0 and NanoString. Results At baseline, expression of the interferon (IFN) response gene was elevated in patients compared with controls, with 75% of patients being positive for this IFN response gene signature. There was, however, substantial heterogeneity of IFN response gene expression and complex relationships among gene networks. The IFN response gene signature was a predictor of time to disease flare, independent of anti–double‐stranded DNA (anti‐dsDNA) antibody and C3 and C4 levels, and overall disease activity. Pharmacodynamically induced changes in gene expression following tabalumab treatment were extensive, occurring predominantly in B cell–related and immunoglobulin genes, and were consistent with other pharmacodynamic changes including anti‐dsDNA antibody, C3, and immunoglobulin levels. Conclusion SLE patients demonstrated increased expression of an IFN response gene signature (75% of patients had an elevated IFN response gene signature) at baseline in ILLUMINATE‐1 and ILLUMINATE‐2. Substantial heterogeneity of gene expression was detected among individual patients and in gene networks. The IFN response gene signature was an independent risk factor for future disease flares. Pharmacodynamic changes in gene expression were consistent with the mechanism of BAFF blockade by tabalumab.
Collapse
Affiliation(s)
| | | | - Marta M E Alarcón-Riquelme
- Oklahoma Medical Research Foundation, Oklahoma City, and Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | | | - Ernst R Dow
- Eli Lilly and Company, Indianapolis, Indiana
| | - Eric Nantz
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | | | | | | | | | | - Yushi Liu
- Eli Lilly and Company, Indianapolis, Indiana
| | | | | |
Collapse
|
44
|
Zharkova O, Celhar T, Cravens PD, Satterthwaite AB, Fairhurst AM, Davis LS. Pathways leading to an immunological disease: systemic lupus erythematosus. Rheumatology (Oxford) 2017; 56:i55-i66. [PMID: 28375453 PMCID: PMC5410978 DOI: 10.1093/rheumatology/kew427] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Indexed: 12/25/2022] Open
Abstract
SLE is a chronic autoimmune disease caused by perturbations of the immune system. The clinical presentation is heterogeneous, largely because of the multiple genetic and environmental factors that contribute to disease initiation and progression. Over the last 60 years, there have been a number of significant leaps in our understanding of the immunological mechanisms driving disease processes. We now know that multiple leucocyte subsets, together with inflammatory cytokines, chemokines and regulatory mediators that are normally involved in host protection from invading pathogens, contribute to the inflammatory events leading to tissue destruction and organ failure. In this broad overview, we discuss the main pathways involved in SLE and highlight new findings. We describe the immunological changes that characterize this form of autoimmunity. The major leucocytes that are essential for disease progression are discussed, together with key mediators that propagate the immune response and drive the inflammatory response in SLE.
Collapse
Affiliation(s)
- Olga Zharkova
- Singapore Immunology Network, 8A Biomedical Grove, Immunos.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Teja Celhar
- Singapore Immunology Network, 8A Biomedical Grove, Immunos
| | | | - Anne B Satterthwaite
- Department of Immunology.,The Rheumatic Diseases Division, Department of Internal Medicine, UT Southwestern Medical Center at Dallas, TX, USA
| | - Anna-Marie Fairhurst
- Singapore Immunology Network, 8A Biomedical Grove, Immunos.,School of Biological Sciences, Nanyang Technological University, Singapore.,Department of Immunology
| | - Laurie S Davis
- The Rheumatic Diseases Division, Department of Internal Medicine, UT Southwestern Medical Center at Dallas, TX, USA
| |
Collapse
|
45
|
Faridi MH, Khan SQ, Zhao W, Lee HW, Altintas MM, Zhang K, Kumar V, Armstrong AR, Carmona-Rivera C, Dorschner JM, Schnaith AM, Li X, Ghodke-Puranik Y, Moore E, Purmalek M, Irizarry-Caro J, Zhang T, Day R, Stoub D, Hoffmann V, Khaliqdina SJ, Bhargava P, Santander AM, Torroella-Kouri M, Issac B, Cimbaluk DJ, Zloza A, Prabhakar R, Deep S, Jolly M, Koh KH, Reichner JS, Bradshaw EM, Chen J, Moita LF, Yuen PS, Li Tsai W, Singh B, Reiser J, Nath SK, Niewold TB, Vazquez-Padron RI, Kaplan MJ, Gupta V. CD11b activation suppresses TLR-dependent inflammation and autoimmunity in systemic lupus erythematosus. J Clin Invest 2017; 127:1271-1283. [PMID: 28263189 PMCID: PMC5373862 DOI: 10.1172/jci88442] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
Genetic variations in the ITGAM gene (encoding CD11b) strongly associate with risk for systemic lupus erythematosus (SLE). Here we have shown that 3 nonsynonymous ITGAM variants that produce defective CD11b associate with elevated levels of type I interferon (IFN-I) in lupus, suggesting a direct link between reduced CD11b activity and the chronically increased inflammatory status in patients. Treatment with the small-molecule CD11b agonist LA1 led to partial integrin activation, reduced IFN-I responses in WT but not CD11b-deficient mice, and protected lupus-prone MRL/Lpr mice from end-organ injury. CD11b activation reduced TLR-dependent proinflammatory signaling in leukocytes and suppressed IFN-I signaling via an AKT/FOXO3/IFN regulatory factor 3/7 pathway. TLR-stimulated macrophages from CD11B SNP carriers showed increased basal expression of IFN regulatory factor 7 (IRF7) and IFN-β, as well as increased nuclear exclusion of FOXO3, which was suppressed by LA1-dependent activation of CD11b. This suggests that pharmacologic activation of CD11b could be a potential mechanism for developing SLE therapeutics.
Collapse
Affiliation(s)
- Mohd Hafeez Faridi
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Samia Q. Khan
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Wenpu Zhao
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Ha Won Lee
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Mehmet M. Altintas
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Kun Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Vinay Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Andrew R. Armstrong
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | | | - Xiaobo Li
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | | | - Erica Moore
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Monica Purmalek
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Jorge Irizarry-Caro
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Tingting Zhang
- Department of Chemistry, University of Miami, Coral Gables, Florida, USA
| | - Rachael Day
- Department of Chemistry and Biochemistry, Dordt College, Sioux Center, Iowa, USA
| | - Darren Stoub
- Department of Chemistry and Biochemistry, Dordt College, Sioux Center, Iowa, USA
| | - Victoria Hoffmann
- Pathology Branch, Division of Veterinary Resources, Office of the Director, NIH, Bethesda, Maryland, USA
| | | | - Prachal Bhargava
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Ana M. Santander
- Sylvester Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Marta Torroella-Kouri
- Sylvester Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Biju Issac
- Sylvester Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - David J. Cimbaluk
- Department of Pathology, Rush University Medical School, Chicago, Illinois, USA
| | - Andrew Zloza
- Section of Surgical Oncology Research, Rutgers Cancer Institute of New Jersey, and Department of Surgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida, USA
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Meenakshi Jolly
- Division of Rheumatology, Department of Internal Medicine, Rush University Medical School, Chicago, Illinois, USA
| | - Kwi Hye Koh
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Jonathan S. Reichner
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Elizabeth M. Bradshaw
- Division of Immunology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - JianFeng Chen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Luis F. Moita
- Innate Immune and Inflammation Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Peter S. Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Wanxia Li Tsai
- Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Bhupinder Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jochen Reiser
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | | | | | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | - Vineet Gupta
- Drug Discovery Center, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| |
Collapse
|
46
|
Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet 2017; 13:e1006641. [PMID: 28263993 PMCID: PMC5358891 DOI: 10.1371/journal.pgen.1006641] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 03/20/2017] [Accepted: 02/17/2017] [Indexed: 12/15/2022] Open
Abstract
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease. Macrophages are immune cells that form the first line of defense against pathogens, but also mediate tissue damage in inflammatory disease. Macrophages initiate inflammation by recognising and responding to components of bacterial cells. Macrophages of the wall of the gut are constantly replenished from the blood. Upon entering the intestine, newly-arrived cells modulate their response to stimuli derived from the bacteria in the wall of the gut. This process fails in chronic inflammatory bowel diseases (IBD). Both the major forms of IBD, Crohn’s disease and ulcerative colitis, run in families. The inheritance is complex, involving more than 200 different regions of the genome. We hypothesised that the genetic risk of IBD is associated specifically with altered regulation of genes that control the development of macrophages. In this study, we used the comprehensive transcriptome dataset produced by the FANTOM5 consortium to identify the sets of promoters and enhancers that are involved in adaptation of macrophages to the gut wall, their response to bacterial stimuli, and how their functions are integrated. A reanalysis of published genome-wide association data based upon regulated genes in monocytes as candidates strongly supports the view that susceptibility to IBD arises from a primary defect in macrophage differentiation.
Collapse
|
47
|
Defining biological subsets in systemic lupus erythematosus: progress toward personalized therapy. Pharmaceut Med 2017; 31:81-88. [PMID: 28827978 DOI: 10.1007/s40290-017-0178-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous disease with respect to disease severity, response to treatment, and organ damage. The pathogenesis of SLE includes immunological mechanisms which are driven by both genetic and environmental factors. There are clear differences in the pathogenesis of SLE between patients of different ancestral backgrounds, including differences in genetic risk factors, immunological parameters, and clinical manifestations. Patients with high vs. low levels of type I interferon (IFN) in circulation represents one major biological subset within SLE, and these two groups of patients are present in all ancestral backgrounds. Genetic factors, autoantibodies, and levels of other cytokines all differ between high and low IFN patients. This distinction has also been important in predicting response to treatment with anti-type I IFN therapies, providing a precedent in SLE for biological subsets predicting treatment response. This review will highlight some recent developments in defining biological subsets of SLE based on disease pathophysiology, and the idea that improved knowledge of disease heterogeneity will inform our efforts to personalize therapy in this disease.
Collapse
|
48
|
Frequency of TNFA, INFG, and IL10 Gene Polymorphisms and Their Association with Malaria Vivax and Genomic Ancestry. Mediators Inflamm 2016; 2016:5168363. [PMID: 27999453 PMCID: PMC5143728 DOI: 10.1155/2016/5168363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in cytokine genes can alter the production of these proteins and consequently affect the immune response. The trihybrid heterogeneity of the Brazilian population is characterized as a condition for the use of ancestry informative markers. The objective of this study was to evaluate the frequency of -1031T>C, -308G>A and -238G>A TNFA, +874 A>T IFNG and -819C>T, and -592C>A IL10 gene polymorphisms and their association with malaria vivax and genomic ancestry. Samples from 90 vivax malaria-infected individuals and 51 noninfected individuals from northern Brazil were evaluated. Genotyping was carried out by using ASO-PCR or PCR/RFLP. The genomic ancestry of the individuals was classified using 48 insertion/deletion polymorphism biallelic markers. There were no differences in the proportions of African, European, and Native American ancestry between men and women. No significant association was observed for the allele and genotype frequencies of the 6 SNPs between malaria-infected and noninfected individuals. However, there was a trend toward decreasing the frequency of individuals carrying the TNF-308A allele with the increasing proportion of European ancestry. No ethnic-specific SNPs were identified, and there was no allelic or genotype association with susceptibility or resistance to vivax malaria. Understanding the genomic mechanisms by which ancestry influences this association is critical and requires further study.
Collapse
|
49
|
Abstract
PURPOSE OF REVIEW The field of systemic lupus erythematosus (SLE) genetics has been advancing rapidly in recent years. This review will summarize recent advances in SLE genetics. RECENT FINDINGS Genome-wide-association and follow-up studies have greatly expanded the list of associated polymorphisms, and much current work strives to integrate these polymorphisms into immune system biology and the pathogenic mediators involved in the disease. This review covers some current areas of interest, including genetic studies in non-European SLE patient populations, studies of pathogenic immune system subphenotypes such as type I interferon and autoantibodies, and a rapidly growing body of work investigating the functional consequences of the genetic polymorphisms associated with SLE. SUMMARY These studies provide a fascinating window into human SLE disease biology. As the work proceeds from genetic association signal to altered human biology, we move closer to tailoring interventions based upon an individual's genetic substrate.
Collapse
|
50
|
Several Critical Cell Types, Tissues, and Pathways Are Implicated in Genome-Wide Association Studies for Systemic Lupus Erythematosus. G3-GENES GENOMES GENETICS 2016; 6:1503-11. [PMID: 27172182 PMCID: PMC4889647 DOI: 10.1534/g3.116.027326] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We aimed to elucidate the cell types, tissues, and pathways influenced by common variants in systemic lupus erythematosus (SLE). We applied a nonparameter enrichment statistical approach, termed SNPsea, in 181 single nucleotide polymorphisms (SNPs) that have been identified to be associated with the risk of SLE through genome-wide association studies (GWAS) in Eastern Asian and Caucasian populations, to manipulate the critical cell types, tissues, and pathways. In the two most significant cells’ findings (B lymphocytes and CD14+ monocytes), we subjected the GWAS association evidence in the Han Chinese population to an enrichment test of expression quantitative trait locus (QTL) sites and DNase I hypersensitivity, respectively. In both Eastern Asian and Caucasian populations, we observed that the expression level of SLE GWAS implicated genes was significantly elevated in xeroderma pigentosum B cells (P ≤ 1.00 × 10−6), CD14+ monocytes (P ≤ 2.74 × 10−4) and CD19+ B cells (P ≤ 2.00 × 10−6), and plasmacytoid dendritic cells (pDCs) (P ≤ 9.00 × 10−6). We revealed that the SLE GWAS-associated variants were more likely to reside in expression QTL in B lymphocytes (q1/q0 = 2.15, P = 1.23 × 10−44) and DNase I hypersensitivity sites (DHSs) in CD14+ monocytes (q1/q0 = 1.41, P = 0.08). We observed the common variants affected the risk of SLE mostly through by regulating multiple immune system processes and immune response signaling. This study sheds light on several immune cells and responses, as well as the regulatory effect of common variants in the pathogenesis of SLE.
Collapse
|