scholarly journals P145 Computational analysis of neutrophil gene expression reveals activation signatures associated with DMARD refractory rheumatoid arthritis

Rheumatology ◽  
2021 ◽  
Vol 60 (Supplement_1) ◽  
Author(s):  
Michele Fresneda Alarcon ◽  
Eva Caamano-Gutierrez ◽  
Philipp Antczak ◽  
Robert J Moots ◽  
Helen L Wright
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Amino Acid ◽  
Gene Networks ◽  
Type I Interferon ◽  
Computational Modelling ◽  
Gene Expression Signature ◽  
Interferon Response ◽  
Type I ◽  
Healthy Controls

Abstract Background/Aims  Neutrophils contribute to disease pathology in inflammatory diseases including rheumatoid arthritis (RA). Activated RA neutrophils release ROS and proteases which damage joints, and produce neutrophil extracellular traps (NETs) that expose citrullinated nuclear proteins leading to the development of ACPA auto-antibodies. We previously described an altered gene expression signature in RA patients compared to healthy controls. This aim of this work was to use computational modelling of neutrophil transcriptomes to provide novel insight into the physiological factors controlling neutrophil phenotype in RA. Methods  RNA from peripheral blood neutrophils (RA patients (DAS28>5.1, cohort 1 n = 23, cohort 2 n = 53), healthy controls (n = 11)) was sequenced using RNAseq. Reads were mapped to the human genome (hg38) using Tophat2 and read counts generated using featureCounts. Partial least squares discriminant analysis (PLS-DA) was carried out using mixOmics (with random sampling and ‘leave one out’ cross-validation). Gene expression network analysis was carried out using tmod, ARACNE2 and GALGO. Gene networks were visualised using Cytoscape. Functional annotation was carried out using Ingenuity Pathway Analysis (IPA) and DAVID. Results  PLS-DA modelling discriminated RA and HC neutrophil transcriptomes with an F1 score of 98.2% +/- 1.6% over 5 repetitions using a model with 1 component. Blood transcriptional modular (tmod) enrichment analysis of gene expression in RA and HC neutrophils from cohort 1 identified the gene networks activated in RA and absent in HC as: myeloid cells activated via NFκB, innate antiviral response, type I interferon response, inflammasome receptors and cell signalling (FDR<0.05, AUC >0.8). Cell cycle and growth arrest was also considerably more enriched in RA compared to HC (RA AUC=0.82, HC AUC=0.57). Activation of type I interferon and inflammasome signalling pathways in cohort 1 was confirmed by IPA and correlated closely with data from a second cohort of RA patients (cohort 2). ARACNE2 identified five major gene modules activated in RA neutrophils (MI threshold 0.5, p < 10-20). IPA and DAVID predicted that Module 1 gene networks regulated amino acid, nucleic acid, carbohydrate and lipid metabolism as well as initiation of gene expression. Module M2 contained a network of genes regulated by integrins and cytokine receptors (e.g. IL-8, JAK/STAT, TNF/NFκB). Module 3 also contained genes activated by NFκB as well as by AMP-protein kinase. Module M4 genes were regulated by activation of type I interferon receptors and pattern recognition receptors (e.g. IRFs, STATs). Module M5 genes regulated amino acid metabolism. Multivariate modelling using GALGO identified genes that predict clinical characteristics, including genes involved in NFκB signalling, apoptosis and kinase activation which were associated with disease activity (DAS28), and cellular stress response genes and chromatin modification that was associated with raised inflammatory markers (ESR, CRP). Conclusion  The results of the computational analyses are currently being validated experimentally. Disclosure  M. Fresneda Alarcon: None. E. Caamano-Gutierrez: None. P. Antczak: None. R.J. Moots: None. H.L. Wright: Grants/research support; H.W. has received funding from Versus Arthritis and the Masonic Charitable Fund.

scholarly journals Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells

2018 ◽  
Author(s):  
Shaylynn Miller ◽  
Patrick Coit ◽  
Elizabeth Gensterblum-Miller ◽  
Paul Renauer ◽  
Nathan C Kilian ◽  
...  
Keyword(s):  
Dna Methylation ◽  
T Cells ◽  
T Cell ◽  
Cd8 T Cells ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Mrna Levels ◽  
Healthy Controls ◽  
Genome Wide

AbstractObjectiveWe examined genome-wide DNA methylation changes in CD8+ T cells from lupus patients and controls, and investigated the functional relevance of some of these changes in lupus.MethodsGenome-wide DNA methylation of lupus and age, sex, and ethnicity-matched control CD8+ T cells was measured using the Infinium MethylationEPIC arrays. Measurement of relevant cell subsets was performed via flow cytometry. Gene expression was quantified by qPCR.ResultsLupus CD8+ T cells had 188 hypomethylated CpG sites compared to healthy matched controls. Among the most hypomethylated were sites associated with HLA-DRB1. Genes involved in the type-I interferon response, including STAT1, were also found to be hypomethylated. IFNα upregulated HLA-DRB1 expression on lupus but not control CD8+ T cells. Lupus and control CD8+ T cells significantly increased STAT1 mRNA levels after treatment with IFNα. The expression of CIITA, a key interferon/STAT1 dependent MHC-class II regulator, is induced by IFNα in lupus CD8+ T cells, but not healthy controls. Co-incubation of naïve CD4+ T cells with IFNα-treated CD8+ T cells led to CD4+ T cell activation, determined by increased expression of CD69, in lupus patients but not in healthy controls. This can be blocked by neutralizing antibodies targeting HLA-DR.ConclusionsLupus CD8+ T cells are epigenetically primed to respond to type-I interferon. We describe an HLA-DRB1+ CD8+ T cell subset that can be induced by IFNα in lupus patients. A possible pathogenic role for CD8+ T cells in lupus that is dependent upon a high type-I interferon environment and epigenetic priming warrants further characterization.

scholarly journals Impact of Intermediate Hyperglycemia and Diabetes on Immune Dysfunction in Tuberculosis

2020 ◽  
Author(s):  
Clare Eckold ◽  
Vinod Kumar ◽  
January Weiner ◽  
Bachti Alisjahbana ◽  
Anca-Lelia Riza ◽  
...  
Keyword(s):  
Gene Expression ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Expression Change ◽  
Tb Treatment ◽  
Increased Risk ◽  
Patients With Diabetes ◽  
Transcriptomic Signature ◽  
Interferon Responses

Abstract Background People with diabetes have an increased risk of developing active tuberculosis (TB) and are more likely to have poor TB-treatment outcomes, which may impact on control of TB as the prevalence of diabetes is increasing worldwide. Blood transcriptomes are altered in patients with active TB relative to healthy individuals. The effects of diabetes and intermediate hyperglycemia (IH) on this transcriptomic signature were investigated to enhance understanding of immunological susceptibility in diabetes-TB comorbidity. Methods Whole blood samples were collected from active TB patients with diabetes (glycated hemoglobin [HbA1c] ≥6.5%) or IH (HbA1c = 5.7% to <6.5%), TB-only patients, and healthy controls in 4 countries: South Africa, Romania, Indonesia, and Peru. Differential blood gene expression was determined by RNA-seq (n = 249). Results Diabetes increased the magnitude of gene expression change in the host transcriptome in TB, notably showing an increase in genes associated with innate inflammatory and decrease in adaptive immune responses. Strikingly, patients with IH and TB exhibited blood transcriptomes much more similar to patients with diabetes-TB than to patients with only TB. Both diabetes-TB and IH-TB patients had a decreased type I interferon response relative to TB-only patients. Conclusions Comorbidity in individuals with both TB and diabetes is associated with altered transcriptomes, with an expected enhanced inflammation in the presence of both conditions, but also reduced type I interferon responses in comorbid patients, suggesting an unexpected uncoupling of the TB transcriptome phenotype. These immunological dysfunctions are also present in individuals with IH, showing that altered immunity to TB may also be present in this group. The TB disease outcomes in individuals with IH diagnosed with TB should be investigated further.

scholarly journals Dynamics of the Type I Interferon Response During Immunosuppressive Therapy in Rheumatoid Arthritis

2019 ◽  
Vol 10 ◽  
Author(s):  
Tamarah D. de Jong ◽  
Tanja Snoek ◽  
Elise Mantel ◽  
Conny J. van der Laken ◽  
Ronald F. van Vollenhoven ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Immunosuppressive Therapy ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I

scholarly journals Suppression of Type I Interferon Signaling by E1A via RuvBL1/Pontin

2017 ◽  
Vol 91 (8) ◽  
Author(s):  
Oladunni Olanubi ◽  
Jasmine Rae Frost ◽  
Sandi Radko ◽  
Peter Pelka
Keyword(s):  
Gene Expression ◽  
Cellular Response ◽  
Type I Interferon ◽  
Early Gene ◽  
Interferon Response ◽  
Type I ◽  
Dependent Manner ◽  
Interferon Signaling ◽  
Interferon Pathway ◽  
Regulated Promoters

ABSTRACT Suppression of interferon signaling is of paramount importance to a virus. Interferon signaling significantly reduces or halts the ability of a virus to replicate; therefore, viruses have evolved sophisticated mechanisms that suppress activation of the interferon pathway or responsiveness of the infected cell to interferon. Adenovirus has multiple modes of inhibiting the cellular response to interferon. Here, we report that E1A, previously shown to regulate interferon signaling in multiple ways, inhibits interferon-stimulated gene expression by modulating RuvBL1 function. RuvBL1 was previously shown to affect type I interferon signaling. E1A binds to RuvBL1 and is recruited to RuvBL1-regulated promoters in an interferon-dependent manner, preventing their activation. Depletion of RuvBL1 impairs adenovirus growth but does not appear to significantly affect viral protein expression. Although RuvBL1 has been shown to play a role in cell growth, its depletion had no effect on the ability of the virus to replicate its genome or to drive cells into S phase. E1A was found to bind to RuvBL1 via the C terminus of E1A, and this interaction was important for suppression of interferon-stimulated gene transcriptional activation and recruitment of E1A to interferon-regulated promoters. Here, we report the identification of RuvBL1 as a new target for adenovirus in its quest to suppress the interferon response. IMPORTANCE For most viruses, suppression of the interferon signaling pathway is crucial to ensure a successful replicative cycle. Human adenovirus has evolved several different mechanisms that prevent activation of interferon or the ability of the cell to respond to interferon. The viral immediate-early gene E1A was previously shown to affect interferon signaling in several different ways. Here, we report a novel mechanism reliant on RuvBL1 that E1A uses to prevent activation of interferon-stimulated gene expression following infection or interferon treatment. This adds to the growing knowledge of how viruses are able to inhibit interferon and identifies a novel target used by adenovirus for modulation of the cellular interferon pathway.

scholarly journals Hypomethylation of STAT1 and HLA-DRB1 is associated with type-I interferon-dependent HLA-DRB1 expression in lupus CD8+ T cells

2019 ◽  
Vol 78 (4) ◽  
pp. 519-528 ◽  
Author(s):  
Shaylynn Miller ◽  
Pei-Suen Tsou ◽  
Patrick Coit ◽  
Elizabeth Gensterblum-Miller ◽  
Paul Renauer ◽  
...  
Keyword(s):  
Dna Methylation ◽  
T Cells ◽  
T Cell ◽  
Cd8 T Cells ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Mrna Levels ◽  
Healthy Controls ◽  
Genome Wide

ObjectiveWe examined genome-wide DNA methylation changes in CD8+ T cells from patients with lupus and controls and investigated the functional relevance of some of these changes in lupus.MethodsGenome-wide DNA methylation of lupus and age, sex and ethnicity-matched control CD8+ T cells was measured using the Infinium MethylationEPIC arrays. Measurement of relevant cell subsets was performed via flow cytometry. Gene expression was quantified by qPCR. Inhibiting STAT1 and CIITA was performed using fludarabine and CIITA siRNA, respectively.ResultsLupus CD8+ T cells had 188 hypomethylated CpG sites compared with healthy matched controls. Among the most hypomethylated were sites associated with HLA-DRB1. Genes involved in the type-I interferon response, including STAT1, were also found to be hypomethylated. IFNα upregulated HLA-DRB1 expression on lupus but not control CD8+ T cells. Lupus and control CD8+ T cells significantly increased STAT1 mRNA levels after treatment with IFNα. The expression of CIITA, a key interferon/STAT1 dependent MHC-class II regulator, is induced by IFNα in lupus CD8+ T cells, but not healthy controls. CIITA knockdown and STAT1 inhibition experiments revealed that HLA-DRB1 expression in lupus CD8+ T cells is dependent on CIITA and STAT1 signalling. Coincubation of naïve CD4+ T cells with IFNα-treated CD8+ T cells led to CD4+ T cell activation, determined by increased expression of CD69 and cytokine production, in patients with lupus but not in healthy controls. This can be blocked by neutralising antibodies targeting HLA-DR.ConclusionsLupus CD8+ T cells are epigenetically primed to respond to type-I interferon. We describe an HLA-DRB1+ CD8+ T cell subset that can be induced by IFNα in patients with lupus. A possible pathogenic role for CD8+ T cells in lupus that is dependent on a high type-I interferon environment and epigenetic priming warrants further characterisation.

scholarly journals Importance of Correlation between Gene Expression Levels: Application to the Type I Interferon Signature in Rheumatoid Arthritis

PLoS ONE ◽  
2011 ◽  
Vol 6 (10) ◽  
pp. e24828 ◽  
Author(s):  
Frédéric Reynier ◽  
Fabien Petit ◽  
Malick Paye ◽  
Fanny Turrel-Davin ◽  
Pierre-Emmanuel Imbert ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Type I Interferon ◽  
Type I ◽  
Interferon Signature ◽  
Expression Levels ◽  
Gene Expression Levels

scholarly journals Interferon- and STING-independent induction of type I interferon stimulated genes during fractionated irradiation

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Ruben S. A. Goedegebuure ◽  
Esther A. Kleibeuker ◽  
Francesca M. Buffa ◽  
Kitty C. M. Castricum ◽  
Syed Haider ◽  
...  
Keyword(s):  
Gene Expression ◽  
Esophageal Cancer ◽  
Cancer Patients ◽  
Cell Lines ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Type I Interferon ◽  
Interferon Response ◽  
Type I ◽  
Fractionated Irradiation

Abstract Background Improvement of radiotherapy efficacy requires better insight in the dynamic responses that occur during irradiation. Here, we aimed to identify the molecular responses that are triggered during clinically applied fractionated irradiation. Methods Gene expression analysis was performed by RNAseq or microarray analysis of cancer cells or xenograft tumors, respectively, subjected to 3–5 weeks of 5 × 2 Gy/week. Validation of altered gene expression was performed by qPCR and/or ELISA in multiple cancer cell lines as well as in pre- and on-treatment biopsies from esophageal cancer patients (NCT02072720). Targeted protein inhibition and CRISPR/Cas-induced gene knockout was used to analyze the role of type I interferons and cGAS/STING signaling pathway in the molecular and cellular response to fractionated irradiation. Results Gene expression analysis identified type I interferon signaling as the most significantly enriched biological process induced during fractionated irradiation. The commonality of this response was confirmed in all irradiated cell lines, the xenograft tumors and in biopsies from esophageal cancer patients. Time-course analyses demonstrated a peak in interferon-stimulated gene (ISG) expression within 2–3 weeks of treatment. The response was accompanied by a variable induction of predominantly interferon-beta and/or -lambda, but blocking these interferons did not affect ISG expression induction. The same was true for targeted inhibition of the upstream regulatory STING protein while knockout of STING expression only delayed the ISG expression induction. Conclusions Collectively, the presented data show that clinically applied fractionated low-dose irradiation can induce a delayed type I interferon response that occurs independently of interferon expression or STING signaling. These findings have implications for current efforts that aim to target the type I interferon response for cancer treatment.

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