TNF induced inflammatory transcription dynamics and epigenetic changes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638409 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11968772_1.fastq.gz | Fastqsanger.gz | |||
| SRR11968772_2.fastq.gz | Fastqsanger.gz | |||
| SRR11968773_1.fastq.gz | Fastqsanger.gz | |||
| SRR11968773_2.fastq.gz | Fastqsanger.gz | |||
| SRR12413947.fastq.gz | Fastqsanger.gz |
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Project description:TNF can induce inflammatory responses in cells, including transcriptional and epigenetic changes. To investigate the long-term influence of TNF stimulation on epigenetic modifications, we did transcriptomic and epigenomic profiling of TNF-treated cells with various time length or stages.
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Project description:TNF is a key inflammatory cytokine that warns recipient cells of a nearby infection or tissue damage. Acute exposure to TNF activates characteristic oscillatory dynamics of the transcription factor NFκB and induces a characteristic gene expression program; these are distinct from the responses of cells directly exposed to pathogen-associated molecular patterns (PAMPs). Here we report that tonic TNF exposure is critical for safeguarding TNF’s specific functions. In the absence of tonic TNF conditioning, acute exposure to TNF causes 1) NFκB signaling dynamics that are less oscillatory and more like PAMP-responsive NFκB dynamics, 2) immune gene expression that is more similar to the Pam3CSK4-response program, 3) broader epigenomic reprogramming that is characteristic of PAMP-responsive changes. We show that tonic TNF signaling effects subtle changes to TNF receptor availability and dynamics such that enhanced pathway activity results in non-oscillatory NFκB. Our results reveal tonic TNF signaling as a key tissue determinant of the specific characteristics of cellular responses to acute paracrine TNF exposure, and their distinction from responses to direct exposure to PAMPs.
2022-07-27 | GSE209565 | GEO
Project description:Drug serum concentrations will be measured at several time-points for inflammatory disease patients treated with anti-TNF agents. The purpose is to determine which patients that will clinically benefit from either discontinue treatment, adjusting the dose, switch to another anti-TNF agent or a different class of medication.
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Project description:Anti-TNF (tumor necrosis factor) monoclonal antibodies have revolutionized management of Inflammatory bowel disease. Their common features include high efficacy but also immunogenicity and increased infection risk. Since 2013, two generics or biosimilars of the first anti-TNF have been registered in Europe, which long lerm safety profile needs yet to be established.
This prospective, multicenter, observational cohort study will assess safety of treatment of anti-TNF monoclonal antibodies in inflammatory bowel disease patients in Poland.
Eligible are consecutive patients in whom anti-TNF is started for Crohn’s disease, ulcerative colitis or indeterminate colitis between January 1st, 2014 and December 31st, 2015. Data to be collected include demography, Montreal classification, indication to treatment, previous treatment, operations, extraintestinal manifestations and concomitant diseases. Data on response, tolerability and safety of anti-TNF and on concomitant treatment will be collected. Adverse events logs will be completed. Majority of IBD centres in Poland, pediatric and adult, academic and regional, have agreed to participate in the study.
As a result of the study, the frequency of adverse events in a cohort of Polish IBD patients on various anti-TNFs will be established.
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Project description:BACKGROUND/RATIONALE:
Treatment outcomes of patients with inflammatory bowel disease (IBD) have improved enormously during the past decade due to the use of anti-tumour necrosis factor (anti-TNF) therapy. As a result, 67 to 91% of paediatric patients and 66% of adult patients is still in sustained remission two years after the initiation of anti-TNF therapy. Prolonged use of anti-TNFs comes with disadvantages such as dose dependent susceptibility to infections and dermatological adverse effects. Preliminary, mostly uncontrolled studies suggest that dose reduction by dosing interval lengthening is a realistic option in a relevant proportion of patients with IBD, provided that intensive follow-up is applied.
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To evaluate whether a faecal calprotectin (FC) guided strategy of anti-TNF dosing interval lengthening is non-inferior in maintaining remission in patients with IBD, compared with an unchanged dosing interval.
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Project description:This SuperSeries is composed of the following subset Series: GSE32050: 5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [5hmC Capture and Seq] GSE32187: 5-hydroxymethylcytosine-mediated epigenetic dynamics during neurodevelopment and aging [mRNA profiling] Refer to individual Series
2011-10-29 | E-GEOD-32188 | biostudies-arrayexpress
Project description:Background: In pediatric inflammatory bowel disease (IBD) up to 30% of patients do not respond to anti-TNF therapy. The aim was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD. Methods: The study population included 29 responders and 9 non-responders to anti-TNF therapy patients aged <18 years with IBD who started treatment with infliximab or adalimumab. Whole gene expression profiles from total RNA isolated from whole-blood samples of 6 responders and 6 non-responders taken before biologic administration and after 2 weeks were analyzed by RNA next-generation sequencing. The expression of 6 selected genes was measured for validation in all of 38 patients recruited using qPCR; Results: Differentially expressed genes in non-responders versus responders to anti-TNF treatment were identified, 32 prior treatment initiation and 44 after 2 weeks (Log2FC (Fold change)>0.6 o <-0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B and GBP1 were overexpressed in non-responders after 2 weeks of anti-TNF treatment (Log2FC 1.05, 1.21 and 1.08, respectively, p value <0.05,); Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.
2021-01-14 | GSE159034 | GEO
Project description:Objectives: This study was undertaken to understand the mechanistic basis of response to anti-TNF therapies and determine if transcriptomic changes in the synovium are reflected in peripheral protein markers. Methods: Synovial tissue from 46 RA patients was profiled with RNA sequencing before and 12 weeks after treatment with anti-TNF therapies. Pathway and gene signature analyses were performed on RNA expression profiles of synovial biopsies to identify mechanisms that could discriminate among EULAR good, moderate and non-responders. Serum proteins encoded by synovial genes differentially expressed between EULAR response groups were measured in the same patients. Results: The gene signatures were able to predict good responder patients and pathway analysis identified elevations in immune pathways including chemokine signaling, Th1 and Th2 cell differentiation, and Toll-like receptor signaling uniquely in good responders. These inflammatory pathways were correspondingly down-modulated by anti-TNF therapy only in good responders. Based on cell signature analysis, lymphocyte, myeloid and fibroblast cell populations were elevated in good responders relative to non-responders, consistent with the increased inflammatory pathways. Cell signatures which decreased following anti-TNF treatment were predominately associated with lymphocytes and fewer were associated with myeloid and fibroblast populations. Following anti-TNF treatment and only in good responders, several peripheral inflammatory proteins decreased consistent with corresponding synovial gene changes. Conclusions: Collectively, these data suggest that RA patients with robust responses to anti-TNF therapies are characterized at baseline by immune pathway activation, which decreases following anti-TNF treatment. Understanding mechanisms that define patient responsiveness to anti-TNF may assist in development of predictive markers of patient response and earlier treatment options.
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Project description:Synovial inflammatory pathways characterize anti-TNF-responsive rheumatoid arthritis patients
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Project description:Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses
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