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Analysis of the polyA+ RNA of LPS-treated human CD14+ monocytes

ABSTRACT: This study aims to investigate the profile and the role of lncRNAs in the IFN response initiated by TLR4 activation of primary human monocytes and their implication in the immune dysregulation present in SSc patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE123532 | GEO | 2019/03/06

REPOSITORIES: GEO

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Transcriptome analysis of CD14+ monocytes from SSc patients

Project description:Transcriptome analysis of CD14+ monocytes from SSc patients

| PRJNA662949 | ENA

Transcriptome analysis of CD14+ monocytes from SSc patients

Project description:Purpose: To compare transcriptome profile of CD14+ blood monocytes from systemic sclerosis (SSc) patients and healthy controls. Methods: CD14+ monocytes were isolated from peripheral blood of lcSSc (n=5, age=54.4±6.7), dcSSc patients (n=5, age=51.8±7.2) and age- and sex-matched healthy controls (HC) (n=5, age=50.8±9.7). Total RNA was isolated and polyA libraries were prepared using TruSeq Stranded mRNA kit. Next Generation Sequencing was performed using Illumina HiSeq 4000 platform. Differentially expressed genes were computed using DESeq2 algorithm. Results: We detected 1440 differentially expressed genes between dcSSc vs HC and 225 between lcSSc and HC respectively (p≤0.01; log2 ratio≥0.5, Fig 1). Among those, in dcSSc 1076 were upregulated (e.g. MMP9, IL1R2, FLT3, MIF, TLR9) and 364 were downregulated (e.g. TGFBR1, CD44, CD244, HLA-DRA, HLA-G). In lcSSc 160 transcripts were upregulated (e.g. CCL2, WNT5B, MMP17) and 65 were downregulated (e.g. KLF11, IRAK2). We identified 123 commonly deregulated genes between SSc subgroups (e.g. CCL3, CD14, IL27, MMP17). Principal component analysis showed close clustering within SSc subgroups and clear separation from healthy controls. Pathway analysis revealed alterations in several biological processes important in fibrogenesis including antigen presentation, MIF-induced immune responses, TGF-β, NOTCH and WNT signalling pathways. qPCR analysis further confirmed differences in gene expression on mRNA level (n HC=8, n SSc=25, p≤0.05). Conclusions: To our knowledge, this is the first global transcriptome analysis of peripheral blood CD14+ monocytes in SSc. Our results suggest a primary activation of monocytes in peripheral blood, which might be further translated into novel cellular biomarker of the disease and potentially used for distinguishing between responders and non-responders to a novel treatment in future clinical trials.

2021-09-10 | GSE157840 | GEO

Analysis of the polyA+ RNA of LPS-treated human CD14+ monocytes

Project description:Analysis of the polyA+ RNA of LPS-treated human CD14+ monocytes

| PRJNA509134 | ENA

Expression data from S100A9 and HMGB1 treated human CD14+ monocytes

Project description:TLR4 signaling was reported to be involved in the upregulation of PD-L1 expression and induction of immunosuppressive properties of human CD14+ monocytes. Damage associated molecular patterns (DAMPs) S100A8, A9, and HMGB1, which act as endogenous TLR4 ligands, drive MDSC activation and were shown to be markedly expressed in the tumor microenvironment (TME) of solid tumors. The role of S100A8/9 and HMGB1 in the acquisition of MDSC immunosuppressive activity remains to be better defined.

2024-07-19 | GSE254271 | GEO

Transcriptional effects of catalytic mTOR inhibiton among LPS-stimulated primary human monocytes

Project description:To better understand the role of mTOR in regulation of the monocyte response to LPS, we obtained mRNA-seq profiles of primary human monocytes stimulated ex vivo through TLR4, with and without pretreatment with a catalytic mTOR inhibitor (mTORi)

2022-07-29 | GSE187403 | GEO

Transcriptome-wide analysis of filarial extract-primed human monocytes reveal changes in LPS-induced PTX3 expression levels

Project description:In vitro priming of human peripheral monocytes with the filarial extract from Brugia malayi and subsequent LPS stimulation to explore the immunmodulatory capacity of filarial extract to subsequent inflammatory LPS responses and thus to identify new candidates to modify TLR4-associated responses/diseases and filarial pathology.

2019-01-31 | E-MTAB-7608 | biostudies-arrayexpress

Transcription profiling by array of human serum-free fibrocytes, serum-containing fibrocytes, CD14++CD16- Monocytes, CD14++CD16+ Monocytes, CD14+CD16++ Monocytes and macrophages

Project description:Serum-free Fibrocytes, Serum-containing Fibrocytes, CD14++CD16- Monocytes, CD14++CD16+ Monocytes, CD14+CD16++ Monocytes, Macrophages were all generated from up to 3 biological replicates from each of 3 separate donors. RNA was extracted (Ambion RNAqueous), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 0.1% FDR. PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment.

2011-01-01 | E-MEXP-2811 | biostudies-arrayexpress

Gene expression profile in freshly isolated monocytes from patients with diffuse cutaneous scleroderma (dcSSc) compared to healthy donors (HDs)

Project description:Monocytes/macrophages are activated in several autoimmune diseases, including systemic sclerosis (scleroderma, SSc), with increased expression of IFN-regulatory genes and inflammatory cytokines, suggesting dysregulation of the innate immune response in autoimmunity. Recently, we found that EBV is deregulated in SSc with abnormal expression of viral lytic-genes in PBMCs and skin. Since monocytes/macrophages are involved in innate immune recognition of EBV/lytic infection, we sought to determine whether EBV might contribute to their activation in SSc. In this study, using recombinant-EBV we infected monocytes from SSc and healthy donors (HDs), we found that viral replication is essential for inducing the expression of TLR8 in EBV-infected primary monocytes. Markers of activated monocytes, such as IFN-regulated genes and chemokines, were up-regulated in SSc- and HD-EBV-infected monocytes. Inhibiting TLR8 expression reduced virally-induced-TLR8 in THP-1 infected cells, demonstrating that innate immune activation by infectious EBV is partially dependent on TLR8. Viral lytic-mRNA and -proteins were detected in freshly isolated SSc monocytes. Microarray analysis substantiated the evidence of an increased IFN signature and altered level of TLR8 expression in SSc monocytes carrying infectious EBV compared to HD monocytes.

2017-06-12 | GSE86984 | GEO

NanoString- Transcriptional profiling of LPS-primed and inflammasome-activated untouched, or platelet-depleted human CD14+ monocytes

Project description:The goal of this experiment was to explore how human platelets affect the transcriptional responses of primary human CD14+ blood monocytes to lipopolysaccharide (LPS), and NLRP3 activation with Nigericin. For this purpose, we analyzed the mRNA expression of 770 myeloid-specific transcripts using the nCounter® Nanostring Human Myeloid Innate Immunity Panel v2. We isolated classical monocytes (CD14+CD16−) from the peripheral blood of healthy volunteers. Monocytes were derived from PBMCs using negative selection with the EasySep™ Human Monocyte Isolation Kit from STEMCELLTM Technologies. We modified this process by either including or excluding a platelet-depleting cocktail, creating two groups: \\"Standard Monocytes (StdMo)\\" and \\"Platelet-depleted Monocytes (PdMo).\\" To examine the impact of platelets further, we supplemented PdMos with fresh autologous platelets at a ratio of 50 platelets per monocyte, resulting in a third group, \\"PdMo + Plts.\\" StdMos were prepared according to the standard protocol provided by the EasySep™ Kit. For the PdMos, a Platelet Removal Component (50 µl ml−1) from the kit was used during isolation. We also reconstituted platelet-depleted monocytes with platelets and analyzed platelets alone to determine their specific mRNA contributions. The groups—StdMo, PdMo, PdMo + Plts, and platelets alone—were then exposed to 2 ng/ml of Ultrapure LPS (from E. coli O111:B4) for 4.5 hours, or stimulated with LPS for 3 hours followed by inflammasome activation with Nigericin (10 µM) for 90 min before extracting RNA for analysis.

2024-05-31 | E-MTAB-14072 | biostudies-arrayexpress

Immune complex stimulation of human monocytes

Project description:Systemic sclerosis (SSc) is an autoimmune disease and several distinct autoantibodies have been described in SSc patients, many correlating with specific clinical presentation. Numerous studies have documented the presence of immune complexes (IC) in sera, lungs and BAL of SSc patients, potentially implicating them in the pathogenesis. Monocyte/macrophage activation also have been observed in fibrotic SSc skin and lung tissue. While the upstream activators remain unknown, it is plausible that IC are amongst the key triggers in activating monocytes and sustaining the chronic inflammation and fibrosis in SSc tissue. To test this hypothesis and find the specific downstream genes regulated by IC, we compare the gene expressions of the monocytes stimulated by control medium, LPS and IC using RNA seq. OPN was one of these IC regulated genes. Our paper further suggested that circulating OPN levels serve as a systemic proxy for IC driven profibrotic macrophage activity, highlighting its potential as a promising biomarker in SSc-ILD.

2020-08-05 | GSE155687 | GEO

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