scholarly journals AB0171 THE IMMUNOMODULATORY AND ANTI-INFLAMMATORY EFFECTS OF BOSENTAN IN SYSTEMIC SCLEROSIS

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1385.2-1386
Author(s):  
M. G. Tinti ◽  
T. Mazza ◽  
L. D’agruma ◽  
A. De Cata
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Systemic Sclerosis ◽  
Differentially Expressed Genes ◽  
Immune Cells ◽  
Differentially Expressed ◽  
Immunomodulatory Activity ◽  
Z Score ◽  
Anti Inflammatory ◽  
Antigen Presenting

Background:Plasma endothelin-1 (ET-1) levels are increased in patients with systemic sclerosis (SSc), playing a central role in the development of fibrosis, vasoconstriction and inflammation1. While the beneficial effect of Bosentan, the endothelin receptor antagonists, have been demonstrated on vasoconstriction and fibrosis, its potential anti-inflammatory and immunomodulatory activity needs to be further investigated.Objectives:To assess whether Bosentan can modulate the gene expression profile of immune cells in sample of patients with limited and diffuse SSc and active digital ulcers.Methods:We enrolled 34 patients affected by SSc. Twenty-four patients were affected by limited SSc and 12 by diffuse SSc. Blood samples were collected from patients before and after 24 weeks of treatment with Bosentan, in the absence of immunosuppressive therapies. All patients received Bosentan 125 mg twice a day for 24 weeks. Gene expression profiles were assessed by GeneChip® Human Transcriptome Array 2.0 microarray technology. Significantly (p-value<0.05) and differentially (|FC|>1.5) expressed genes pre/post treatment were obtained by paired t-statistics, as implemented in Partek Genomics Suite ver. 6.6. These genes were subjected to functional enrichment analysis by Ingenuity Pathway Analysis. The effect of Bosentan on patients was studied on the “diffuse” and “limited” sub-cohorts, individually, as well as on the whole cohort.Results:Contrary to the limited cohort where differentially expressed genes resulted to be all non-coding genes which are almost all over-expressed before treatment, the diffuse cohort was characterized by 19 differentially expressed genes that enrich biological functions and pathways related to the immune system and its organic response (in particular T-cells). Comparing the limited to the diffuse cohort, pre- and post- treatment, a distinct genetic fingerprint emerges, that characterizes the response to Bosentan by the latter cohort as increased apoptosis of lymphocytes (z-score=3.28) and a decreased quantity of antigen presenting cells (from z-score=1.06 (pre) to -0.75 (post)).Conclusion:The presence of an inflammatory microenvironment, as occur in SSc, influence the relative expression of ET-1 receptors on immune cells, which in turn further contribute to the amplification of cellular responses to inflammation. The observed difference response to therapy between the two cohorts of patients was attributed to influence of ET-1 levels on the relative expression of ET-1 receptors on immune cells surface. Interestingly Bosentan, beside the already-known effect on promoting antigen presenting cells apoptosis, seem to exert its immunomodulatory activity also by deregulating functions that mainly involves the T cells and by promoting their apoptosis, which in turn reflect also its anti-inflammatory proprieties.References:[1]Tinazzi E, Puccetti A, Patuzzo G, et al. Endothelin receptors expressed by immune cells are involved in modulation of inflammation and in fibrosis: relevance to the pathogenesis of systemic sclerosis. J Immunol Res. 2015;2015:147616.Disclosure of Interests:None declared

scholarly journals HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 244 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Rossella Gratton ◽  
João Paulo Britto de Melo ◽  
José Leandro Andrade-Santos ◽  
Rafael Lima Guimarães ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Differentially Expressed Genes ◽  
Cd4 T Cells ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Infected Cells ◽  
Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

scholarly journals Gene expression and DNA methylation analyses suggest that two immune related genes are prognostic factors of colorectal cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xiao-Liang Xing ◽  
Zhi-Yong Yao ◽  
Chaoqun Xing ◽  
Zhi Huang ◽  
Jing Peng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Risk Assessment ◽  
Dna Methylation ◽  
Differentially Expressed Genes ◽  
Risk Score ◽  
Immune Cells ◽  
Assessment Model ◽  
Differentially Expressed ◽  
Risk Assessment Model

Abstract Background Colorectal cancer (CRC) is the second most prevalent cancer, as it accounts for approximately 10% of all annually diagnosed cancers. Studies have indicated that DNA methylation is involved in cancer genesis. The purpose of this study was to investigate the relationships among DNA methylation, gene expression and the tumor-immune microenvironment of CRC, and finally, to identify potential key genes related to immune cell infiltration in CRC. Methods In the present study, we used the ChAMP and DESeq2 packages, correlation analyses, and Cox regression analyses to identify immune-related differentially expressed genes (IR-DEGs) that were correlated with aberrant methylation and to construct a risk assessment model. Results Finally, we found that HSPA1A expression and CCRL2 expression were positively and negatively associated with the risk score of CRC, respectively. Patients in the high-risk group were more positively correlated with some types of tumor-infiltrating immune cells, whereas they were negatively correlated with other tumor-infiltrating immune cells. After the patients were regrouped according to the median risk score, we could more effectively distinguish them based on survival outcome, clinicopathological characteristics, specific tumor-immune infiltration status and highly expressed immune-related biomarkers. Conclusion This study suggested that the risk assessment model constructed by pairing immune-related differentially expressed genes correlated with aberrant DNA methylation could predict the outcome of CRC patients and might help to identify those patients who could benefit from antitumor immunotherapy.

scholarly journals Gene Expression Profiling of Sorted Peripheral Blood Cells Using Microarray and Next Generation Sequencing Reveals Distinct Molecular Signatures in the Polymorphonuclear and Mononuclear Cells of Patients with Polycythemia Vera and Primary Myelofibrosis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 5201-5201
Author(s):  
Chieh Lee Wong ◽  
Baoshan Ma ◽  
Gareth Gerrard ◽  
Martyna Adamowicz-Brice ◽  
Zainul Abidin Norziha ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Gene Expression Profiling ◽  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Expression Profiling ◽  
Differentially Expressed ◽  
Cell Type ◽  
Cell Type Specific ◽  
Generation Sequencing

Abstract Background The past decade has witnessed a significant progress in the understanding of the molecular pathogenesis of myeloproliferative neoplasms (MPN). A large number of genes have now been implicated in the pathogenesis of MPN but their relative importance, the mechanisms by which they cause different cell types to predominate and their implications for prognosis remain unknown. We hypothesized that there are other genes which may contribute to the pathogenesis of the different disease subtypes detectable only by cell-type specific analysis. Aim The aim of this study was to perform gene expression profiling on different cell types from patients with MPN in order to identify novel variants and driver mutations, to elucidate the pathogenesis and to identify predictors of survival in patients with MPN in a multiracial country. Methods We performed gene expression profiling on normal controls (NC) and patients with MPN from 3 different races (Malay, Chinese and Indian) in Malaysia who were diagnosed with essential thrombocythemia (ET), polycythemia vera (PV) and primary myelofibrosis (PMF) according to the 2008 WHO diagnostic criteria for MPN. Two cohorts of patients, the patient and validation cohorts, from 3 tertiary-level hospitals were recruited prospectively over 3 years and informed consents were obtained. Peripheral blood samples were taken and sorted into polymorphonuclear cells (PMNs), mononuclear cells (MNCs) and T cells. RNA was extracted from each cell population. Gene expression profiling was performed using the Illumina HumanHT-12 Expression Beadchip for microarray and the Illumina Nextera XT DNA Sample Preparation Kit for next generation sequencing on the patient and validation cohorts respectively. Results Twenty-eight patients (10 ET, 11 PV and 7 PMF) and 11 NC were recruited into the patient cohort. Twelve patients (4 ET, 4 PV and 4 PMF) and 4 NC were recruited into the validation cohort. Gene expression levels for each cell type in each disease were compared with NC. In the patient cohort, the number of differentially expressed genes in ET, PV and PMF was 0, 141 and 15 respectively for PMNs (p < 0.05 after multiple testing correction) and 5, 170 and 562 respectively for MNCs (p < 0.05). No differentially expressed genes were identified for T cells in any of the three disease groups. RNA-seq analysis of samples from the validation cohort was used to corroborate these findings. After combination, we were able to confirm differential expression of 0, 14 and 7 genes in ET, PV and PMF respectively for PMNs (p < 0.05) and 51 genes in only PMF for MNCs (p < 0.05). The validated differentially expressed genes for PMNs and MNCs were mutually exclusive except for one gene. The differentially expressed genes in PV and PMF for PMNs were involved in cellular processes and metabolic pathways whereas the differentially expressed genes for PMF in MNCs were involved in regulation of cytoskeleton, focal adhesion and cell signaling pathways. Conclusion This is the first study to use microarray and next generation sequencing techniques to compare cell type-specific expression of genes between different subtypes of MPN. The lack of differential expression in T cells validates the techniques used and indicates that they are not part of the neoplastic clone. Differential expression of genes for MNCs was seen only in PMF which may be related to their more severe phenotype. Interestingly, there were fewer differentially expressed genes in PMF compared to PV for PMNs. The lack of differential expression in ET may either reflect the relatively milder phenotype of the disease or that differential expression is limited to megakaryocytes-platelets which were not studied. The lists of mutually exclusive cell type-specific differentially expressed genes for PMNs and MNCs provide further insight into the pathogenesis of MPN and into the differences between its different forms. The identified genes also indicate further routes for investigation of pathogenesis and possible disease-specific targets for therapy. Disclosures Aitman: Illumina: Honoraria.

scholarly journals Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

2020 ◽  
Vol 26 (1) ◽  
Author(s):  
Lara Kim Brackmann ◽  
Alicia Poplawski ◽  
Caine Lucas Grandt ◽  
Heike Schwarz ◽  
Thomas Hankeln ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ionizing Radiation ◽  
Differentially Expressed Genes ◽  
Human Fibroblasts ◽  
Differentially Expressed ◽  
High Dose ◽  
Z Score ◽  
Time Points ◽  
Dose Irradiation ◽  
Time Point

Abstract Background Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. Methods Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2 h and 4 h after exposure. Differentially expressed genes with an adjusted p-value < 0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis. Results More genes were differentially expressed 4 h after exposure to low and high doses of radiation than after 2 h. In experiments with high dose irradiation and RNA sequencing after 4 h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (< 0.05) and (in) activating z-score (≥2.00 or ≤ − 2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p < 0.05 and z-score ≥ 2.00 or ≤ − 2.00) activated or inactivated pathways for both time points. Conclusions Compared to 2 h after irradiation, a higher number of differentially expressed genes were found 4 h after exposure to low and high dose ionizing radiation. Differences in gene expression were related to signal transduction pathways of the DNA damage response after 2 h and to metabolic pathways, that might implicate cellular senescence, after 4 h. The time point 4 h will be used to conduct further irradiation experiments in a larger sample.

Changes in Differential Gene and Protein Expression Patterns during Development of Cord Blood (CB) Versus Adult Peripheral Blood (APB) Monocyte (Mo) into Mature Dendritic Cells (mDC): Insight into Immaturity of CB DC Immunity.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 5204-5204
Author(s):  
Hong Jiang ◽  
Cheryl Wade-Harris ◽  
Megan Lim ◽  
Laxmi Baxi ◽  
Mitchell S. Cairo
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Oligonucleotide Microarray ◽  
Differentially Expressed ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Hla Dqa1 ◽  
Antigen Presenting

Abstract It has been recognized that dysfunction of CB immune system is in part due to the immaturity of CB cellular immunity (Cairo, Blood,1997). The molecular mechanisms associated with the immaturity of CB cellular immunity including DC subset remain to be defined. The maturation status of DC greatly influences its antigen presentation capacity. Recently, we have utilized oligonucleotide microarray to demonstrate differential gene expression profiles of CB vs APB Mo (Jiang/Cairo, JI, 2004). In the current study, differential expressed genes and proteins were examined in Mo-derived CB vs. APB DC during DC developmental stages: Mo, immature DC (iDC) and mDC, by utilizing oligonucleotide microarray and proteomics. Briefly, Mo isolated from CB or APB and cultured for 8 days with GM-CSF/IL-4 (iDC) and further stimulated with LPS (mDC). Oligonucleotide microarray was carried out using U133A gene chip (Affymetrix). The representative differentially expressed genes resulted from microarray analysis were selected and analyzed by quantitative RT-PCR (Roche). The proteomic technique was conducted by liquid chromatography (LC) and mass spectrometry (MS) (Lim, Mol Cell Proteomics, 2006). The differentially expressed proteins were compared in CB vs. APB for iDC and mDC. We identified different gene expression patterns that were significantly lower in CB vs. APB in different stages during DC differentiation: Mo, iDC and mDC. These differentially expressed genes included RELA (5F), JUNB (6F), IRF-1 (3F) in Mo; CREB5 (3F), MAP7 (5F), IL1R2 (6F) in iDC; and HLA-DQA1 (4F), CD80 (3F), IRF-5 (3F) in mDC. The proteomic studies demonstrated Tyrosine Kinase Fer (12.5F), Actin regulator 3 (2.5F), Rap guanine nucleotide exchange factor 1 (2.4F) and Myeloid cell nuclear differentiation antigen (1.5F) were expressed higher in APB vs.CB iDC, while MAX binding protein MNT (5.5F), IRS2 (2.2F) and Zinc-Finger Proteins (514, 212, 462) (3–14F) were expressed higher in CB vs. APB iDC. Further, the proteomic results also indicated other Zinc-Finger Proteins (292, 221, 474) (2–5F), Fibrillin 1 precursor (2.5F) and interleukin-4 (7.7F) were expressed higher in APB vs. CB mDC. In contrast, cyclin I (3F), Rb-like protein 2 (4.35 F) and PKC theta (2F) were significantly lower in APB vs. CB DC. Moreover, the comparison of CB vs. APB DC antigen presenting activity by ELISPOT was performed and the influenza-peptide loaded CB-mDC demonstrated weaker ability to induce T cells to produce IFNg compared with APB-mDC. In summary, these differentially expressed genes in Mo (RELA, JUN) may play key roles in initiating Mo differentiation toward DC. The increased expression of genes in APB vs. CB iDC, like CREB5, IL1R2, may be involved in mediating maturation process of iDC to mDC. Lastly, the elevated expression of genes in APB vs. CB mDC, such as HLA-DQA1, CD80, IRF5 among others, may be likely to control mDC functionality as demonstrated by weaker antigen presenting activity of CB vs. APB mDC. We postulate that decreased expression of specific genes in CB vs. APB DC during DC developmental stages may in part be responsible for the lack of maturity of CB, and ultimately may partially be responsible for differential CB vs. APB innate and adaptive immunity.

scholarly journals UNIQUE GENE EXPRESSION IN GUT-DERIVED PHAGOCYTIC IMMUNE CELLS FROM IBD PATIENTS

2021 ◽  
Vol 27 (Supplement_1) ◽  
pp. S31-S32
Author(s):  
Gillian Jacobsen ◽  
Irina Fernandez ◽  
Maria Alejandra Quintero Cusguen ◽  
Ana Santander ◽  
Judith Pignac-Kobinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Immune Cells ◽  
Differential Expression Analysis ◽  
Cell Activity ◽  
Acid Synthesis ◽  
Differentially Expressed ◽  
Patient Treatment ◽  
Phagocytic Cells ◽  
Immune Pathways

Abstract Introduction/Aim Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), have a complex immunopathogenesis involving chronic, dysregulated inflammation of the gut in response to commensal microbes. Current therapies, such as Anti-TNF drugs, target this immune dysregulation, but many patients exhibit recurrent inflammation despite treatment (refractoriness). Research shows that IBD patient phagocytic immune cells have altered cytokine production and bacterial clearing defects. We thus set out to analyze the transcriptome of phagocytic cells (CD11b+) isolated from patient gut biopsies. To shed light on potential causes of refractoriness, we examined cells from both not inflamed (successfully treated) and inflamed (refractory) patients on Anti-TNF therapy. Methods We used magnetic sorting to isolate CD11b+ cells from the lamina propria of a diverse set of IBD patient biopsies and performed RNA sequencing (n = 61). We used differential expression analysis to compare combinations of four patient biopsy variables: location (ileum or colon), condition (inflamed or uninflamed), IBD type (CD or UC), and patient treatment (Anti-TNF therapy or other). We also performed pathway analysis on genes significantly upregulated or downregulated (p &lt; 0.05) between these variables. Results The highest number of differentially expressed genes was found in the colon (5578 genes upregulated) vs ileum (5582). Genes upregulated in colon mapped to innate immune pathways, while ileum pathways were mainly metabolic. Only 29 genes were differentially expressed in UC vs CD, regardless of inflammation status or location. 26 genes were differentially expressed between inflamed and uninflamed biopsies on Anti-TNF therapy (n = 16). Genes upregulated in inflamed biopsies were associated with neutrophils, while genes in uninflamed biopsies were associated with adaptive immunity, short chain fatty acid synthesis, transcription and translation, and protein secretion. Conclusion CD11b+ cells of the colon are more immunologically active, likely due to their interaction with the dense microbiome of the colon. In contrast, the metabolic pathways upregulated in ileum may point to a role for phagocytes in digestion and metabolism. These results suggest that intestinal CD11b+ gene expression is highly influenced by regional microenvironment. Fewer differences were seen comparing CD11b+ cells from CD vs UC, suggesting that this cell population is not solely responsible for the clinical differences between these diseases. The small number of differentially expressed genes in Anti-TNF refractoriness shows a clear difference between innate and adaptive immune pathways, as well as increased general cell activity in Anti-TNF responders. These genes should be further investigated to determine their precise role in refractoriness.

scholarly journals SNAP25 Is a Potential Prognostic Biomarker for Prostate Cancer

2021 ◽  
Author(s):  
Longjiang Di ◽  
Maoli Gu ◽  
Yan Wu ◽  
Guoqiang Liu ◽  
Lishuo Zhang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
T Cells ◽  
Gene Ontology ◽  
Differentially Expressed Genes ◽  
Gleason Score ◽  
Immune Cells ◽  
Prognostic Biomarker ◽  
Differentially Expressed ◽  
Normal Prostate ◽  
Immune Infiltration

Abstract Background Prostate cancer is one of the most lethal cancers in male individuals. The Synaptosome associated protein 25 (SNAP25) gene is a key mediator of multiple biological functions in tumours. However, its significant impact on the prognosis in prostate cancer remains to be elucidated.Methods We performed a comprehensive analysis of the Cancer Genome Atlas dataset (TCGA) to identify the differentially expressed genes between prostate cancer and normal prostate tissue. We subjected the differentially expressed genes to gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes functional analysis, and constructed a protein-protein interaction network. We then screened for pivotal genes to identify the hub genes of prognostic significance by performing Cox regression analysis. We identified SNAP25 as one such gene and analysed the relationship between its expression in prostate cancer to poor prognosis using Studio R. Results TCGA database demonstrated that SNAP25 was significantly downregulated in prostate cancer, and that its expression was significantly correlated with the Gleason score and pathological TNM stage of patients. The association between SNAP25 expression and tumour-infiltrating immune cells was evaluated using the Tumour Immune Estimation Resource site. Gene set enrichment and gene ontology analyses were used to analyse the function of SNAP25. We found that SNAP25 expression strongly correlated with overall survival in the Gleason score. In addition, SNAP25 was involved in the activation, differentiation, and migration of immune cells, and its expression was positively correlated with immune infiltration, including of B cells, CD8+ T cells, CD4+ T cells, neutrophils, dendritic cells, macrophages, and natural killer cells. SNAP25 expression was also positively correlated with chemokines/chemokine receptors, suggesting that SNAP25 might regulate the migration of immune cells. These molecular experiment results validate the low expression of SNAP25 seen in prostate cancer cells.Conclusion Our findings indicate a relationship between SNAP25 expression and prostate cancer, demonstrating that SNAP25 is a potential prognostic biomarker due to its vital role in immune infiltration.

scholarly journals Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Miranda Houtman ◽  
Espen Hesselberg ◽  
Lars Rönnblom ◽  
Lars Klareskog ◽  
Vivianne Malmström ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
T Cells ◽  
Mhc Class Ii ◽  
Immune Cells ◽  
Mononuclear Cells ◽  
Class Ii ◽  
Differentially Expressed ◽  
Healthy Individuals ◽  
Hla Dq

HLA-DRB1 alleles have been associated with several autoimmune diseases. For anti-citrullinated protein antibody positive rheumatoid arthritis (RA), HLA-DRB1 shared epitope (SE) alleles are the major genetic risk factors. In order to study the genetic regulation of major histocompatibility complex (MHC) Class II gene expression in immune cells, we investigated transcriptomic profiles of a variety of immune cells from healthy individuals carrying different HLA-DRB1 alleles. Sequencing libraries from peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of 32 genetically pre-selected healthy female individuals were generated, sequenced and reads were aligned to the standard reference. For the MHC region, reads were mapped to available MHC reference haplotypes and AltHapAlignR was used to estimate gene expression. Using this method, HLA-DRB and HLA-DQ were found to be differentially expressed in different immune cells of healthy individuals as well as in whole blood samples of RA patients carrying HLA-DRB1 SE-positive versus SE-negative alleles. In contrast, no genes outside the MHC region were differentially expressed between individuals carrying HLA-DRB1 SE-positive and SE-negative alleles, thus HLA-DRB1 SE alleles have a strong cis effect on gene expression. Altogether, our findings suggest that immune effects associated with different allelic forms of HLA-DR and HLA-DQ may be associated not only with differences in the structure of these proteins, but also with differences in their expression levels.

scholarly journals Comparative Analysis on Abnormal Methylome of Differentially Expressed Genes and Disease Pathways in the Immune Cells of RA and SLE

2021 ◽  
Vol 12 ◽  
Author(s):  
Qinghua Fang ◽  
Tingyue Li ◽  
Peiya Chen ◽  
Yuzhe Wu ◽  
Tingting Wang ◽  
...  
Keyword(s):  
T Cells ◽  
B Cells ◽  
Differentially Expressed Genes ◽  
Immune Cells ◽  
Differentially Expressed ◽  
Receiver Operating Curve ◽  
Data Sets ◽  
Hub Genes ◽  
Differentially Methylated Genes ◽  
Disease Pathways

We identified abnormally methylated, differentially expressed genes (DEGs) and pathogenic mechanisms in different immune cells of RA and SLE by comprehensive bioinformatics analysis. Six microarray data sets of each immune cell (CD19+ B cells, CD4+ T cells and CD14+ monocytes) were integrated to screen DEGs and differentially methylated genes by using R package “limma.” Gene ontology annotations and KEGG analysis of aberrant methylome of DEGs were done using DAVID online database. Protein-protein interaction (PPI) network was generated to detect the hub genes and their methylation levels were compared using DiseaseMeth 2.0 database. Aberrantly methylated DEGs in CD19+ B cells (173 and 180), CD4+ T cells (184 and 417) and CD14+ monocytes (193 and 392) of RA and SLE patients were identified. We detected 30 hub genes in different immune cells of RA and SLE and confirmed their expression using FACS sorted immune cells by qPCR. Among them, 12 genes (BPTF, PHC2, JUN, KRAS, PTEN, FGFR2, ALB, SERB-1, SKP2, TUBA1A, IMP3, and SMAD4) of RA and 12 genes (OAS1, RSAD2, OASL, IFIT3, OAS2, IFIH1, CENPE, TOP2A, PBK, KIF11, IFIT1, and ISG15) of SLE are proposed as potential biomarker genes based on receiver operating curve analysis. Our study suggests that MAPK signaling pathway could potentially differentiate the mechanisms affecting T- and B- cells in RA, whereas PI3K pathway may be used for exploring common disease pathways between RA and SLE. Compared to individual data analyses, more dependable and precise filtering of results can be achieved by integrating several relevant data sets.

scholarly journals Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis

2020 ◽  
Vol 11 ◽  
Author(s):  
Lori Garman ◽  
Richard C. Pelikan ◽  
Astrid Rasmussen ◽  
Caleb A. Lareau ◽  
Kathryn A. Savoy ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Differentially Expressed Genes ◽  
Immune Cells ◽  
Immune Dysregulation ◽  
Differentially Expressed ◽  
Cell Type ◽  
Cell Type Specific ◽  
Classical Monocytes

Sarcoidosis is a systemic inflammatory disease characterized by infiltration of immune cells into granulomas. Previous gene expression studies using heterogeneous cell mixtures lack insight into cell-type-specific immune dysregulation. We performed the first single-cell RNA-sequencing study of sarcoidosis in peripheral immune cells in 48 patients and controls. Following unbiased clustering, differentially expressed genes were identified for 18 cell types and bioinformatically assessed for function and pathway enrichment. Our results reveal persistent activation of circulating classical monocytes with subsequent upregulation of trafficking molecules. Specifically, classical monocytes upregulated distinct markers of activation including adhesion molecules, pattern recognition receptors, and chemokine receptors, as well as enrichment of immunoregulatory pathways HMGB1, mTOR, and ephrin receptor signaling. Predictive modeling implicated TGFβ and mTOR signaling as drivers of persistent monocyte activation. Additionally, sarcoidosis T cell subsets displayed patterns of dysregulation. CD4 naïve T cells were enriched for markers of apoptosis and Th17/Treg differentiation, while effector T cells showed enrichment of anergy-related pathways. Differentially expressed genes in regulatory T cells suggested dysfunctional p53, cell death, and TNFR2 signaling. Using more sensitive technology and more precise units of measure, we identify cell-type specific, novel inflammatory and regulatory pathways. Based on our findings, we suggest a novel model involving four convergent arms of dysregulation: persistent hyperactivation of innate and adaptive immunity via classical monocytes and CD4 naïve T cells, regulatory T cell dysfunction, and effector T cell anergy. We further our understanding of the immunopathology of sarcoidosis and point to novel therapeutic targets.

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