O18 Integrated molecular analysis of systemic sclerosis skin and blood shows significant differences between major autoantibody subgroups

Abstract Background/Aims The major antinuclear autoantibodies of systemic sclerosis (SSc) associate with different skin score trajectories and risk of internal organ manifestations. To elucidate molecular differences between ANA-defined subgroups, we utilised the prospective BIOPSY cohort of well-characterised SSc patients. Methods The prospectively collected BIOPSY cohort recruited 52 SSc patients (21 early dcSSc, 15 established dcSSc, 16 lcSSc) and 16 healthy controls (HC). 36 (69%) of the SSc patients are female. Mean disease duration in the early dcSSc cohort was 24 months (sd 12 months), and in established dcSSc was 11.3 years. ANA frequency in BIOPSY reflected the overall dcSSc population: anti-topoisomerase-1 (ATA) n = 14 (27%), anti-RNA pol III (ARA) n = 12 (23%) and other n = 26 (50%). Mean baseline skin score (MRSS) for early dcSSc was 21 (sd 11.2). At a group level mRSS peak was 21.9 (11.8) at 3 months and fell to 19.1(10.5) at 12 months. Serum biomarkers of ECM turnover and fibrosis were measured three monthly and genome-wide transcriptomic profiling of whole skin and whole blood performed by RNA-Seq. Statistical analysis used RStudio with ANOVA, and Tukey post-hoc test. Differential gene expression used the Bioconductor limma software, with standard thresholds for significance. Results At baseline, there were differences in soluble markers between clinical SSc sugroups and HC but not for major ANA subgroups. However, we found clear differences in early dcSSc analysed by major ANA subset for longitudinal change in serum markers of fibrosis and in whole skin gene expression, suggesting a mechanistic basis for the distinct clinical phenotypes associated with hallmark ANAs. During follow-up, significant differences were observed in HA, TIMP1, and PIIINP at 6 and 12 months (p < 0.05), with stable levels in ATA+ patients compared to progressively increased levels in the other subgroups. There were 564 significantly differentially expressed genes in skin between early dcSSc and HC. Unsupervised clustering differentiated patients with ARA and ATA positivity with early dcSSc. 54 genes were significantly differentially expressed in skin between ATA and ARA patients. Whilst 179 genes were differentially expressed in whole blood between early dcSSc compared with HC, no genes could significantly differentiate ATA from ARA. Functional analysis using HALLMARK pathway analysis identified both shared pathways associated with SSc across ANA groups (e.g. TGF beta signaling, IL6 JAK STAT3 signalling, inflammatory response), and pathways only upregulated in patients with ATA (e.g. Wnt beta catenin signaling, Notch signaling), and ARA (e.g. interferon gamma response, adipogenesis). Conclusion We have found significant differences in skin gene expression and longitudinal change in serum markers by autoantibody specificity in dcSSc. Our findings have implications for SSc pathogenesis and support stratification by ANA subgroup in clinical studies. Disclosure K.E. Clark: None. C. Campochiaro: None. E. Csomor: Corporate appointments; employee of GSK. A. Taylor: Corporate appointments; employee of GSK. K. Nevin: Corporate appointments; employee of GSK. N. Galwey: Corporate appointments; employee of GSK. M.A. Morse: Corporate appointments; employee of GSK. V.H. Ong: None. E. Derrett-Smith: None. N. Wisniacki: Corporate appointments; employee of GSK. S. Flint: Corporate appointments; employee of GSK. C.P. Denton: Consultancies; Actelion, GlaxoSmithKline, Bayer, Sanofi, lnventiva, Boehringer Ingelheim, Roche, Bristol Myers Squibb, CSL Behring, UCB, Leadiant Biosciences, Corbus, Servier, Arxx Therapeutics.

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OP0021 IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN EARLY RHEUMATOID ARTHRITIS PATIENTS RESPONDING TO TOCILIZUMAB

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2021-eular.3668 ◽

2021 ◽

Vol 80 (Suppl 1) ◽

pp. 12.2-12

Author(s):

I. Muller ◽

M. Verhoeven ◽

H. Gosselt ◽

M. Lin ◽

T. De Jong ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gene Expression ◽

T Cells ◽

Gene Ontology ◽

Regulatory T Cells ◽

Early Rheumatoid Arthritis ◽

Whole Blood ◽

Differentially Expressed ◽

Rna Seq ◽

Double Blind

Background:Tocilizumab (TCZ) is a monoclonal antibody that binds to the interleukin 6 receptor (IL-6R), inhibiting IL-6R signal transduction to downstream inflammatory mediators. TCZ has shown to be effective as monotherapy in early rheumatoid arthritis (RA) patients (1). However, approximately one third of patients inadequately respond to therapy and the biological mechanisms underlying lack of efficacy for TCZ remain elusive (1). Here we report gene expression differences, in both whole blood and peripheral blood mononuclear cells (PBMC) RNA samples between early RA patients, categorized by clinical TCZ response (reaching DAS28 < 3.2 at 6 months). These findings could lead to identification of predictive biomarkers for TCZ response and improve RA treatment strategies.Objectives:To identify potential baseline gene expression markers for TCZ response in early RA patients using an RNA-sequencing approach.Methods:Two cohorts of RA patients were included and blood was collected at baseline, before initiating TCZ treatment (8 mg/kg every 4 weeks, intravenously). DAS28-ESR scores were calculated at baseline and clinical response to TCZ was defined as DAS28 < 3.2 at 6 months of treatment. In the first cohort (n=21 patients, previously treated with DMARDs), RNA-sequencing (RNA-seq) was performed on baseline whole blood PAXgene RNA (Illumina TruSeq mRNA Stranded) and differential gene expression (DGE) profiles were measured between responders (n=14) and non-responders (n=7). For external replication, in a second cohort (n=95 therapy-naïve patients receiving TCZ monotherapy), RNA-seq was conducted on baseline PBMC RNA (SMARTer Stranded Total RNA-Seq Kit, Takara Bio) from the 2-year, multicenter, double-blind, placebo-controlled, randomized U-Act-Early trial (ClinicalTrials.gov identifier: NCT01034137) and DGE was analyzed between 84 responders and 11 non-responders.Results:Whole blood DGE analysis showed two significantly higher expressed genes in TCZ non-responders (False Discovery Rate, FDR < 0.05): urotensin 2 (UTS2) and caveolin-1 (CAV1). Subsequent analysis of U-Act-Early PBMC DGE showed nine differentially expressed genes (FDR < 0.05) of which expression in clinical TCZ non-responders was significantly higher for eight genes (MTCOP12, ZNF774, UTS2, SLC4A1, FECH, IFIT1B, AHSP, and SPTB) and significantly lower for one gene (TND2P28M). Both analyses were corrected for baseline DAS28-ESR, age and gender. Expression of UTS2, with a proposed function in regulatory T-cells (2), was significantly higher in TCZ non-responders in both cohorts. Furthermore, gene ontology enrichment analysis revealed no distinct gene ontology or IL-6 related pathway(s) that were significantly different between TCZ-responders and non-responders.Conclusion:Several genes are differentially expressed at baseline between responders and non-responders to TCZ therapy at 6 months. Most notably, UTS2 expression is significantly higher in TCZ non-responders in both whole blood as well as PBMC cohorts. UTS2 could be a promising target for further analyses as a potential predictive biomarker for TCZ response in RA patients in combination with clinical parameters (3).References:[1]Bijlsma JWJ, Welsing PMJ, Woodworth TG, et al. Early rheumatoid arthritis treated with tocilizumab, methotrexate, or their combination (U-Act-Early): a multicentre, randomised, double-blind, double-dummy, strategy trial. Lancet. 2016;388(10042):343-55.[2]Bhairavabhotla R, Kim YC, Glass DD, et al. Transcriptome profiling of human FoxP3+ regulatory T cells. Human Immunology. 2016;77(2):201-13.[3]Gosselt HR, Verhoeven MMA, Bulatovic-Calasan M, et al. Complex machine-learning algorithms and multivariable logistic regression on par in the prediction of insufficient clinical response to methotrexate in rheumatoid arthritis. Journal of Personalized Medicine. 2021;11(1).Disclosure of Interests:None declared

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Whole Blood Transcriptome Analysis in Children with Sickle Cell Anemia

Frontiers in Genetics ◽

10.3389/fgene.2021.737741 ◽

2022 ◽

Vol 12 ◽

Author(s):

Beatrice E. Gee ◽

Andrea Pearson ◽

Iris Buchanan-Perry ◽

Roger P. Simon ◽

David R. Archer ◽

...

Keyword(s):

Gene Expression ◽

Rna Sequencing ◽

Sickle Cell ◽

Sickle Cell Anemia ◽

Whole Blood ◽

Differentially Expressed ◽

Mrna Levels ◽

Control Subjects ◽

Non Coding Rna ◽

And Control

Whole transcriptome RNA-sequencing was performed to quantify RNA expression changes in whole blood samples collected from steady state sickle cell anemia (SCA) and control subjects. Pediatric SCA and control subjects were recruited from Atlanta (GA)—based hospital(s) systems and consented for RNA sequencing. RNA sequencing was performed on an Ion Torrent S5 sequencer, using the Ion Total RNA-seq v2 protocol. Data were aligned to the hg19 reference genome and analyzed in the Partek Genomics studio package (v7.0). 223 genes were differentially expressed between SCA and controls (± 1.5 fold change FDR p < 0.001) and 441 genes show differential transcript expression (± 1.5 fold FDR p < 0.001). Differentially expressed RNA are enriched for hemoglobin associated genes and ubiquitin-proteasome pathway genes. Further analysis shows higher gamma globin gene expression in SCA (33-fold HBG1 and 49-fold HBG2, both FDR p < 0.05), which did not correlate with hemoglobin F protein levels. eQTL analysis identified SNPs in novel non-coding RNA RYR2 gene as having a potential regulatory role in HBG1 and HBG2 expression levels. Gene expression correlation identified JHDM1D-AS1(KDM7A-DT), a non-coding RNA associated with angiogenesis, enhanced GATA1 and decreased JAK-STAT signaling to correlate with HBG1 and HBG2 mRNA levels. These data suggest novel regulatory mechanisms for fetal hemoglobin regulation, which may offer innovative therapeutic approaches for SCA.

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Systemic sclerosis

Oxford Textbook of Rheumatology ◽

10.1093/med/9780199642489.003.0121_update_001 ◽

2013 ◽

pp. 971-988 ◽

Cited By ~ 1

Author(s):

Christopher P. Denton ◽

Pia Moinzadeh

Keyword(s):

Systemic Sclerosis ◽

Cell Injury ◽

Rna Polymerase Iii ◽

Systematic Investigation ◽

Clinical Markers ◽

Topoisomerase 1 ◽

Skin Sclerosis ◽

Female Predominance ◽

Organ Manifestations ◽

Pulmonary Arterial

The term ’scleroderma’ describes a group of conditions in which the development of thickened, fibrotic skin is a cardinal feature. This includes localized forms of scleroderma (e.g. morphoea) and also systemic forms of the disease that are more correctly termed systemic sclerosis. Systemic sclerosis (SSc) is a multiorgan, autoimmune disease that has a high clinical burden and mortality, due to affecting the skin as well as internal organs. As with other related diseases there is a female predominance and marked clinical diversity. The pathogenesis of SSc is not fully elucidated; it includes endothelial cell injury fibroblast activation and autoimmunity that lead to skin and internal organ manifestations. The majority of cases exhibit characteristic serum autoantibodies. Some of these antibodies are scleroderma-specific reactivities including anti-centromere (ACA), anti-topoisomerase-1 (ATA or Scl 70) or anti-RNA polymerase III antibodies. These anti-nuclear antibody (ANA) patterns are generally mutually exclusive and serve as useful clinical markers of disease subgroups. Additional subsetting of scleroderma cases, based on the extent of skin sclerosis, permits classification into limited and diffuse subsets. Because of the heterogeneity of the disease patients may suffer from different organ manifestations, such as lung fibrosis, hypertensive renal crisis, severe cardiac disease, gastrointestinal involvement, and pulmonary arterial hypertension. Although outcomes have improved recently, systemic sclerosis still has the highest case-specific mortality of any of the autoimmune rheumatic diseases and requires careful and systematic investigation, management and follow-up. Treatment includes symptomatic strategies with attention to each involved organ system; it is still an area where therapeutic progress and better understanding of pathogenesis is increasingly anticipated.

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Gene expression profiling in whole blood of patients with coronary artery disease

Clinical Science ◽

10.1042/cs20100043 ◽

2010 ◽

Vol 119 (8) ◽

pp. 335-343 ◽

Cited By ~ 86

Author(s):

Chiara Taurino ◽

William H. Miller ◽

Martin W. McBride ◽

John D. McClure ◽

Raya Khanin ◽

...

Keyword(s):

Gene Expression ◽

Coronary Artery Disease ◽

Coronary Artery ◽

Gene Expression Profiling ◽

Whole Blood ◽

Expression Profiling ◽

Gene Expression Analysis ◽

Differentially Expressed ◽

Differentially Expressed Mirnas ◽

Artery Disease

Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10−16). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease.

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hnRNP U is differentially expressed in whole blood from patients with sepsis.

10.31219/osf.io/2ab9s ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Differential Expression ◽

Whole Blood ◽

Differentially Expressed ◽

Significant Differential Expression ◽

Hnrnp U ◽

Significant Gene ◽

Nuclear Ribonucleoprotein ◽

Microarray Datasets

We probed published and public microarray datasets (1, 2) to discover the most significant gene expression changes in the blood of patients with sepsis. We identified significant differential expression of the heterogenous nuclear ribonucleoprotein hnRNP U in whole blood from patients with sepsis.

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The interleukin-18 receptor is differentially expressed in the blood during sepsis.

10.31219/osf.io/wved6 ◽

2020 ◽

Author(s):

Shahan Mamoor

Keyword(s):

Gene Expression ◽

Whole Blood ◽

Differentially Expressed ◽

Interleukin 18 ◽

Genes Encoding ◽

Significant Gene ◽

Microarray Datasets

We probed published and public microarray datasets (1, 2) to discover the most significant gene expression changes in the blood of patients with sepsis. We found significant induction expression of IL18RAP and IL18R1, genes encoding subunits of the interleukin-18 receptor, in whole blood from patients with sepsis.

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Systemic sclerosis

10.1093/med/9780199642489.003.0121 ◽

2013 ◽

Cited By ~ 3

Author(s):

Christopher P. Denton ◽

Pia Moinzadeh

Keyword(s):

Systemic Sclerosis ◽

Cell Injury ◽

Rna Polymerase Iii ◽

Systematic Investigation ◽

Clinical Markers ◽

Topoisomerase 1 ◽

Skin Sclerosis ◽

Female Predominance ◽

Organ Manifestations ◽

Pulmonary Arterial

The term 'scleroderma' describes a group of conditions in which the development of thickened, fibrotic skin is a cardinal feature. This includes localized forms of scleroderma (e.g. morphoea) and also systemic forms of the disease that are more correctly termed systemic sclerosis. Systemic sclerosis (SSc) is a multiorgan, autoimmune disease that has a high clinical burden and mortality, due to affecting the skin as well as internal organs. As with other related diseases there is a female predominance and marked clinical diversity. The pathogenesis of SSc is not fully elucidated; it includes endothelial cell injury fibroblast activation and autoimmunity that lead to skin and internal organ manifestations. The majority of cases exhibit characteristic serum autoantibodies. Some of these antibodies are scleroderma-specific reactivities including anti-centromere (ACA), anti-topoisomerase-1 (ATA or Scl 70) or anti-RNA polymerase III antibodies. These anti-nuclear antibody (ANA) patterns are generally mutually exclusive and serve as useful clinical markers of disease subgroups. Additional subsetting of scleroderma cases, based on the extent of skin sclerosis, permits classification into limited and diffuse subsets. Because of the heterogeneity of the disease patients may suffer from different organ manifestations, such as lung fibrosis, hypertensive renal crisis, severe cardiac disease, gastrointestinal involvement, and pulmonary arterial hypertension. Although outcomes have improved recently, systemic sclerosis still has the highest case-specific mortality of any of the autoimmune rheumatic diseases and requires careful and systematic investigation, management and follow-up. Treatment includes symptomatic strategies with attention to each involved organ system; it is still an area where therapeutic progress and better understanding of pathogenesis is increasingly anticipated.

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Whole Blood Transcriptional Profiling of DLBCL At Diagnosis: Evidence of Systemic Changes Altering T-Cell Signaling Pathways

Blood ◽

10.1182/blood.v118.21.2435.2435 ◽

2011 ◽

Vol 118 (21) ◽

pp. 2435-2435

Author(s):

Delphine Rossille ◽

Céline Pangault ◽

Xavier Cahu ◽

Thierry Lamy ◽

Burgun Anita ◽

...

Keyword(s):

Gene Expression ◽

Healthy Volunteers ◽

Signaling Pathways ◽

Differentially Expressed Genes ◽

Whole Blood ◽

Transcriptional Profiling ◽

The Body ◽

Differentially Expressed ◽

Cytokine Signaling ◽

Upregulated Genes

Abstract Abstract 2435 DLBCLs are the most prevalent lymphomas in adults and great advances have been made in understanding molecular effects on tumor cells as well as tissue environment, leading to determining gene prognosis signatures using transcriptional profiling techniques. As blood cells interact with cells in almost all tissues in the body, blood-derived total RNA gene expressions have been investigated for the past years including for solid cancers [Clin Cancer Res. 2006:3374.], infections [Nature 2010;446:973.] and autoimmune disorders [Genes Immun. 2010;11:269., Immunity 2008;29:150.]. Blood-based microarray approaches were able to identify differentially expressed genes distinguishing patients from healthy volunteers. Interested in the potential of this noninvasive and easy-to-use technique, we hypothesized that aggressive DLBCLs at diagnosis cause molecular perturbations on the whole blood allowing identifying gene expression differentiation compared to healthy controls. Whole blood was collected into PAXgene™ Blood RNA tubes ensuring blood stabilization and sent within 24 hours to be stored at −80°C before extraction. Our study involved high-quality RNA samples from 75 DLBCL patients taken at diagnosis prior to any anti-cancer treatment and 87 healthy volunteers, sex and gender matched. All patients were less than 60 and enrolled in a multicentric & prospective clinical trial for aggressive form of DLBCL, GOELAMS 075, which compares the autologous stem cell treatment to regular R-CHOP procedure. The median age was 52 for patients and 48 for controls. Gene expression profiling (GEP) was assessed using Affymetrix GeneChip® Human Exon 1.0 ST arrays. Unsupervised hierarchical clustering analysis (HCA) distinguished DLBCLs from controls. Two gene lists were identified based on HCA (Figure 1): listA consisted in 3,323 upregulated genes for a subgroup of patients and inversely, listB in 2,966 upregulated genes for controls. Canonical pathways were generated for both lists for genes meeting p<5% and FC >1.2 through the use of IPA (Ingenuity® Systems). The upregulated genes for patients (listA) were found associated with cytokine signaling pathways (Interleukins, NF-κB) while the down-regulated genes (listB) were implicated in T lymphocytes signaling pathways. Further investigations of the dataset by univariate analysis (Mann-Whitney test, FDR<5%, FC >1.5) found 1047 differentially expressed genes, confirming the systemic alteration. A set of 20 genes, selected as the best predictive genes for which the misclassification error rate is minimal, was able to discriminate DLBCLs from control samples (sensitivity= 88% & specificity=95%). No correlation was found between genes and biological parameters such as hemoglobin, leucocytes, lymphocytes, platelets or polynuclear neutrophils. The down-regulated genes were located in the nucleus and involved in transcription deregulation, DNA repair and apoptosis. Upregulated genes were related to the immune response as well as the inflammatory response with for instance S100 proteins which are implicated in myeloid-derived suppressor cell biology. Conclusion: Despite the complex mixture of cell types in blood, whole blood has shown strong systemic perturbations in DLBCLs at diagnosis. Biological investigation indicated an over-expression of the inflammation and immune responses combined to perturbations of the T-lymphocyte pattern. Our findings concerning inflammation-related gene expression including NF-κB activation and upregulated cytokine transcripts, with for instance IL-1, IL-6 & IL-10, invite us to determine whether a specific DLBCL-induced inflammation process exists compared to other nonmalignant diseases [Clin Microbiol Rev. 2002 Jul; 15(3):414-29]. Comparison to other lymphoma and inflammatory diseases as well as with tumor status are under way allowing to better characterizing DLBCL-specific biomarkers. These results shed new lights on DLBCL biology deciphering disease's heterogeneity at the RNA whole blood level. They encourage us to investigate whole blood GEP for prognosis and as a new parameter useful for disease classification. Disclosures: No relevant conflicts of interest to declare.

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Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort

Scientific Reports ◽

10.1038/s41598-020-80158-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nikita Baiju ◽

Torkjel M. Sandanger ◽

Pål Sætrom ◽

Therese H. Nøst

Keyword(s):

Gene Expression ◽

Whole Blood ◽

Smoking Status ◽

Expression Profiles ◽

Differentially Expressed ◽

P Value ◽

Smoking Exposure ◽

Former Smokers ◽

Never Smokers ◽

Free Women

AbstractActive smoking has been linked to modulated gene expression in blood. However, there is a need for a more thorough understanding of how quantitative measures of smoking exposure relate to differentially expressed genes (DEGs) in whole-blood among ever smokers. This study analysed microarray-based gene expression profiles from whole-blood samples according to smoking status and quantitative measures of smoking exposure among cancer-free women (n = 1708) in the Norwegian Women and Cancer postgenome cohort. When compared with never smokers and former smokers, current smokers had 911 and 1082 DEGs, respectively and their biological functions could indicate systemic impacts of smoking. LRRN3 was associated with smoking status with the lowest FDR-adjusted p-value. When never smokers and all former smokers were compared, no DEGs were observed, but LRRN3 was differentially expressed when never smokers were compared with former smokers who quit smoking ≤ 10 years ago. Further, LRRN3 was positively associated with smoking intensity, pack-years, and comprehensive smoking index score among current smokers; and negatively associated with time since cessation among former smokers. Consequently, LRRN3 expression in whole-blood is a molecular signal of smoking exposure that could supplant self-reported smoking data in further research targeting blood-based markers related to the health effects of smoking.

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Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patients

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-217116 ◽

2020 ◽

Vol 79 (9) ◽

pp. 1218-1226

Author(s):

Lorenzo Beretta ◽

Guillermo Barturen ◽

Barbara Vigone ◽

Chiara Bellocchi ◽

Nicolas Hunzelmann ◽

...

Keyword(s):

Systemic Sclerosis ◽

Differentially Expressed Genes ◽

Whole Blood ◽

P53 Protein ◽

Differentially Expressed ◽

Type I ◽

Geographical Differences ◽

Rna Transcripts ◽

Cell Counts ◽

Genome Wide

ObjectivesThe analysis of annotated transcripts from genome-wide expression studies may help to understand the pathogenesis of complex diseases, such as systemic sclerosis (SSc). We performed a whole blood (WB) transcriptome analysis on RNA collected in the context of the European PRECISESADS project, aiming at characterising the pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations.MethodsSamples from 162 patients and 252 controls were collected in RNA stabilisers. Cases and controls were divided into a discovery (n=79+163; Southern Europe) and validation cohort (n=83+89; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the Functional Analysis of Individual Microarray Expression (FAIME) algorithm. In parallel, immunophenotyping of 28 circulating cell populations was performed. We tested the presence of differentially expressed genes/pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated.ResultsOverall, 15 224 genes and 1277 functional pathways were available; of these, 99 and 225 were significant in both sets. Among replicated pathways, we found a deregulation in type-I interferon, Toll-like receptor cascade, tumour suppressor p53 protein function, platelet degranulation and activation. RNA transcripts or FAIME scores were jointly correlated with cell subtypes with strong geographical differences; neutrophils were the major determinant of gene expression in SSc-WB samples.ConclusionsWe discovered a set of differentially expressed genes/pathways validated in two independent sets of patients with SSc, highlighting a number of deregulated processes that have relevance for the pathogenesis of autoimmunity and SSc.

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