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Table 1 Genomics studies in rheumatic diseases

From: Transcription profiling of rheumatic diseases

Disease Tissue Number of samples Approximate number of genes on array Comparison Results Reference
RA Synovium 13 RA 16,164 Intra- and interindividual patients Gene expression differences between patients are greater than between biopsies obtained from the same joint [7]
RA Synovium 5 RA and 10 OA 5,760 RA versus OA Genes differentially expressed between RA and OA [5]
RA Synovium 21 RA and 9 OA 11,500 and 18,000 Within RA and versus OA Evidence for the existence of multiple pathways of tissue destruction and repair [8, 9]
RA Synovium 12 early and 4 late 23,040 Early versus longstanding RA Early RA fell into two groups based on differences in genes critical for proliferative inflammation [16]
RA Synovium 10 RA 30,000 cDNA spots Before versus after about 9 weeks of infliximab Genes specifically changed in patients who have a good response to infliximab treatment. [53]
RA Synovium 18 RA 18,000 Responders versus nonresponders to infliximab treatment Patients with high expression levels of genes involved in tissue inflammation before treatment are more likely to benefit from Infliximab therapy. [54]
RA Synovium 12 RA 11,500 and 18,000 Within RA Identification of IL-7 signalling pathway in tissues characterized by lymphoid neogenesis [15]
RA FLS 19 RA 18,000 Within RA Heterogeneity between synovial tissues is reflected in FLSs [27]
RA FLS 2 RA 12,600 Resting versus TNF-α or IL-1β4-hour stimulated cells Identification of TNF-α and IL-1β regulated genes in RA FLSs [26]
RA FLS 5 RA and 5 HC 588 RA versus HC Over-expression of genes responsible for tumor-like growth in RA FLSs [24]
RA Whole blood 35 RA and 15 HC 18,000 Within RA and versus HC Assignment of a type I IFN signature in a subpopulation of Patients [39, 40]
RA PBMC 19 4,300 Early versus longstanding RA Gene signature in early disease overlaps with normal response to virus [38]
RA PBMC 29 RA and 21 HC 12,626 RA versus HC Monocyte associated gene signature increased in RA [36]
RA PBMC 33 10,000 Before versus 3 months after infliximab Gene expression profile correlating with treatment response [51]
RA PBMC 8 RF+, 6 RF- and 7 HC 10,000 RF+ versus RF- and versus HC No genes differentially expressed between RF+ and RF- RA patients. Increased expression of immunoinflammatory response genes, especially those related to phagocytic functions, in RA [35]
RA PBMC 19 18,500 Before versus 72 hours after etanercept Gene pairs and triplets predictive for response to treatment at an early stage of treatment [52]
RA B-cells 8 RA versus 8 HC 21,329 RA versus HC Dysregulated B-cell biology in RA is multifaceted [37]
SSc Skin biopsies 24 SSc and 6 HC 33,000 Within SSc and versus HC A 177-gene signature associated with severity of skin disease in diffuse SSc [14]
SSc Dermal fibroblasts 15 SSc twins and 5 HC 16,659 Lesional versus nonlesional and versus twin pair and versus HC At the molecular level, concordance for the SSc fibroblast phenotype is high in MZ twins and greatly exceeds that in DZ twins [31]
SSc Dermal non-lesional fibroblasts 21 SSc and 18 HC 16,659 Lesional versus nonlesional and versus HC Fibroblasts from nonlesional sites in SSc have detectable abnormalities in a variety of cellular processes, including ECM formation, fibrillogenesis, angiogenesis and complement activation [30]
SSc PBMC 18 SSc and 18 HC 16,659 SSc versus HC Differentially regulated expression of genes involved in IFN and vasculopathy [42]
SSc PBMC 9 early diffuse SSc and 4 HC 38,500 SSc versus HC Type I IFN induced Siglec-1 is increased on circulating SSc CD14+ monocytes [43]
SS Minor salivary glands 10 SS and 10 HC 6,803 SS versus HC Increased expression of genes involved in chronic inflammation and type I IFN [13]
SS Minor salivary glands 7 SS and 7 HC 7,261 SS versus HC Activation of IFN pathways in SS [17]
SS Whole saliva 10 SS and 8 HC 38,500 SS versus HC Activation of IFN pathway in SS [18]
SLE Synovium 6 SLE, 7 RA and 6 OA 38,500 SLE versus RA versus OA The different diseases were characterized by distinct molecular signatures. Upregulation of IFN-induced genes and downregulation of genes involved in ECM homeostasis in SLE [6]
SLE Glomeruli 12 SLE and 4 HC 3,602 and 4,030 SLE versus HC and within SLE Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis [12]
Paediatric SLE PBMC 30 SLE, 12 JCA and 9 controls 12,626 SLE versus JCA versus controls IFN signature in the majority of SLE patients and upregulation of granulocyte specific transcripts [32]
SLE PBMC 48 SLE and 42 HC 10,260 Within SLE and versus HC About half of the patients studied exhibited dysregulated expression of genes in the IFN pathway associated with more severe disease [33]
SLE Whole blood 269 patients 256 Within SLE Categorization of SLE patients into two groups based on a high or low IFN signature. Disease activity correlates with the high IFN signature [34]
Paediatric SoJIA PBMC 44 SoJIA, 94 infected patients, 38 SLE, 6 PAPA and 39 healthy controls 17,454 SoJIA versus controls A SoJIA-specific gene signature containing 88 genes. Blood transcriptional patterns in the systemic phase of SoJIA are more similar to those of patients with infections than to those of SoJIA patients in a later arthritic stage of disease [45]
Paediatric SoJIA PBMC 8 untreated and 5 infliximab treated SoJIA 17,454 Treated versus untreated Patients Increased expression of type I IFN regulated genes in the anti-TNF treated SoJIA patients, suggesting cross-regulation between TNF and type I IFN [55]
Autoimmune diseases PBMC 20 RA, 24 SLE, 5 type I diabetes, 4 MS and 9 HC 4,329 Between autoimmune disease Overlapping gene expression profiles in RA, SLE, type I diabetes and MS, which is distinct from a normal immune response profile [48, 58, 59]
RA, SLE Whole blood 6 HC, 4 RA, 4 SLE and 5 family members 4,000 RA versus SLE versus HC versus family Shared autoimmune gene expression signature in patients and unaffected first-degree relatives [47]
  1. DZ, dizygotic twin; ECM, extracellular matrix; FLS, fibroblast-like synoviocyte; HC, healthy control individuals; OA, osteoarthritis; IFN, interferon; IL, interleukin; JCA, juvenile chronic arthritis; MS, multiple sclerosis; MZ, monozygotic; PAPA syndrome, a familial autoinflammatory disease that causes pyogenic sterile arthritis, pyoderma gangrenosum and acne; PBMC, peripheral blood mononuclear cell; RA, rheumatoid arthritis; RF, rheumatoid factor; SLE, systemic lupus erythematosus; SoJIA, systemic onset juvenile idiopathic arthritis; SS, Sjögren's syndrome; SSc, scleroderma; TNF, tumour necrosis factor.