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 | |
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 | |
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 | |
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] |