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Table 1
Genomics studies in 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]

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.
van Baarsen et al. Arthritis Research & Therapy 2009 11:207 doi:10.1186/ar2557

Table 1