Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.
BACKGROUND
Here we integrate verified signals from previous genetic association studies with gene expression and pathway analysis for discovery of new candidate genes and signaling networks, relevant for rheumatoid arthritis (RA).


METHODS
RNA-sequencing-(RNA-seq)-based expression analysis of 377 genes from previously verified RA-associated loci was performed in blood cells from 5 newly diagnosed, non-treated patients with RA, 7 patients with treated RA and 12 healthy controls. Differentially expressed genes sharing a similar expression pattern in treated and untreated RA sub-groups were selected for pathway analysis. A set of "connector" genes derived from pathway analysis was tested for differential expression in the initial discovery cohort and validated in blood cells from 73 patients with RA and in 35 healthy controls.


RESULTS
There were 11 qualifying genes selected for pathway analysis and these were grouped into two evidence-based functional networks, containing 29 and 27 additional connector molecules. The expression of genes, corresponding to connector molecules was then tested in the initial RNA-seq data. Differences in the expression of ERBB2, TP53 and THOP1 were similar in both treated and non-treated patients with RA and an additional nine genes were differentially expressed in at least one group of patients compared to healthy controls. The ERBB2, TP53. THOP1 expression profile was successfully replicated in RNA-seq data from peripheral blood mononuclear cells from healthy controls and non-treated patients with RA, in an independent collection of samples.


CONCLUSIONS
Integration of RNA-seq data with findings from association studies, and consequent pathway analysis implicate new candidate genes, ERBB2, TP53 and THOP1 in the pathogenesis of RA.
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden. klementy.shchetynsky@ki.se.
Klementy
http://orcid.org/0000-0003-4578-5588
K
Shchetynsky
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Lina-Marcella
LM
Diaz-Gallo
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Lasse
L
Folkersen
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Aase Haj
AH
Hensvold
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Anca Irinel
AI
Catrina
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Louise
L
Berg
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Lars
L
Klareskog
Rheumatology Unit, Department of Medicine Centre of Molecular Medicine, CMM:L8:04, Karolinska Institutet/Karolinska University Hospital Solna, 171 61, Stockholm, Sweden.
Leonid
L
Padyukov
D018501:Antirheumatic Agents / Q000627:therapeutic use; D001172:Arthritis, Rheumatoid / Q000188:drug therapy / Q000235:genetics*; D016000:Cluster Analysis; D015331:Cohort Studies; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D008666:Metalloendopeptidases / Q000235:genetics; D008727:Methotrexate / Q000627:therapeutic use; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
D018501:Antirheumatic Agents; D008666:Metalloendopeptidases; D008727:Methotrexate; D018719:Erb-b2 Receptor Tyrosine Kinases; D016159:Tumor Suppressor Protein p53; C495901:TP53 protein, human; C508053:ERBB2 protein, human; C022510:thimet oligopeptidase
Genome-wide; Immunology; Molecular genetics; RNA-seq; Rheumatoid arthritis