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2016 ; 6
(6
): 1503-11
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Several Critical Cell Types, Tissues, and Pathways Are Implicated in Genome-Wide
Association Studies for Systemic Lupus Erythematosus
#MMPMID27172182
Liu L
; Yin X
; Wen L
; Yang C
; Sheng Y
; Lin Y
; Zhu Z
; Shen C
; Shi Y
; Zheng Y
; Yang S
; Zhang X
; Cui Y
G3 (Bethesda)
2016[Jun]; 6
(6
): 1503-11
PMID27172182
show ga
We aimed to elucidate the cell types, tissues, and pathways influenced by common
variants in systemic lupus erythematosus (SLE). We applied a nonparameter
enrichment statistical approach, termed SNPsea, in 181 single nucleotide
polymorphisms (SNPs) that have been identified to be associated with the risk of
SLE through genome-wide association studies (GWAS) in Eastern Asian and Caucasian
populations, to manipulate the critical cell types, tissues, and pathways. In the
two most significant cells' findings (B lymphocytes and CD14+ monocytes), we
subjected the GWAS association evidence in the Han Chinese population to an
enrichment test of expression quantitative trait locus (QTL) sites and DNase I
hypersensitivity, respectively. In both Eastern Asian and Caucasian populations,
we observed that the expression level of SLE GWAS implicated genes was
significantly elevated in xeroderma pigentosum B cells (P ? 1.00 × 10(-6)), CD14+
monocytes (P ? 2.74 × 10(-4)) and CD19+ B cells (P ? 2.00 × 10(-6)), and
plasmacytoid dendritic cells (pDCs) (P ? 9.00 × 10(-6)). We revealed that the SLE
GWAS-associated variants were more likely to reside in expression QTL in B
lymphocytes (q1/q0 = 2.15, P = 1.23 × 10(-44)) and DNase I hypersensitivity sites
(DHSs) in CD14+ monocytes (q1/q0 = 1.41, P = 0.08). We observed the common
variants affected the risk of SLE mostly through by regulating multiple immune
system processes and immune response signaling. This study sheds light on several
immune cells and responses, as well as the regulatory effect of common variants
in the pathogenesis of SLE.