Genetics of systemic sclerosis

IRF5

Interferon regulatory factor 5 (IRF5) is a crucial regulator of type I interferon (IFN) signaling. IFN signatures, IFN-inducible genes, similar to those of SLE in the peripheral blood cells of SSc patients have also been determined. ³⁹

Dieude et al. ²⁰ found an association between the IRF5 intron 1 rs2004640T allele and SSc, especially the ATA(+) dcSSc with fibrosing alveolitis (FA) in French population, suggesting that the rs2004640 could influence the fibrotic phenotype via type I IFN activation. They further performed genotype–phenotype–haplotype correlation analyses of IRF5 with the SNPs rs3757385, rs2004640, and rs10954213, and found that the “R” haplotype (C-T-A) conferred susceptibility to SSc, especially dcSSc, and the “P” haplotype (A-G-G) had protective effect on both dcSSc and FA. ⁴⁰ The “R” haplotype is known to infer the CGGGG insertion risk allele, which leads to increased binding of SP1 transcriptional factor and also known as the causative variant of SLE and Sjogren syndrome. ⁴¹ As all single markers failed to detect association signals, the study suggested the haplotype analyses may be more informative than single-marker analyses.

Association of IRF5 with SSc was also confirmed in the GWAS of SSc,^14,19 and the meta-analysis conducted by Xu et al., ²³ suggesting its association beyond populations. Collectively, these studies strongly indicated a key role of IRF5 in SSc pathogenesis.

STAT4

Signal transducer activator transcriptional factor 4 (STAT4) is a member of the STAT transcription factor family and is essential in mediating interleukin-12 (IL-12) signaling, as well as in helper T-cell differentiation. ⁴² STAT4 also links the innate and the adaptive immune responses through type I IFN-mediated IFN-γ production. ²⁷

Rueda et al. ²⁵ first reported the association of STAT4 in their Caucasian case–control study. The tag SNP rs7574865 (intron 3) T allele, which is correlated with STAT4 mRNA expression ²⁸ and known for its association with other AIDs, ²³ significantly associated with susceptibility to lcSSc as well as lacked the association with dcSSc. A dosage effect was also observed (rs7574865 TT genotype, p = 1.02 × 10⁻⁷). Subsequent two Caucasian GWASs^14,19 also showed significant associations, although the study conducted by Allanore et al. might include populations overlapped with the first case–control study.

On the other hand, a Chinese case–control study conducted by Yi et al. reported different results. The T-allele carriers of rs7574865 as well as rs10168266 were associated with ATA (p = 0.0012 and p = 3.1 × 10⁻⁴, respectively) and PF (p = 1.2 × 10⁻⁴ and p = 7.7 × 10⁻⁴, respectively), as well as with dcSSc (p = 6.4 × 10⁻⁴ and p = 0.0015, respectively). The presence of ACA and lcSSc did not show significant association with any of the examined SNPs in this study. ²⁶

According to a meta-analysis of six case–control studies including the studies above conducted by Xu et al., the rs7574865T allele showed a significant association with SSc susceptibility (p < 0.00001) in the overall population, and both lcSSc and dcSSc showed a significant association with each of the genetic models (lcSSc, p < 1.0 × 10⁻⁵; dcSSc, p < 5.0 × 10⁻⁴ to 1.0 × 10⁻⁵). ²³

Furthermore, our transethnic meta-analysis of GWAS in the Japanese and European populations found a GWS association of rs7574865T allele with overall SSc. ²²

The different effects of rs7574865T allele on SSc subtypes and autoantibody profiles among different ethnicities indicated that an association of the rs7574865T allele with ACA(+) SSc may be limited in European populations while that in Asian populations remained questionable partly because of small sample size of the studies. It might also be possible that different SNPs might be more important for non-European populations.

Notably, Dieude et al. observed that additive effects of STAT4 rs7574865 and IRF5 rs2004640 polymorphisms on susceptibility to both SSc and SSc-related FA. ²⁹ The STAT4 rs7574865T allele and the IRF5 rs2004640T allele resulted in 1.28-fold higher risk of SSc and the odds ratio (OR) for SSc was 2.72 (1.86–3.99) for combinations of genotypes with ⩾3 risk alleles.

The functional role in SSc pathogenesis was also tested in Stat4-knockout mice, which presented decreased cytokine production and protection from skin fibrosis in bleomycin-induced model. ⁴³ Despite several questions remaining to be answered, all the studies above further strongly supported functional consequences caused by STAT4 polymorphisms and their roles in SSc pathophysiology.

IL12, IL12RB1, and IL12RB2

The protein encoded by IL12, the p35 subunit, promotes type 1 helper T-cell differentiation and in combination with IFN-γ antagonizes type 2 helper T-cell differentiation. ⁴⁴

IL12A was one of the non-HLA loci identified by ImmunoChip study conducted by Mayes et al. The missense SNP rs77583790 in an intergenic region between IL12A and SCHIP1 encoding schwannomin interacting protein 1 was significantly associated with overall SSc, and the association was also significant in the lcSSc and ACA(+) subgroup. ⁷

IL12RB1 and IL12RB2 encode both chains of the IL-12 receptor, and both of genes showed suggestive associations with SSc in Caucasian GWAS. ¹⁴ Bossini-Castillo et al. ³¹ subsequently conducted a follow-up study using an independent cohort and observed GWS association of an intronic SNP rs3790567 of IL12RB2 with SSc. The SNP may be a tag of certain functional variant or may have a yet unknown functional implication.

According to the suggestive association signals of IL12RB1 locus in immunoChip study, ⁷ Lopez-Isac et al. ³⁰ conducted a follow-up study, in which four SNPs showed GWS associations with SSc susceptibility (rs8109496, rs2305743, rs436857, and rs11668601). They also suggested that SNP rs436857 in IL12RB1 promoter region was the most likely causal variant. The minor allele of this SNP showed a protective effect and was located in an IL12RB1 cis-eQTL that decreased IL12RB1 expression, ⁴⁵ which would lead to a reduced IL-12 response consistent with a lower SSc susceptibility. ¹² Furthermore, they also reported an association of a common variant (V362F) of TYK2, which encodes tyrosine kinase 2 involved in IL-12 pathway, with SSc susceptibility. ⁴⁶

Collectively, these data in conjunction with those of STAT4, IL-12/STAT4 axis are further implicated as parts of the central roles in the pathogenesis of SSc.

CD247

CD247 encodes CD3ζ chain, ⁴⁷ and altered low expression of CD3ζ chain results in impaired immune response. ⁴⁸ Genetic variants in the 3′ untranslated region of this gene have shown functional implications leading to a reduced expression of the CD3ζ chain that could be manifested in systemic autoimmunity. ⁴⁹

Radstake et al. ¹⁴ identified CD247 (rs2056626) as a susceptibility locus for SSc by European ancestry GWAS. An independent French study confirmed the association and indicated that the minor allele rs2056656G was associated with a protective effect. ³² In sharp contrast, there was no association between the same variant and SSc or any SSc subtypes in a Han Chinese cohort, ⁵⁰ and our transethnic meta-GWAS analysis also failed to replicate the association observed in the European studies above. ²² Further studies to better explain the exact role of CD247 in SSc in different ethnic populations will be of great interest.

PRDM1

PRDM1, B-lymphocyte-induced maturation protein 1, also known as BLIMP1, is a transcription factor influencing a broad range of genes involved with cell proliferation and immune systems. PRDM1 is also critical for epithelial and B-cell differentiation and associated with immune functions and other AIDs. ⁵¹

Our meta-GWAS analysis in the Japanese and European populations identified a significant association of PRDM1 rs4134466 with SSc susceptibility. ²² The rs4134466 was not dependent on rs9373839 in ATG5, a previously reported susceptibility gene to SSc. ⁷ Intriguingly, the rs4134466 provided the highest score of H3K4me3 in naïve CD4+ T cell among the SSc susceptibility variants, suggesting a functional consequence of this variant.

Tumor necrosis factor-α-related genes

TNFAIP3 and TNIP1 encode for tumor necrosis factor (TNF)-α-induced protein (A20) ⁵² and TNFAIP3-interacting protein, respectively. Both A20 and TNIP1 are involved in negatively regulating the TNF-induced nuclear factor (NF)-κB signaling pathway. ⁵³

A European GWAS conducted by Allanore et al. found a significant association of TNIP1 rs4958881 with SSc. ¹⁹ They also observed a markedly reduced expression of the TNIP1 gene and its protein product both in skin lesions and in cultured dermal fibroblasts from SSc patients. Furthermore, TNIP1 showed in vitro inhibitory effects on inflammatory cytokine-induced collagen production. On the other hand, Bossini-Castillo et al. ³³ conducted a replication study in independent Caucasian populations and confirmed the association of rs4958881 (p = 3.26 × 10⁻⁵) as well as other variants (rs2233287, p = 1.94 × 10⁻⁴; rs3792783, p = 2.16 × 10⁻⁴) with SSc and its subgroups.

Multiple studies with different ethnicities have repeatedly reported the associations of TNFAIP3 SNP variants with susceptibility of SSc and its subtypes.^{22,24,34 –37} However, only one of them reached GWS in its association with dcSSc. ³⁴ Considering the close relationship between TNIP1 and TNFAIP3 as described above, it may be important to consider the effects of both of these gene polymorphisms simultaneously.

CSK

C-Src kinase, CSK, is a tyrosine-protein kinase that negatively regulates lymphocyte activation through phosphorylation of the Src-family kinases. ⁵⁴ It has been reported that Src kinases play a central role in the activation of fibroblasts and in the development of experimental fibrosis and Src kinase inhibition reduced the transcriptional activity of COL1A1, COL1A2, and FN1 (which encode collagen type 1 α1, α2 chains, and fibronectin 1) and prevented experimental dermal fibrosis. ⁵⁵

In the GWAS follow-up study conducted by Martin et al., ³⁶ CSK was newly identified as a gene associated with SSc with genome-wide significance (rs1378942). Although the functional relevance of the CSK associated SNP is unknown, genetic variants affecting its inhibitory effect may contribute to the uncontrolled fibroblast activation in SSc pathogenesis. ¹²

GSDMA

Our transethnic meta-GWAS analysis identified a missense variant rs3894194 in GSDMA, which encodes gasdermin A, was associated with overall SSc as well as lcSSc. ²² GSDMA also showed a significant association with other AIDs including RA ⁵⁶ and IBD.^57,58 Importantly, the rs3894194 showed enhancer activity and enrichment of histone marks, and strongly associated with expression of neighboring genes, GSDMB, and ORMDL3, encoding gasdermin B and ORMDL sphingolipid biosynthesis regulator 3, respectively, suggesting this variant as a potential causative SNP. On the other hand, Moreno-Moral et al. ³⁸ recently reported that the rs3894194 conferred changes of transcriptome signatures in SSc macrophages. Although lack of GWS or replications, TLR (toll-like receptor) ⁵⁹ and NLRP (NLR family pyrin domain) ⁶⁰ were also reported to be associated with SSc and encoding proteins as well as gasdermin A are essential components for inflammasome formation and pyroptosis induction, implicating their roles in the innate immune/inflammasome pathway underlying SSc pathogenesis.