ITGAM encodes the α-chain of αMβ2-intergin (CD11b) 16 and plays a role in phagocytosis and leukocyte adhesion 17. GWASs have reported that variants at this locus are associated with SLE, and single-nucleotide polymorphism (SNP) rs9888739 showed the strongest association (P = 1.61 × 10⁻²³, odds ratio (OR) = 1.62). However, a trans-ancestral study in European-Americans and African-Americans 18 indicated the causal variant as rs1143679, which has been reported to cause two functional changes in ITGAM. The first of these functional changes is an amino acid mutation at R77H (Arg-His) which modifies the tertiary and quaternary structures of the αMβ2 ligand-binding domain 18. αMβ2-integrin interacts with a number of ligands such as intracellular adhesion molecule 1 (ICAM-1) and the complement C3 degradation product, C3bi; these ligands play a role in leukocyte activation, migration, and phagocytosis 16. Variants in the αMβ2 ligand-binding domain may alter binding affinity, hence leukocyte trafficking, phagocytosis 16, and IC clearing 19. The second functional change is with rs1143679, which impairs the phagocytosis of C3bi-coated particles 20 and propagates the deficient clearance of ICs and increased inflammation 20. However, the exact mechanism of how both of these variants influence the pathogenesis of SLE warrants further investigation.

The FCGR genes encode diverse Fcγ receptors that recognize the Fc portion of immunoglobulin G (IgG) molecules. Several missense polymorphisms in FCGR2A, FCGR2B, and FCGR3A 212223 are associated with SLE. Three of the five FCGR genes (FCGR3A, FCGR2C, and FCGR3B) have been reported to show CNV 24 and expression of Fcγ receptors on the cell surface is dependent on the number of copies expressed 2526. A CNV that resulted in a reduced number of FCGR3B molecules expressed on the cell surface of neutrophils is associated with SLE. The exact mechanism by which the CNV incorporating FCGR3B promotes disease is not fully established, although reduced binding of ICs by neutrophils is a possible mechanism.

TNFAIP3 encodes the ubiquitin-editing enzyme A20 2829, which alters ubiquitin patterns, which then alter targeting for proteosome degradation and termination of nuclear factor-kappa-B (NF-κB)-derived pro-inflammatory responses. This occurs through the ubiquitination of IKKγ and phosphorylation of IκBα 3031, facilitating the release of NF-κB (Figure 2). A20 is a key regulator of NF-κB through ubiquitin modifications of receptor-interacting protein kinase (RIP) and tumor necrosis factor receptor-associated kinase 6 (TRAF6) 32.Multiple associations have been found in TNFAIP3 in a range of autoimmune diseases 28; of these associations, rs2230926 has shown the strongest significance (P = 1.37×10⁻¹⁷, OR = 1.72) in SLE. This non-synonymous SNP 33 causes an amino acid change from a Phe-Cys. This amino acid change propagates A20 protein to be less effective at inhibiting tumor necrosis factor (TNF)-induced NF-κB activity 34. Variants at this locus could potentially lead to reduced inhibitory activity of NF-κB and reduced expression of A20.

Owing to increased NF-κB signaling, Tnfaip3^−/− mice develop spontaneous inflammation and lymphocyte cell death 35. This shows the importance of TNFAIP3 in NF-κB regulation through the ubiquitination of adaptors such as RIP 35. Therefore, it can be seen that TNFAIP3 is an important locus that contributes to SLE pathogenesis through its downregulation. The downregulation of TNFAIP3 facilitates hyperactive NF-κB signaling, chronic inflammation, and reduced apoptosis, all characteristics of SLE.

TNIP1, an adaptor protein that binds to A20, has also been reported to be associated with SLE. TNIP1 is expressed on lymphocytes and its expression is inducedby NF-κB 36. However, overexpression of TNIP1 inhibits NF-κB activation by TNF 37. Variants in TNIP1 could potentially play a role in negatively regulating the NF-κB pathway 38. SNP rs7708392 has been reportedto play a role in TNIP1 splicing, rendering the inhibition of the NF-κB pathway less effective. This would propagate pro-inflammatory responses and chronic inflammation. This variant has been shown to be associated with Caucasian and Asian populations 36.

UBE2L3 is a ubiquitin-carrier enzyme gene and is expressed widely on all lymphocytes 39. It plays a key role in the maturation of transcription factors (for example, p53 and p105, the latter of which is an NF-κB precursor) 4041. This enzyme regulates IFN through TLR7/9 4243. The exact mechanism of UBE2L3 is still not fully understood, but variants in this locus have been shown to be associated with SLE (rs463426,P = 1.48×10⁻¹⁶, OR = 0.78).

ETS1 and IKZF1 are transcription factors that regulate lymphocyte differentiation and lymphocyte development 4647. ETS1 has been reported as a negative regulator of B-cell differentiation and T helper 17 (Th₁₇) cell proliferation 48. Patients with SLE demonstrate a reduced expression of ETS1, which may contribute to abnormal B-cell differentiation into immunoglobulin-secreting plasma cells and an increased number of Th₁₇ cells 495051. While having increased proliferation of Th₁₇ cells causes increased inflammation through the secretion of interleukin-17 (IL-17), ETS1-deficient Th₁ cells secrete higher amounts of anti-inflammatory cytokine IL-10 52. Interestingly, these ETS1-deficient Th₁ cells have reduced secretion of IL-2, which is a potent Th₁₇ inhibitor 52. The top associated variant at this locus, rs6590330 (P = 1.77×10⁻²⁵, OR = 1.37), could potentially play a role in decreasing ETS1 expression.

Patients with SLE have also been reported to express low IKZF1 levels in peripheral blood 48. The strongest association found at this locus is rs4917014 (P = 2.75×10⁻²³, OR = 1.23) 53, which may play a role in downregulating IKZF1 expression. This reduced level of expression contributes to SLE pathogenesis through interactions with other genes; for example, IKZF1 has been reported to play a role in trans-activating STAT4, a confirmed risk locus in SLE 54. IKZF1 is important for lymphocyte differentiation 55 and regulation of self-tolerance through B-cell receptor (BCR) signaling 56. Downregulation of this locus would therefore promote loss of self-tolerance, a hallmark of SLE.

The gene products of BANK1, BLK, and LYN operate in the BCR signaling pathway and have been reported to be associated with SLE 58, which together attest to the importance of this pathway in disease pathogenesis.rs10516487, located in the BANK1-binding region 59, has shown the strongest association with SLE (P = 3.1 × 10⁻¹⁰, OR = 1.38). After B-cell activation, BANK1 becomes tyrosine-phosphorylated, resulting in phosphorylation of type 1 inositol-1,2,4-triphosphate(IP(3)R). This phosphorylation event serves to augment calcium mobilization and hence B-cell activation 60. The associated variant at BANK1 increases its expression by influencing splicing efficiency, creating a splicing enhancer 59. The expression increase propagatesstronger binding affinity between BANK1 and IP(3)R, resulting in hyper-responsiveness 61. Cells expressing the risk allele of this variant also have higher protein levels, which can sustain BCR signaling and hyperactive B cells, as shown in SLE 59.

Associated allelic variants in BLK (rs7812879,P = 2.09×10⁻²⁴, OR = 0.69) and LYN (rs7829819,P = 5.40×10⁻⁹, OR = 0.77), in comparison with BANK1, have been shown to decrease their respective expressions 6162. LYN kinase mediates inhibitory signals from CD22, which modulates the B-cell activation threshold 63. Downregulation of LYN causes hyper-responsiveness of BCR stimulation, triggering autoimmunity 64 asshown in Lyn^−/− mice 65. Compared with BLK, which affects pre-BCR signaling, active BLK enhances BCR responsiveness 66. Blk^−/− mice have shown no phenotype 67; thus, an interaction with BANK1 could potentially explain the association with SLE 61. As LYN and BLK share similarities of genomic structure 64, it is believed that, in BCR signaling, BLK plays a role similar to that of LYN.

RasGRP3 regulates Ras-ERK signaling, which is crucial in lymphocyte development and activity 68, and is involved in B-cell proliferation and immunoglobulin production 53. rs13385731 (P = 1.25 × 10⁻¹⁵, OR = 0.70) at the RasGRP3 locus has been reported to be associated with SLE and may cause an underexpression of RasGRP3, which blocks its inhibitory role in B-cell proliferation.

NCF2 is a cytosolic subunit of NADPH oxidase, which is expressed on B cells 69. It is thought to play a role in the increased production and release of free radicals, propagating B-cell activation. rs10911363 (P = 2.87 × 10⁻¹¹, OR = 1.18) has been shown to have reached genome-wide significance in SLE 69 and could play a role in increased NCF2 expression in patients with SLE.

STAT4 is a Th₁ transcription factor that has been reported to mediate Th₁ T-cell response, Th₁ cytokines, IL-12 and IL-23 7475, and IFNγ signaling 7677. rs7574865 has been reported to have the strongest association with SLE (P = 5.17 × 10⁻⁴², OR = 1.51) and has also been described for other autoimmune diseases such as rheumatoid arthritis (RA) 74, Sjögren's syndrome 78, inflammatory bowel disease, and type 1 diabetes(T1D) 79. rs7574865 has been described as being associated with many SLE clinical features, such as lupus nephritis 80. STAT4 propagates a Th₁ T-cell response, increasing IFNγ release 81. As seen in Figure 1, this influx of IFNγ would target organs such as the kidneys, propagating further IFNγ release and chronic inflammation. rs7574865 may act to increase STAT4 expression and hence IFNγ production. Further reports have shown that other associated variants, such as rs7582694 (intronic), show overexpression of the risk allele (C) in mesenchymal cells but not in B cells 82. Th is STAT4 risk allele was also reported to be overexpressed in cells carrying the risk haplotype in comparison with cells not carrying this haplotype 82.

PTPN22 encodes the lymphoid tyrosine phosphate protein, LYP, which is involved in the down regulation of T-cell activation through the inter action with cytoplasmic tyrosine kinase (CSK) and suppression of T regulatory cells 83. rs2476601 (P = 3.4 × 10⁻¹², OR = 1.35) has been reported to be associated with SLE and also with T1D and RA 84. Furthermore, a trans-ancestral study has shown that rs2476601 is associated with SLE in Europeans, Hispanics, and African-Americans 85. The associated variant causes the amino acid change of Arg-Try, preventing PTPN22 interaction with CSK 8687. However, the experimental evidence suggests that rs2476601 reduces TCR signaling 88. Furthermore, PTPN22 expressing the associated risk allele (A) has been reported to bind CSK less effectively than those expressing the G allele, producing hyper-responsive T cells 85. Therefore, the current experimental evidence does not give us the full understanding of PTPN22 function and warrants further investigation.

TNFSF4 is expressed on the surface of antigen-presenting cells (APCs), B cells, and macrophages, and its unique ligand CD123 (OX40) is expressed on activated CD4⁺ and CD8⁺ T cells 89. The strongest association in TNFSF4 is with the upstream variant rs2205960 (P = 2.5 × 10⁻³², OR = 1.46), and protective and risk haplotypes that carry alternate alleles of rs2205960 have been observed 90. The risk haplotype has been reported to be associated with increased TNFSF4 transcript levels 9192. This increased expression of OX40L promotes OX40/OX40L interactions and increases the co-stimulatory signal between APCs and T cells, and this in turn increases T-cell survival and thereby propagates autoimmunity. OX40L has been shown in vitro to inhibit the generation of IL-10-producing T regulatory cells needed for tolerance, and it is known that mutations in this pathway cause loss of tolerance and autoimmunity 93.

The major histocompatibility complex (MHC) region has been shown to exert the strongest genetic association and effect in SLE to date; the top association was found atHLA-DRB1 (P = 2.0 × 10⁻⁶⁰, OR = 1.98). Studies examining the association with HLA class II have implicated both HLA-DRB1*03:01 and HLA-DRB1*15:01 94 in SLE. The MHC is composed of 250 genes subdivided into three classes (I, II, and III) with a strong linkage disequilibrium (LD) spanning the region. There appear to be multiple independent signals at the MHC in SLE, accounting for the overall strength of the association seen with the region. One paper reported a 180-kb region of class II, spanning HLA-DRB1, HLA-DQA1, and HLADQB 95, whereas the second signal was found in a marker of the class III gene SKIV2L. Other immunologically relevant genes such as complement C4A and C4B are also in this region of MHC. The strong LD covering the extended MHC region makes it difficult to identify whether the association arises from the associated variants currently identified or from variants within this LD region. For this reason, further fine mapping of the region is needed and the region may also benefit from trans-ancestral mapping 96.

IRF5, IRF7, and IRF8 are transcription factors that play a role in type 1 IFN signaling and immune cell development 99. SNPs in IRF5, IRF7, and IRF8 (P = 5.8 × 10⁻²⁴, OR = 1.88; P = 3.0 × 10⁻¹⁰, OR = 0.78; and P = 1.24 × 10⁻⁸, OR = 1.17, respectively) (as shown in Table 1) have been shown to be associated with increased risk of SLE 98. These variants have been shown to increase the levels of IRF5, IRF7, and IRF8 transcript and protein expressions 100. Of these three loci, IRF5 exhibits the largest effect. An IRF5 risk haplotype has been observed and carries multiple mutations, including rs2004640, which has been reported to create a novel splicing variant. Another variant found at the 3' untranslated region, rs10954213, has been reported to create a more functional polyadenlyation site, which creates a more stable transcript 101. Variants in the IRF5 locus influence alternatively spliced transcripts, which alter or prolong IRF5 expression. Hence, increased expression of IRF5 propagates increased IFNα production. Little is reported for IRF7 and IRF8; therefore, these loci warrant further investigation to determine the functional consequences of the associated variants.

IFIH1 is a DEAD box helicase that senses intracellular RNA and induces IFN (type 1) activation 102. Variants at this locus have been associated with other autoimmune diseases such as T1D 103, autoimmune thyroid disease 104, and psoriasis 105. The top associated SNP in SLE is rs1990760 (P = 1.63 × 10⁻⁸, OR = 1.23), which has been shown to increase expression of IFIH1. This increased expression could contribute to an IFN cascade initiated by nucleic acids.

TYK2 plays an important role in the pro-inflammatory immune response, being involved in cytokine signaling and the phosphorylation of IFN receptors, triggering a type 1 IFN response 69. Variants in TYK2 have been reported to increase type 1 IFN gene expression 106 and deregulate the Th₁/Th₁₇ response. Th₁₇ cells are pro-inflammatory, and their differentiation is dependent on IL-6 and transforming growth factor-beta (TGFβ), both of which are cytokines that are regulated by TYK2 107. The top associated SNP in SLE, rs280519 (P = 3.88 × 10⁻⁸), has been shown to play a role in increasing gene expression and IFN production. Variants propagating increased TYK2 function have also been reported to lead to a pro-inflammatory phenotype with increased levels of Th₁/Th₁₇ cells 107. Multiple variants in TYK2 have been reported to be associated with other autoimmune and inflammatory diseases 108.

The PRDM1-ATG5 gene region has shown a significant association with increased risk of SLE at the intergenic variant rs548234 (P = 5.1 × 10⁻¹², OR = 1.25) 109. This variant has been shown to increase the expression of ATG5 in individuals who are homozygous for the C allele 109. Since ATG5 is important for the formation of autophagosomes 110, increased expression of this gene increases autophagy, which in turn stimulates the IFNα and NF-κB pathways 109 and exacerbates the immune response. However, PRDM1 (BLIMP1) has been reported to play a role in B-cell differentiation 111, and so variants that affect PRDM1 could allow plasma cell differentiation, which further propagates hyperactive B cells and auto-antibody production. PRDM1 has also been reported to maintain immune tolerance and has been shown to alter DC function in female mice that lack PRDM1 expression on DCs. These mice also develop lupus-like auto-antibodies 112. Therefore, both ATG5 and PRDM1 could potentially have causal effects for lupus. Consequently, further experiments will be required to establish whether one (or perhaps both) of these genes plays a role in genetic susceptibility to SLE.

One trans-ancestral study (Europeans, African-Americans,and Asians) reported two intergenic SNPs between PDHX-CD44 113. PDHX plays a role in the pyruvate dehydrogenase complex, and CD44 is an integral cell membrane glycoprotein, which plays a role in cell-cell interactions and regulation of IFNγ and LCK 58. Variants in CD44 alone have been shown to be associated with SLE 58. CD4⁺ and CD8⁺ T cells of patients withSLE have been shown to overexpress CD44, causing an influx of IFNγ, inflammation, and tissue damage 113. This fact suggests that the intergenic associations are pointing toward CD44 as a more likely candidate gene for SLE than PDHX.