WDFY4基因导致系统性红斑狼疮易感的功能变异鉴定及机制研究
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摘要
系统性红斑狼疮(Systemic Lupus Erythematosus, SLE)是一种典型的自身免疫性疾病,患者体内大量自身抗体的产生和免疫复合物的沉积导致了严重的炎症反应和多器官损伤。SLE具有高度的家族聚集现象,同卵双生子的患病一致率达到了24-56%,因此,SLE的发生很大程度上受到遗传因素的影响。
2005年,全基因组关联分析(Genome Wide Association Study, GWAS)的出现,极大地促进了SLE的遗传学研究,目前GWAS已经鉴定出40多个SLE的易感位点。2009年,针对亚洲人群SLE的两个GWAS研究发现,位于10q21的WDFY4-LRRC18区域是SLE的一个易感区域。该区域中的rs877819,rs7097397和rs1913517与亚洲人群SLE相关,其中rs1913517同时位于LRRC18和WDFY4基因的内含子。2013年,有研究发现rs1913517也是高加索人群SLE的易感变异位点。
WDFY4是WDFY家族的第四位成员,主要表达于一些免疫组织,如淋巴结、脾脏、胸腺和扁桃体等,提示它有可能参与机体的免疫功能。WDFY4含有多个转录本,最大的转录本可编码一个含有3184个氨基酸的巨大蛋白。WDFY4最近的同源体是同一家族的WDFY3,它们的C末端都含有BEACH (Beige and chediak-kigashi)和WD40(WD-repeat)结构域,不同的是WDFY4没有该家族特有的FYVE锌指结构域。WD40结构域存在于一系列真核蛋白中,包含该结构域的蛋白主要参与细胞信号转导调控、pre-mRNA的加工和细胞骨架的形成等。大多数包含有BEACH结构域的蛋白通常可以作为支架蛋白参与膜事件,例如：促进质膜的融合和解离。最近的研究结果发现BEACH蛋白突变可以导致多种疾病以及各种细胞畸变,如溶酶体畸变、细胞凋亡和自噬等。另外,WDFY4蛋白在多个物种间具有高度的保守性。到目前为止,关于这一保守蛋白的功能研究,仍是一个空白。
虽然GWAS研究已经证实了WDFY4-LRRC18区域与中国汉族人群SLE的相关性,但是这些研究主要是在中国南方汉族人群中开展的。由于关联分析的结果具有人群差异,那么,WDFY4-LRRC18是否也与中国北方汉族人群SLE有关?在该区域的3个SLE易感SNP位点中,哪个为功能变异?功能变异是如何影响SLE发生的?该区域导致SLE易感的分子机制又是什么?为了解决这些问题,我们进行了以下研究。
第一部分
WFY4-LRRC18区域与中国北方汉族人群SLE的关联分析
为了研究WDFY4-LRRC18区域中rs877819, rs1913517和rs7097397位点与中国北方汉族人群SLE的相关性,我们利用病例-对照关联研究的方法,对这三个SNP位点进行了关联分析。400例SLE患者均来自山东大学齐鲁医院和省立医院的风湿免疫科,1000例健康对照则是来自这两家医院的健康查体者,他们的年龄、种族和地理区域等相匹配。
所有三个位点等位基因频率及基因型频率符合Hardy-Weinberg平衡(P>0.05),具有群体代表性。其中,2个SNP位点rs877819和rs7097397与SLE具有显著的相关性(P=0.015, OR1.36,95%CI1.06-1.75; P=0.0004, OR1.36595%CI1.148-1.622)。在病例与对照中,rs1913517位点的等位基因频率则没有明显差异(P=0.244,OR1.13195%CI0.929-1.392),说明rs1913517与中国北方汉族人群SLE没有相关性。连锁不平衡分析表明,这3个SNP的连锁不平衡性较弱,r2<0.75。
本部分结果验证了GWAS的结果,表明WDFY4-LRRC18区域也是中国北方汉族人群SLE的易感位点,2个SNP位点rs877819和rs7097397与中国北方汉族人群SLE显著相关。
第二部分
WDFY4-LRRC18导致SLE易感的基因及功能变异的鉴定
由于与SLE相关联的rs1913517同时位于WDFY4和LRRC18基因的内含子,那么,哪个基因才是与SLE直接相关的呢?为了鉴别出真正参与SLE发生的易感基因,我们分别检测了58名SLE患者和58名健康对照外周血单核细胞中WDFY4和LRRC18基因的相对表达水平。结果发现,与健康对照相比,SLE患者中WDFY4基因的相对表达水平显著下降(P<0.05),而LRRC18基因的表达则没有明显差异,说明WDFY4是SLE的易感基因,并且低表达的WDFY4与SLE的发生有关。
既然WDFY4是SLE的易感基因,但是与SLE有关的功能变异还不清楚。因此,我们首先选取了70名健康对照个体,对他们WDFY4基因的61个外显子进行测序,结果没有发现可能具有功能作用的新变异。
GWAS研究表明rs877819, rs7097397和rs1913517是WDFY4基因中SLE的易感位点,但是尚不能确定哪个是功能变异。为了从3个SNP位点中鉴别出SLE的功能变异,我们首先分析了rs877819和rs1913517位点与SLE的相关性。连锁不平衡分析表明这两个位点是强连锁的(r2=0.93)。logistic回归分析结果表明rs877819是SLE的易感SNP, P=2.5×10-4,利用独立贡献检验,在屏蔽了rs877819的作用后,rs1913517与SLE没有相关性,P=0.7758。以上结果说明rs1913517位点不是SLE的功能变异,它与SLE的易感性依赖于rs877819。
对于外显子中的rs7097397位点,我们采用焦磷酸测序的方法检测了rs7097397位点的等位基因特异表达(Allele Specific Expression, ASE)。我们选取了31个rs7097397位点AG基因型的杂合子健康个体,对其外周血单核细胞中的cDNA和基因组DNA进行焦磷酸测序,结果发现rs7097397位点等位基因表达没有差异,该位点可能不是SLE的功能变异。
由于rs877819位点位于内含子中,所以我们利用实时定量PCR的方法分析了rs877819等位基因对WDFY4和LRRC18基因表达的影响。鉴于rs877819A的频率非常低,AA基因型个体较少,我们只选取了rs877819位点40个GG基因型和15个AG基因型的个体,分别检测了他们外周血单核细胞中WDFY4和LRRC18基因的相对表达水平。结果发现,AG基因型个体中WDFY4基因的相对表达水平明显低于GG基因型的个体(P<0.05),而LRRC18的相对表达水平没有明显的差异,说明rs877819A与WDFY4基因的低表达有关。
本部分研究结果表明,WDFY4是SLE真正的易感基因。位于该基因内含子中的rs877819可能是导致SLE易感的功能变异,危险等位基因A与WDFY4的低表达有关,这可能是导致SLE患者中WDFY4基因低表达的原因。
第三部分分
功能变异rs877819导致SLE易感的分子机制
由于内含子变异rs877819的危险等位基因A与WDFY4的低表达有关,所以我们推测该位点有可能影响了基因的转录活性。为了检测rs877819不同等位基因转录活性的差异,我们进行了双荧光素酶报告基因分析。与预期相一致,在HeLa和HEK293T细胞中,rs877819罕见等位基因A的相对转录活性显著低于常见等位基因G(P<0.001),因此,rs877819等位基因A可能导致了WDFY4的低表达。
由于rs877819等位基因影响了WDFY4的转录活性,所以我们针对rs877819位点等位基因进行了电泳凝胶迁移率实验(EMSA),验证该SNP是否为转录因子结合位点。结果发现rs877819确实能与细胞核蛋白相结合,并且等位基因G与该蛋白的结合亲和力大于等位基因A。
MatInspector软件预测,与rs877819位点结合的转录因子可能是Freac2, ZBTB7和Yinyang1(YY1)。所以我们合成了这3个转录因子的保守结合序列,进行竞争实验。结果发现,只有YY1的保守结合序列能完全竞争掉结合条带,所以YY1可能是与rs877819结合的转录因子。超迁移率实验(Supershift)结果也表明YY1抗体能够结合到rs877819位点的DNA-蛋白结合复合物上,而突变的YY1保守序列不能竞争结合条带,说明rs877819位点所在序列能够与转录因子YY1特异结合。与EMSA结果相一致,染色质免疫共沉淀实验(ChIP)也表明,rs877819位点也能够与转录因子YY1相结合。
我们的结果说明WDFY4基因的内含子变异rs877819能够与内源性YY1蛋白发生特异结合,并且罕见等位基因A与YY1的亲和力低于等位基因G,这可能是rs877819A导致WDFY4低表达的原因。
为了研究转录因子YY1对rs877819等位基因转录活性的影响,我们将rs877819等位基因G或A连入荧光素酶报告基因载体,并且与YY1的干扰RNA(siRNA)或表达载体(CMV-YY1)共转染细胞,进行双荧光素酶报告基因分析。结果表明,YY1对rs877819等位基因G的转录活性起正调控作用,却几乎不影响等位基因A的转录活性。
本部分研究结果表明,起正调控作用的转录因子YYl能够结合到rs877819位点,并且与等位基因A的亲和力较低,使得等位基因A转录活性下降,从而导致了WDFY4的低表达,而低表达的WDFY4导致了SLE的易感。
第四部分WDFY4基因对自噬通路的影响
WDFY4最相近的同源体是同一家族的WDFY3,它们的C末端都包含了相对保守的BEACH结构域和WD40结构域。WDFY3编码了一个自噬相关蛋白ALFY(autophagy-linked FYVE protein),参与选择性自噬。已经有越来越多的研究表明自噬可能参与了自身免疫病的发生。既然WDFY4蛋白与WDFY3结构如此相似,那么WDFY4是否也参与自噬呢?它导致SLE的易感是否是通过自噬通路实现的呢?带着这些问题,我们首先检测了WDFY4基因的表达模式以及狼疮小鼠脾脏中的自噬水平。结果发现,无论是人类还是小鼠的脾脏、胸腺等免疫组织中,WDFY4的表达水平高于其它组织。另外,与对照小鼠相比,狼疮小鼠脾脏中,Wdfy4表达水平下降,自噬水平升高。那么,自噬水平的升高是否与Wdfy4的低表达有关呢?
我们检测了WDFY4在Jurkat, NK92, Raji和THP-1等不同免疫细胞中的表达模式,结果发现,B淋巴瘤细胞Raji中WDFY4的表达水平远高于其它3种细胞,表明该基因在B细胞中高表达。我们还将WDFY4的shRNA和包含BEACH-WD40结构域表达载体(由于WDFY4蛋白太大,无法构建全长的表达载体)转染细胞,氯喹处理后,免疫印迹法检测细胞自噬流。结果发现低表达的WDFY4促进了自噬流,而BEACH-WD40结构域的高表达则抑制了自噬流。
为了研究WDFY4抑制自噬的分子机制,我们检测了shWDFY4细胞以及BEACH-WD40结构域高表达细胞中,自噬相关蛋白的表达水平。结果发现,低表达WDFY4的细胞中,Bcl2表达水平下调；而高表达BEACH-WD40结构域的细胞中,Bcl2表达水平升高。Bc12是一个抗凋亡蛋白,它的高表达会抑制细胞凋亡。另外,Bc12可以与自噬蛋白Beclinl相结合,使参与自噬的Beclinl蛋白减少,从而抑制细胞自噬。由于过度自噬也可能导致细胞自噬性死亡,所以Bc12可能直接抑制细胞凋亡,也可能抑制细胞自噬性死亡。
接下来,我们用流式细胞术的方法,检测了低表达的WDFY4和高表达的BEACH-WD40结构域对细胞凋亡的影响。与预期相一致,低表达的WDFY4促进了细胞凋亡,高表达的BEACH-WD40结构域则抑制细胞凋亡。
Systemic lupus erythematosus (SLE) is a prototype autoimmune disease, characterized by autoantibody production and immune complex (IC) deposition leading to severe inflammatory reaction multi-organ damage. Epidemiological studies suggest strong contribution of genetic factors in the etiology of SLE. SLE has high tendency of familial aggregation and a higher concordance rates between monozygotic twins (25-56%).
Since2005, Genome-wide association studies (GWASs) have greatly drived the genetics study of SLE. By now, GWASs have confirmed genetic associations of over40genes/loci with SLE during the past several years. In2009, two GWASs in east Asian populations have discovered WDFY4-LRRC18region was a genetic locus for SLE, with3susceptibility SNPs rs877819, rs7097397and rs1913517. Wang C et al have confirmed the association of rs1913517, which is located both in WDFY4and LRRC18, with Caucasian populations.
As the fourth member in WDFY family, WDFY4encodes multiple transcripts and the longest transcript encodes a huge protein with3184amino acids residues. Its closest paralog is WD repeat and FYVE domain containing3(WDFY3), and both proteins contain five WD40domains and a BEACH (Beige and chediak-kigashi) domain. However, the best characterized FYVE zinc finger domain in the family is truncated for WDFY4. WD40domain is found in a number of eukaryotic proteins which are mainly involved in a wide variety of functions including adaptor modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. Most of BEACH domain containing proteins (BDCPs) act as scaffolding proteins that facilitate membrane events, including both fission and fusion, and recent studies found that mutations in individual BDCPs cause several human diseases and cell dysfunction, such as abnormal lysosome size, apoptosis and autophagy. In a variety of mammals, the sequence of WDFY4protein is highly conserved. So far, very little is known about the potential function of this well conserved protein. An interesting phenomenon is that WDFY4is predominantly expressed in immune tissues such as lymph node, spleen, thymus and tonsil, which implies the important role on immunity of organism.
Although GWASs have shown that the association of WDFY4-LRRC18with SLE in Chinese Han population, given the genetic heterogeneity between different populations, the restriction of previous studies to only Central and Southern Chinese Han populations limited the generalizability of this association to the whole Chinese Han ethnicity. Then, whether WDFY4-LRRC18is the susceptibility region of SLE in Northern Chinese Han population? Whether there is the functional variation in the three SNPs in WDFY4-LRRC18gene or not? And how to involved in SLE pathogenesis? What is the mechanisms of susceptibility gene contributing to the pathogenesis of SLE? To answer these questions, we carried out the following study.
Part I
Replicated association of WDFY4-LRRC18with Systemic Lupus Erythematosus in a Northern Chinese Han Population
To explore the possible association of WDFY4-LRRC18variants with SLE in a Northern Chinese Han population, the3SNPs rs877819, rs7097397and rs1913517were genotyped by a case-control association study.400patients with SLE were recruited from the Department of Rheumatology and Immunology of Qilu Hospital and Provincial Hospital affiliated to Shandong University, and1000unrelated, random-sampled healthy controls from the two hospitals were recruited during the same time. All healthy individuals were matched to cases by age, ethnicity and geographic region.
The allelic and genotypic frequency distributions of the three SNPs were in agreement with Hardy-Weinberg Equilibrium(HWE)(P>0.05) for both patients and controls, with the MAFs consistent with the International HapMap Project data for CHB. The SNPs rs877819and rs7097397presented strong associations with SLE (P=0.015, OR1.36,95%CI1.06-1.75; P=0.0004, OR1.365,95%CI1.148-1.622). Whereas rs1913517was not observed association with SLE (P=0.244, OR1.131,95%CI0.919-1.392).
Our replication study revealed that two SNPs, rs877819and rs7097397in WDFY4gene, were significantly associated with SLE in a Northern Chinese Han population.
Part II
Identifying susceptibility gene and the functional variant in WDFY4-LRRC18region associated with SLE
Although WDFY4-LRRC18is a susceptibility region of SLE, but the functional variant is still unclear. Usually, the SNPs rs877819, rs7097397and rs1913517, which were found to be related to SLE by GWASs, are not functional, and they might be just in strong linkage disequilibrium (LD) with the causal variation.
The susceptibility SNP rs1913517is located in an intron in LRRC18, which itself is located in an intron of WDFY4, thus the exact susceptibility gene with SLE is unclear. To identify the susceptibility gene, we examined the mRNA levels of the two genes in peripheral blood mononuclear cell (PBMC) samples from58SLE patients and58healthy controls. Relative WDFY4mRNA expression was lower in patients with SLE than in controls (P<0.05), with no significant difference in LRRC18expression.
Because the novel variant in WDFY4-LRRC18might have a functional effect on SLE susceptibility, we sequenced all61coding exons of WDFY4in70normal individuals, however, no novel variant was found in the coding sequences.
To identify the functional variant among3SNPs, we conducted an independent contribution test and allele specific expression (ASE) assay. We found rs1913517and rs877819were in strong linkage disequilibrium (LD) with r2=0.93. Conditional logistic regression revealed rs877819had an independent contribution to SLE with P=2.5×10-4, when controlling the effect of rs1913517. However, the P value for independent rs1913517was just0.7758, with no significant assiociation with SLE. These results suggest the assiociation of rs1913517with SLE was dependent on rs877819.
To detect whether WDFY4expression was associated with rs877819or rs7097397, we performed allele specific expression (ASE) assay. For rs7097397located at the transcript sequence, pyrosequencing was performed in31healthy subjects heterozygous for rs7097397, and no significant difference of ASE was identified on rs7097397.
To determine whether intronic variant rs877819was associated with WDFY4and LRRC18expression, we analyzed the expression of subjects with different genotypes on the SNP. Quantitative PCR analysis showed significantly lower WDFY4expression was seen in AG heterozygotes than in GG homozygotes (P<0.05), but no difference on LRRC18expression. Thus, risk allele A of rs877819was significantly associated with a lower WDFY4expression.
The result in this part suggest WDFY4is directly associated with SLE. The functional variant might be the intronic SNP rs877819, with the risk allele A associated with the lower expression of WDFY4, which might be consistent with the result that the expression of WDFY4is decreased in SLE.
Part Ⅲ
The mechanisms of the functional variant rs877819involved in the pathogenesis of SLE
Since the risk allele A of rs877819is associated with the decreased expression of WDFY4, the intronic SNP might affect gene expression through transcriptional regulation. We examed the transcriptional activity of the allele G or A on rs877819by the luciferase reporter activity assay. As expected, the activity was significantly lower for the A allele than G allele in HeLa and HEK-293T cells (P<0.001), which was consistent with our observation of the rs877819risk allele A associated with decreased expression of WDFY4.
Gene transcription might be modulated by transcription factor binding sites in intronic regions. Electrophoretic mobility shift assay (EMSA) was used to investigate whether the allelic difference in transcription activity on rs877819might be explained by their different binding capacities for nuclear factors. We found both alleles on rs877819could form DNA-protein complexes with the nuclear extracts, with the higher affinity of G allele than A.
Three transcriptional factors Freac2, ZBTB7and Yinyangl (YY1), predicted by Matlnspector, might bind with rs877819, so we synthesized conserved motifs for the three factors as competition probes. The detected complex was completely abrogated only by the conserved YY1binding motif, thus YY1might be the transcription factor binding to the rs877819site. Supershift assay suggested YY1 antibody could bind with the DNA-protein complex, while the mutant YY1conserved motifs could not. Chromatin immunoprecipitation assay (ChIP) also indicated that YY1could bind to the rs877819site in vivo.
These DNA-protein binding analyses indicated that endogenous YY1protein specifically interacted with intronic variant rs877819within WDFY4, and the risk allele A had lower affinity than the G allele with transcription factor YY1, which might explain that allele A was associated with reduced transcription of WDFY4.
To investigate the effect of transcription factor YY1on different alleles of rs877819, we transfected HeLa cells with the luciferase vector containing rs877819-G or-A and siYYl or the expression vector of YY1(CMV-YY1). The result showed that YY1had a positive regulation on rs877819G, with little effect on the allele A.
In this part, our findings suggest transcription factor YY1could bind to rs877819, with lower affinity to the A allele, which might lead to the reduced transcriptional activity of WDFY4.
Part IV
The effects of WDFY4gene on the autophagy pathway
The closest paralog of WDFY4is WDFY3in the same gene family and both contains WD40domains and a BEACH domain, however, the best characterized FYVE zinc finger domain in the family is truncated for WDFY4. WDFY3protein, involved in selective autophagy, is also called autophagy-linked FYVE protein (ALFY). There has been a growing studies for the possibility that autophagy may be involved in autoimmune disease. In addition, the elevated autophagy has been detected in lupus mice. Since the protein structure of WDFY4is so similar with ALFY, whether WDFY4is also involved in autophagy? Whether the susceptibility of WDFY4to SLE is related to autophagy process?
With these questions, we first examined the expression patterns of Wdfy4and autophagy in spleen from lupus mice. We found WDFY4gene was predominantly expressed in immune tissues in both human and mouse, such as spleen, thymus and bone marrow. In addition, compared with the wild-type mice, the expression of Wdjy4decreased in lupus mice spleen, however, the level of autophagy increased.
What's more, the expression level of WDFY4in Raji (B lymphoma cells) was higher than Jurkat, NK92and THP-1. In order to investigate the effect of WDFY4on autophagy, we transfected cells with the shRNA of WDFY4and expression vector of WDFY4containing WD40-BEACH domain with starvation induced and chloroquine (CQ) treatment, and autophagy was detected by Western Blot. Our results showed that decreased expression of WDFY4led to a higher autophagy flux, and expression of BEACH-WD40domain inhibited autophagy flux.
To study the mechinsms of WDFY4involved in autophagy, the expression of several key proteins in autophagy pathyway were detected in cells transfected with shWDFY4and BEACH-WD40domain expression vector. We found the expression of Bc12decreased in cell with shWDFY4, while increased in cell with BEACH-WD40domain expression vector. Bc12is an apoptosis-related protein, and its high expression might inhibit cell apoptosis. In addition, Bc12is also involved in the autophagic process, and it can be combined with the autophagy protein Beclinl, which cause Beclinl involved in autophagy reduced. As we all known, autophagy can lead to autophagic cell death. Therefore, Bc12can directly inhibit cell apoptosis, or inhibit autophagic cell death.
Next, the effects of WDFY4gene on cell apoptosis was analysed by flow cytometry. Consistent with our expectation, the result indicated that decreased expression of WDFY4promoted cell apoptosis, and the expression of BEACH-WD40domain inhbited cell apoptosis to a certain extent.
In this part, the expression of WDFY4gene is higher in B cells than other immunocyte. Knockdown of WDFY4increased cell autophagy and downregulated the expression of Bcl-2, which might contribute to the elevated cell apoptosis. Consistently, the expression vector containing BEACH-WD40domain caused cell autophagy decreased and the expression level of Bcl2increased evidently, protecting cells from apoptosis. Therefore, WDFY4may contribute to the pathogenesis of SLE through the autophagy pathway.
2005年,全基因组关联分析(Genome Wide Association Study, GWAS)的出现,极大地促进了SLE的遗传学研究,目前GWAS已经鉴定出40多个SLE的易感位点。2009年,针对亚洲人群SLE的两个GWAS研究发现,位于10q21的WDFY4-LRRC18区域是SLE的一个易感区域。该区域中的rs877819,rs7097397和rs1913517与亚洲人群SLE相关,其中rs1913517同时位于LRRC18和WDFY4基因的内含子。2013年,有研究发现rs1913517也是高加索人群SLE的易感变异位点。
WDFY4是WDFY家族的第四位成员,主要表达于一些免疫组织,如淋巴结、脾脏、胸腺和扁桃体等,提示它有可能参与机体的免疫功能。WDFY4含有多个转录本,最大的转录本可编码一个含有3184个氨基酸的巨大蛋白。WDFY4最近的同源体是同一家族的WDFY3,它们的C末端都含有BEACH (Beige and chediak-kigashi)和WD40(WD-repeat)结构域,不同的是WDFY4没有该家族特有的FYVE锌指结构域。WD40结构域存在于一系列真核蛋白中,包含该结构域的蛋白主要参与细胞信号转导调控、pre-mRNA的加工和细胞骨架的形成等。大多数包含有BEACH结构域的蛋白通常可以作为支架蛋白参与膜事件,例如：促进质膜的融合和解离。最近的研究结果发现BEACH蛋白突变可以导致多种疾病以及各种细胞畸变,如溶酶体畸变、细胞凋亡和自噬等。另外,WDFY4蛋白在多个物种间具有高度的保守性。到目前为止,关于这一保守蛋白的功能研究,仍是一个空白。
虽然GWAS研究已经证实了WDFY4-LRRC18区域与中国汉族人群SLE的相关性,但是这些研究主要是在中国南方汉族人群中开展的。由于关联分析的结果具有人群差异,那么,WDFY4-LRRC18是否也与中国北方汉族人群SLE有关?在该区域的3个SLE易感SNP位点中,哪个为功能变异?功能变异是如何影响SLE发生的?该区域导致SLE易感的分子机制又是什么?为了解决这些问题,我们进行了以下研究。
第一部分
WFY4-LRRC18区域与中国北方汉族人群SLE的关联分析
为了研究WDFY4-LRRC18区域中rs877819, rs1913517和rs7097397位点与中国北方汉族人群SLE的相关性,我们利用病例-对照关联研究的方法,对这三个SNP位点进行了关联分析。400例SLE患者均来自山东大学齐鲁医院和省立医院的风湿免疫科,1000例健康对照则是来自这两家医院的健康查体者,他们的年龄、种族和地理区域等相匹配。
所有三个位点等位基因频率及基因型频率符合Hardy-Weinberg平衡(P>0.05),具有群体代表性。其中,2个SNP位点rs877819和rs7097397与SLE具有显著的相关性(P=0.015, OR1.36,95%CI1.06-1.75; P=0.0004, OR1.36595%CI1.148-1.622)。在病例与对照中,rs1913517位点的等位基因频率则没有明显差异(P=0.244,OR1.13195%CI0.929-1.392),说明rs1913517与中国北方汉族人群SLE没有相关性。连锁不平衡分析表明,这3个SNP的连锁不平衡性较弱,r2<0.75。
本部分结果验证了GWAS的结果,表明WDFY4-LRRC18区域也是中国北方汉族人群SLE的易感位点,2个SNP位点rs877819和rs7097397与中国北方汉族人群SLE显著相关。
第二部分
WDFY4-LRRC18导致SLE易感的基因及功能变异的鉴定
由于与SLE相关联的rs1913517同时位于WDFY4和LRRC18基因的内含子,那么,哪个基因才是与SLE直接相关的呢?为了鉴别出真正参与SLE发生的易感基因,我们分别检测了58名SLE患者和58名健康对照外周血单核细胞中WDFY4和LRRC18基因的相对表达水平。结果发现,与健康对照相比,SLE患者中WDFY4基因的相对表达水平显著下降(P<0.05),而LRRC18基因的表达则没有明显差异,说明WDFY4是SLE的易感基因,并且低表达的WDFY4与SLE的发生有关。
既然WDFY4是SLE的易感基因,但是与SLE有关的功能变异还不清楚。因此,我们首先选取了70名健康对照个体,对他们WDFY4基因的61个外显子进行测序,结果没有发现可能具有功能作用的新变异。
GWAS研究表明rs877819, rs7097397和rs1913517是WDFY4基因中SLE的易感位点,但是尚不能确定哪个是功能变异。为了从3个SNP位点中鉴别出SLE的功能变异,我们首先分析了rs877819和rs1913517位点与SLE的相关性。连锁不平衡分析表明这两个位点是强连锁的(r2=0.93)。logistic回归分析结果表明rs877819是SLE的易感SNP, P=2.5×10-4,利用独立贡献检验,在屏蔽了rs877819的作用后,rs1913517与SLE没有相关性,P=0.7758。以上结果说明rs1913517位点不是SLE的功能变异,它与SLE的易感性依赖于rs877819。
对于外显子中的rs7097397位点,我们采用焦磷酸测序的方法检测了rs7097397位点的等位基因特异表达(Allele Specific Expression, ASE)。我们选取了31个rs7097397位点AG基因型的杂合子健康个体,对其外周血单核细胞中的cDNA和基因组DNA进行焦磷酸测序,结果发现rs7097397位点等位基因表达没有差异,该位点可能不是SLE的功能变异。
由于rs877819位点位于内含子中,所以我们利用实时定量PCR的方法分析了rs877819等位基因对WDFY4和LRRC18基因表达的影响。鉴于rs877819A的频率非常低,AA基因型个体较少,我们只选取了rs877819位点40个GG基因型和15个AG基因型的个体,分别检测了他们外周血单核细胞中WDFY4和LRRC18基因的相对表达水平。结果发现,AG基因型个体中WDFY4基因的相对表达水平明显低于GG基因型的个体(P<0.05),而LRRC18的相对表达水平没有明显的差异,说明rs877819A与WDFY4基因的低表达有关。
本部分研究结果表明,WDFY4是SLE真正的易感基因。位于该基因内含子中的rs877819可能是导致SLE易感的功能变异,危险等位基因A与WDFY4的低表达有关,这可能是导致SLE患者中WDFY4基因低表达的原因。
第三部分分
功能变异rs877819导致SLE易感的分子机制
由于内含子变异rs877819的危险等位基因A与WDFY4的低表达有关,所以我们推测该位点有可能影响了基因的转录活性。为了检测rs877819不同等位基因转录活性的差异,我们进行了双荧光素酶报告基因分析。与预期相一致,在HeLa和HEK293T细胞中,rs877819罕见等位基因A的相对转录活性显著低于常见等位基因G(P<0.001),因此,rs877819等位基因A可能导致了WDFY4的低表达。
由于rs877819等位基因影响了WDFY4的转录活性,所以我们针对rs877819位点等位基因进行了电泳凝胶迁移率实验(EMSA),验证该SNP是否为转录因子结合位点。结果发现rs877819确实能与细胞核蛋白相结合,并且等位基因G与该蛋白的结合亲和力大于等位基因A。
MatInspector软件预测,与rs877819位点结合的转录因子可能是Freac2, ZBTB7和Yinyang1(YY1)。所以我们合成了这3个转录因子的保守结合序列,进行竞争实验。结果发现,只有YY1的保守结合序列能完全竞争掉结合条带,所以YY1可能是与rs877819结合的转录因子。超迁移率实验(Supershift)结果也表明YY1抗体能够结合到rs877819位点的DNA-蛋白结合复合物上,而突变的YY1保守序列不能竞争结合条带,说明rs877819位点所在序列能够与转录因子YY1特异结合。与EMSA结果相一致,染色质免疫共沉淀实验(ChIP)也表明,rs877819位点也能够与转录因子YY1相结合。
我们的结果说明WDFY4基因的内含子变异rs877819能够与内源性YY1蛋白发生特异结合,并且罕见等位基因A与YY1的亲和力低于等位基因G,这可能是rs877819A导致WDFY4低表达的原因。
为了研究转录因子YY1对rs877819等位基因转录活性的影响,我们将rs877819等位基因G或A连入荧光素酶报告基因载体,并且与YY1的干扰RNA(siRNA)或表达载体(CMV-YY1)共转染细胞,进行双荧光素酶报告基因分析。结果表明,YY1对rs877819等位基因G的转录活性起正调控作用,却几乎不影响等位基因A的转录活性。
本部分研究结果表明,起正调控作用的转录因子YYl能够结合到rs877819位点,并且与等位基因A的亲和力较低,使得等位基因A转录活性下降,从而导致了WDFY4的低表达,而低表达的WDFY4导致了SLE的易感。
第四部分WDFY4基因对自噬通路的影响
WDFY4最相近的同源体是同一家族的WDFY3,它们的C末端都包含了相对保守的BEACH结构域和WD40结构域。WDFY3编码了一个自噬相关蛋白ALFY(autophagy-linked FYVE protein),参与选择性自噬。已经有越来越多的研究表明自噬可能参与了自身免疫病的发生。既然WDFY4蛋白与WDFY3结构如此相似,那么WDFY4是否也参与自噬呢?它导致SLE的易感是否是通过自噬通路实现的呢?带着这些问题,我们首先检测了WDFY4基因的表达模式以及狼疮小鼠脾脏中的自噬水平。结果发现,无论是人类还是小鼠的脾脏、胸腺等免疫组织中,WDFY4的表达水平高于其它组织。另外,与对照小鼠相比,狼疮小鼠脾脏中,Wdfy4表达水平下降,自噬水平升高。那么,自噬水平的升高是否与Wdfy4的低表达有关呢?
我们检测了WDFY4在Jurkat, NK92, Raji和THP-1等不同免疫细胞中的表达模式,结果发现,B淋巴瘤细胞Raji中WDFY4的表达水平远高于其它3种细胞,表明该基因在B细胞中高表达。我们还将WDFY4的shRNA和包含BEACH-WD40结构域表达载体(由于WDFY4蛋白太大,无法构建全长的表达载体)转染细胞,氯喹处理后,免疫印迹法检测细胞自噬流。结果发现低表达的WDFY4促进了自噬流,而BEACH-WD40结构域的高表达则抑制了自噬流。
为了研究WDFY4抑制自噬的分子机制,我们检测了shWDFY4细胞以及BEACH-WD40结构域高表达细胞中,自噬相关蛋白的表达水平。结果发现,低表达WDFY4的细胞中,Bcl2表达水平下调；而高表达BEACH-WD40结构域的细胞中,Bcl2表达水平升高。Bc12是一个抗凋亡蛋白,它的高表达会抑制细胞凋亡。另外,Bc12可以与自噬蛋白Beclinl相结合,使参与自噬的Beclinl蛋白减少,从而抑制细胞自噬。由于过度自噬也可能导致细胞自噬性死亡,所以Bc12可能直接抑制细胞凋亡,也可能抑制细胞自噬性死亡。
接下来,我们用流式细胞术的方法,检测了低表达的WDFY4和高表达的BEACH-WD40结构域对细胞凋亡的影响。与预期相一致,低表达的WDFY4促进了细胞凋亡,高表达的BEACH-WD40结构域则抑制细胞凋亡。
Systemic lupus erythematosus (SLE) is a prototype autoimmune disease, characterized by autoantibody production and immune complex (IC) deposition leading to severe inflammatory reaction multi-organ damage. Epidemiological studies suggest strong contribution of genetic factors in the etiology of SLE. SLE has high tendency of familial aggregation and a higher concordance rates between monozygotic twins (25-56%).
Since2005, Genome-wide association studies (GWASs) have greatly drived the genetics study of SLE. By now, GWASs have confirmed genetic associations of over40genes/loci with SLE during the past several years. In2009, two GWASs in east Asian populations have discovered WDFY4-LRRC18region was a genetic locus for SLE, with3susceptibility SNPs rs877819, rs7097397and rs1913517. Wang C et al have confirmed the association of rs1913517, which is located both in WDFY4and LRRC18, with Caucasian populations.
As the fourth member in WDFY family, WDFY4encodes multiple transcripts and the longest transcript encodes a huge protein with3184amino acids residues. Its closest paralog is WD repeat and FYVE domain containing3(WDFY3), and both proteins contain five WD40domains and a BEACH (Beige and chediak-kigashi) domain. However, the best characterized FYVE zinc finger domain in the family is truncated for WDFY4. WD40domain is found in a number of eukaryotic proteins which are mainly involved in a wide variety of functions including adaptor modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. Most of BEACH domain containing proteins (BDCPs) act as scaffolding proteins that facilitate membrane events, including both fission and fusion, and recent studies found that mutations in individual BDCPs cause several human diseases and cell dysfunction, such as abnormal lysosome size, apoptosis and autophagy. In a variety of mammals, the sequence of WDFY4protein is highly conserved. So far, very little is known about the potential function of this well conserved protein. An interesting phenomenon is that WDFY4is predominantly expressed in immune tissues such as lymph node, spleen, thymus and tonsil, which implies the important role on immunity of organism.
Although GWASs have shown that the association of WDFY4-LRRC18with SLE in Chinese Han population, given the genetic heterogeneity between different populations, the restriction of previous studies to only Central and Southern Chinese Han populations limited the generalizability of this association to the whole Chinese Han ethnicity. Then, whether WDFY4-LRRC18is the susceptibility region of SLE in Northern Chinese Han population? Whether there is the functional variation in the three SNPs in WDFY4-LRRC18gene or not? And how to involved in SLE pathogenesis? What is the mechanisms of susceptibility gene contributing to the pathogenesis of SLE? To answer these questions, we carried out the following study.
Part I
Replicated association of WDFY4-LRRC18with Systemic Lupus Erythematosus in a Northern Chinese Han Population
To explore the possible association of WDFY4-LRRC18variants with SLE in a Northern Chinese Han population, the3SNPs rs877819, rs7097397and rs1913517were genotyped by a case-control association study.400patients with SLE were recruited from the Department of Rheumatology and Immunology of Qilu Hospital and Provincial Hospital affiliated to Shandong University, and1000unrelated, random-sampled healthy controls from the two hospitals were recruited during the same time. All healthy individuals were matched to cases by age, ethnicity and geographic region.
The allelic and genotypic frequency distributions of the three SNPs were in agreement with Hardy-Weinberg Equilibrium(HWE)(P>0.05) for both patients and controls, with the MAFs consistent with the International HapMap Project data for CHB. The SNPs rs877819and rs7097397presented strong associations with SLE (P=0.015, OR1.36,95%CI1.06-1.75; P=0.0004, OR1.365,95%CI1.148-1.622). Whereas rs1913517was not observed association with SLE (P=0.244, OR1.131,95%CI0.919-1.392).
Our replication study revealed that two SNPs, rs877819and rs7097397in WDFY4gene, were significantly associated with SLE in a Northern Chinese Han population.
Part II
Identifying susceptibility gene and the functional variant in WDFY4-LRRC18region associated with SLE
Although WDFY4-LRRC18is a susceptibility region of SLE, but the functional variant is still unclear. Usually, the SNPs rs877819, rs7097397and rs1913517, which were found to be related to SLE by GWASs, are not functional, and they might be just in strong linkage disequilibrium (LD) with the causal variation.
The susceptibility SNP rs1913517is located in an intron in LRRC18, which itself is located in an intron of WDFY4, thus the exact susceptibility gene with SLE is unclear. To identify the susceptibility gene, we examined the mRNA levels of the two genes in peripheral blood mononuclear cell (PBMC) samples from58SLE patients and58healthy controls. Relative WDFY4mRNA expression was lower in patients with SLE than in controls (P<0.05), with no significant difference in LRRC18expression.
Because the novel variant in WDFY4-LRRC18might have a functional effect on SLE susceptibility, we sequenced all61coding exons of WDFY4in70normal individuals, however, no novel variant was found in the coding sequences.
To identify the functional variant among3SNPs, we conducted an independent contribution test and allele specific expression (ASE) assay. We found rs1913517and rs877819were in strong linkage disequilibrium (LD) with r2=0.93. Conditional logistic regression revealed rs877819had an independent contribution to SLE with P=2.5×10-4, when controlling the effect of rs1913517. However, the P value for independent rs1913517was just0.7758, with no significant assiociation with SLE. These results suggest the assiociation of rs1913517with SLE was dependent on rs877819.
To detect whether WDFY4expression was associated with rs877819or rs7097397, we performed allele specific expression (ASE) assay. For rs7097397located at the transcript sequence, pyrosequencing was performed in31healthy subjects heterozygous for rs7097397, and no significant difference of ASE was identified on rs7097397.
To determine whether intronic variant rs877819was associated with WDFY4and LRRC18expression, we analyzed the expression of subjects with different genotypes on the SNP. Quantitative PCR analysis showed significantly lower WDFY4expression was seen in AG heterozygotes than in GG homozygotes (P<0.05), but no difference on LRRC18expression. Thus, risk allele A of rs877819was significantly associated with a lower WDFY4expression.
The result in this part suggest WDFY4is directly associated with SLE. The functional variant might be the intronic SNP rs877819, with the risk allele A associated with the lower expression of WDFY4, which might be consistent with the result that the expression of WDFY4is decreased in SLE.
Part Ⅲ
The mechanisms of the functional variant rs877819involved in the pathogenesis of SLE
Since the risk allele A of rs877819is associated with the decreased expression of WDFY4, the intronic SNP might affect gene expression through transcriptional regulation. We examed the transcriptional activity of the allele G or A on rs877819by the luciferase reporter activity assay. As expected, the activity was significantly lower for the A allele than G allele in HeLa and HEK-293T cells (P<0.001), which was consistent with our observation of the rs877819risk allele A associated with decreased expression of WDFY4.
Gene transcription might be modulated by transcription factor binding sites in intronic regions. Electrophoretic mobility shift assay (EMSA) was used to investigate whether the allelic difference in transcription activity on rs877819might be explained by their different binding capacities for nuclear factors. We found both alleles on rs877819could form DNA-protein complexes with the nuclear extracts, with the higher affinity of G allele than A.
Three transcriptional factors Freac2, ZBTB7and Yinyangl (YY1), predicted by Matlnspector, might bind with rs877819, so we synthesized conserved motifs for the three factors as competition probes. The detected complex was completely abrogated only by the conserved YY1binding motif, thus YY1might be the transcription factor binding to the rs877819site. Supershift assay suggested YY1 antibody could bind with the DNA-protein complex, while the mutant YY1conserved motifs could not. Chromatin immunoprecipitation assay (ChIP) also indicated that YY1could bind to the rs877819site in vivo.
These DNA-protein binding analyses indicated that endogenous YY1protein specifically interacted with intronic variant rs877819within WDFY4, and the risk allele A had lower affinity than the G allele with transcription factor YY1, which might explain that allele A was associated with reduced transcription of WDFY4.
To investigate the effect of transcription factor YY1on different alleles of rs877819, we transfected HeLa cells with the luciferase vector containing rs877819-G or-A and siYYl or the expression vector of YY1(CMV-YY1). The result showed that YY1had a positive regulation on rs877819G, with little effect on the allele A.
In this part, our findings suggest transcription factor YY1could bind to rs877819, with lower affinity to the A allele, which might lead to the reduced transcriptional activity of WDFY4.
Part IV
The effects of WDFY4gene on the autophagy pathway
The closest paralog of WDFY4is WDFY3in the same gene family and both contains WD40domains and a BEACH domain, however, the best characterized FYVE zinc finger domain in the family is truncated for WDFY4. WDFY3protein, involved in selective autophagy, is also called autophagy-linked FYVE protein (ALFY). There has been a growing studies for the possibility that autophagy may be involved in autoimmune disease. In addition, the elevated autophagy has been detected in lupus mice. Since the protein structure of WDFY4is so similar with ALFY, whether WDFY4is also involved in autophagy? Whether the susceptibility of WDFY4to SLE is related to autophagy process?
With these questions, we first examined the expression patterns of Wdfy4and autophagy in spleen from lupus mice. We found WDFY4gene was predominantly expressed in immune tissues in both human and mouse, such as spleen, thymus and bone marrow. In addition, compared with the wild-type mice, the expression of Wdjy4decreased in lupus mice spleen, however, the level of autophagy increased.
What's more, the expression level of WDFY4in Raji (B lymphoma cells) was higher than Jurkat, NK92and THP-1. In order to investigate the effect of WDFY4on autophagy, we transfected cells with the shRNA of WDFY4and expression vector of WDFY4containing WD40-BEACH domain with starvation induced and chloroquine (CQ) treatment, and autophagy was detected by Western Blot. Our results showed that decreased expression of WDFY4led to a higher autophagy flux, and expression of BEACH-WD40domain inhibited autophagy flux.
To study the mechinsms of WDFY4involved in autophagy, the expression of several key proteins in autophagy pathyway were detected in cells transfected with shWDFY4and BEACH-WD40domain expression vector. We found the expression of Bc12decreased in cell with shWDFY4, while increased in cell with BEACH-WD40domain expression vector. Bc12is an apoptosis-related protein, and its high expression might inhibit cell apoptosis. In addition, Bc12is also involved in the autophagic process, and it can be combined with the autophagy protein Beclinl, which cause Beclinl involved in autophagy reduced. As we all known, autophagy can lead to autophagic cell death. Therefore, Bc12can directly inhibit cell apoptosis, or inhibit autophagic cell death.
Next, the effects of WDFY4gene on cell apoptosis was analysed by flow cytometry. Consistent with our expectation, the result indicated that decreased expression of WDFY4promoted cell apoptosis, and the expression of BEACH-WD40domain inhbited cell apoptosis to a certain extent.
In this part, the expression of WDFY4gene is higher in B cells than other immunocyte. Knockdown of WDFY4increased cell autophagy and downregulated the expression of Bcl-2, which might contribute to the elevated cell apoptosis. Consistently, the expression vector containing BEACH-WD40domain caused cell autophagy decreased and the expression level of Bcl2increased evidently, protecting cells from apoptosis. Therefore, WDFY4may contribute to the pathogenesis of SLE through the autophagy pathway.
引文
1. Hewagama, A. and B. Richardson, The genetics and epigenetics of autoimmune diseases. J Autoimmun,2009.33(1):p.3-11.
2. D'Cruz, D.P., M.A. Khamashta, and G.R. Hughes, Systemic lupus erythematosus. Lancet,2007.369(9561):p.587-96.
3. Tsao, B.P., The genetics of human systemic lupus erythematosus. Trends Immunol,2003.24(11):p.595-602.
4. Kariuki, S.N. and T.B. Niewold, Genetic regulation of serum cytokines in systemic lupus erythematosus. Transl Res,2010.155(3):p.109-17.
5. Cohen-Solal, J.F., et al., Hormonal regulation of B-cell function and systemic lupus erythematosus. Lupus,2008.17(6):p.528-32.
6. Ramos-Casals, M., et al., Acute viral infections in patients with systemic lupus erythematosus:description of 23 cases and review of the literature. Medicine (Baltimore),2008.87(6):p.311-8.
7. Bultink, I.E., Osteoporosis and fractures in systemic lupus erythematosus. Arthritis Care Res (Hoboken),2012.64(1):p.2-8.
8. Ortega, L.M., et al., Review:Lupus nephritis:pathologic features, epidemiology and a guide to therapeutic decisions. Lupus,2010.19(5):p. 557-74.
9. Mok, C.C., Biomarkers for lupus nephritis:a critical appraisal. J Biomed Biotechnol,2010.2010:p.638413.
10. Anaya, J.M., et al., Lupus nephritis in Colombians:contrasts and comparisons with other populations. Clin Rev Allergy Immunol,2011.40(3):p.199-207.
11. de Zubiria Salgado, A. and C. Herrera-Diaz, Lupus nephritis:an overview of recent findings. Autoimmune Dis,2012.2012:p.849684.
12. Varela, D.C., et al., Delayed lupus nephritis. Ann Rheum Dis,2008.67(7):p. 1044-6.
13. Moser, K.L., et al., Recent insights into the genetic basis of systemic lupus erythematosus. Genes Immun,2009.10(5):p.373-9.
14. Selmi, C., Q. Lu, and M.C. Humble, Heritability versus the role of the environment in autoimmunity. J Autoimmun,2012.39(4):p.249-52.
15. Ngalamika, O., et al., Epigenetics, autoimmunity and hematologic malignancies:a comprehensive review. J Autoimmun,2012.39(4):p.451-65.
16. Kaiser, R. and L.A. Criswell, Genetics research in systemic lupus erythematosus for clinicians:methodology, progress, and controversies. Curr Opin Rheumatol,2010.22(2):p.119-25.
17. Zhou, Y. and Q. Lu, DNA methylation in T cells from idiopathic lupus and drug-induced lupus patients. Autoimmun Rev,2008.7(5):p.376-83.
18. Freimer, N. and C. Sabatti, The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology. Nat Genet, 2004.36(10):p.1045-51.
19. Lander, E. and L. Kruglyak, Genetic dissection of complex traits:guidelines for interpreting and reporting linkage results. Nat Genet,1995.11(3):p. 241-7.
20. Sabatti, C., S. Service, and N. Freimer, False discovery rate in linkage and association genome screens for complex disorders. Genetics,2003.164(2):p. 829-33.
21. Frazer, K.A., et al., A second generation human haplotype map of over 3.1 million SNPs. Nature,2007.449(7164):p.851-61.
22. Purcell, S., et al., PLINK:a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet,2007.81(3):p.559-75.
23. Klein, R.J., et al., Complement factor H polymorphism in age-related macular degeneration. Science,2005.308(5720):p.385-9.
24. Hindorff, L.A., et al., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A,2009.106(23):p.9362-7.
25. Kingsley, C.B., Identification of causal sequence variants of disease in the next generation sequencing era. Methods Mol Biol,2011.700:p.37-46.
26. Harley, J.B., et al., Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet,2008.40(2):p.204-10.
27. Han, J.W., et al., Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1234-7.
28. Yang, W., et al., Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet,2010.6(2):p. e1000841.
29. Cui, Y., Y. Sheng, and X. Zhang, Genetic susceptibility to SLE:recent progress from GWAS. J Autoimmun,2013.41:p.25-33.
30. Wang, C., et al., Genes identified in Asian SLE GWASs are also associated with SLE in Caucasian populations. Eur J Hum Genet,2013.21(9):p.994-9.
31. Barbosa, M.D., et al., Identification of the homologous beige and Chediak-Higashi syndrome genes. Nature,1996.382(6588):p.262-5.
32. Cullinane, A.R., A.A. Schaffer, and M. Huizing, The BEACH is hot:a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic,2013.14(7):p.749-66.
33. Lemmon, M.A., Structural basis for high-affinity phosphoinositide binding by pleckstrin homology domains. Biochem Soc Trans,1999.27(4):p.617-24.
34. Lemmon, M.A., Pleckstrin homology domains:not just for phosphoinositides. Biochem Soc Trans,2004.32(Pt 5):p.707-11.
35. Smith, T.F., et al., The WD repeat:a common architecture for diverse functions. Trends Biochem Sci,1999.24(5):p.181-5.
36. Li, D. and R. Roberts, WD-repeat proteins:structure characteristics, biological function, and their involvement in human diseases. Cell Mol Life Sci,2001.58(14):p.2085-97.
37. Tchernev, V.T., et al., The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. Mol Med,2002.8(1):p.56-64.
38. Wang, J.W., et al., Identification of a novel lipopolysaccharide-inducible gene with key features of both A kinase anchor proteins and chsl/beige proteins. J Immunol,2001.166(7):p.4586-95.
39. Lopez-Herrera, G, et al., Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity. Am J Hum Genet,2012. 90(6):p.986-1001.
40. Montfort, A., et al., FAN stimulates TNF(alpha)-induced gene expression, leukocyte recruitment, and humoral response. J Immunol,2009.183(8):p. 5369-78.
41. Segui, B., et al., Involvement of FAN in TNF-induced apoptosis. J Clin Invest, 2001.108(1):p.143-51.
42. Finley, K.D., et al., blue cheese mutations define a novel, conserved gene involved in progressive neural degeneration. J Neurosci,2003.23(4):p. 1254-64.
43. Hocking, L.J., et al., Functional interaction between sequestosome-1/p62 and autophagy-linked FYVE-containing protein WDFY3 in human osteoclasts. Biochem Biophys Res Commun,2010.402(3):p.543-8.
44. Klionsky, D.J., Autophagy revisited:a conversation with Christian de Duve. Autophagy,2008.4(6):p.740-3.
45. Klionsky, D.J., et al., A unified nomenclature for yeast autophagy-related genes. Dev Cell,2003.5(4):p.539-45.
46. Majeski, A.E. and J.F. Dice, Mechanisms of chaperone-mediated autophagy. Int J Biochem Cell Biol,2004.36(12):p.2435-44.
47. Levine, B. and J. Yuan, Autophagy in cell death:an innocent convict? J Clin Invest,2005.115(10):p.2679-88.
48. Lockshin, R.A. and Z. Zakeri, Apoptosis, autophagy, and more. Int J Biochem Cell Biol,2004.36(12):p.2405-19.
49. Bhattacharya, A. and N.T. Eissa, Autophagy and autoimmunity crosstalks. Front Immunol,2013.4:p.88.
50. Pierdominici, M., et al., Role of autophagy in immunity and autoimmunity, with a special focus on systemic lupus erythematosus. FASEB J,2012.26(4): p.1400-12.
51. Zhou, X.J., et al., Genetic association of PRDM1-ATG5 intergenic region and autophagy with systemic lupus erythematosus in a Chinese population. Ann Rheum Dis,2011.70(7):p.1330-7.
52. Parkes, M, et al., Sequence variants in the autophagy gene 1RGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet,2007.39(7):p.830-2.
53. Lichtman, E.I., S.M. Helfgott, and M.A. Kriegel, Emerging therapies for systemic lupus erythematosus--focus on targeting interferon-alpha. Clin Immunol,2012.143(3):p.210-21.
54. Lee, H.K., et al., Autophagy-dependent viral recognition by plasmacytoid dendritic cells. Science,2007.315(5817):p.1398-401.
55. Cao, W., et al., Toll-like receptor-mediated induction of type I interferon in plasmacytoid dendritic cells requires the rapamycin-sensitive PI(3)K-mTOR-p70S6Kpathway. Nat Immunol,2008.9(10):p.1157-64.
56. Wu, T., et al., Metabolic disturbances associated with systemic lupus erythematosus. PLoS One,2012.7(6):p. e37210.
57. Zhou, R., et al., A role for mitochondria in NLRP3 inflammasome activation. Nature,2011.469(7329):p.221-5.
58. Kaspar, J.W., S.K. Niture, and A.K. Jaiswal, Nrf2:INrf2 (Keapl) signaling in oxidative stress. Free Radic Biol Med,2009.47(9):p.1304-9.
59. Komatsu, M., et al., Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell,2007.131(6):p.1149-63.
60. He, Y., et al., Identification of a lysosomal pathway that modulates glucocorticoid signaling and the inflammatory response. Sci Signal,2011. 4(180):p. ra44.
61. Hochberg, M.C., Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum, 1997.40(9):p.1725.
62. Gateva, V., et al., A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1228-33.
63. Plenge, R.M., Recent progress in rheumatoid arthritis genetics:one step towards improved patient care. Curr Opin Rheumatol,2009.21(3):p.262-71.
64. Kochi, Y., et al., Genetics of rheumatoid arthritis:underlying evidence of ethnic differences. J Autoimmun,2009.32(3-4):p.158-62.
65. Tian, C., P.K. Gregersen, and M.F. Seldin, Accounting for ancestry: population substructure and genome-wide association studies. Hum Mol Genet,2008.17(R2):p. R143-50.
66. Greene, C.S., et al., Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One,2009.4(6):p. e5639.
67. Hardy, J. and A. Singleton, Genomewide association studies and human disease. N Engl J Med,2009.360(17):p.1759-68.
68. Graham, R.R., et al., Review of recent genome-wide association scans in lupus. J Intern Med,2009.265(6):p.680-8.
69. Lee, H.S. and S.C. Bae, What can we learn from genetic studies of systemic lupus erythematosus? Implications of genetic heterogeneity among populations in SLE. Lupus,2010.19(12):p.1452-9.
70. Guerra, S.G., T.J. Vyse, and D.S. Cunninghame Graham, The genetics of lupus: a functional perspective. Arthritis Res Ther,2012.14(3):p.211.
71. Kaplan, M.H., STAT4:a critical regulator of inflammation in vivo. Immunol Res,2005.31(3):p.231-42.
72. Nath, S.K., et al., A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet,2008.40(2):p.152-4.
73. Han, S., et al., Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Hum Mol Genet,2009.18(6):p.1171-80.
74. Molineros, J.E., et al., Admixture mapping in lupus identifies multiple functional variants within IFIHl associated with apoptosis, inflammation, and autoantibodyproduction. PLoS Genet,2013.9(2):p. e1003222.
75. Kawasaki, A., et al., Association of IRF5 polymorphisms with systemic lupus erythematosus in a Japanese population:support for a crucial role of intron 1 polymorphisms. Arthritis Rheum,2008.58(3):p.826-34.
76. Barnes, B.J., et al., Global and distinct targets of IRF-5 and IRF-7 during innate response to viral infection. J Biol Chem,2004.279(43):p.45194-207.
77. Novais, R.C. and Y.R. Thorstenson, The evolution of Pyrosequencing(R) for microbiology:From genes to genomes. J Microbiol Methods,2011.86(1):p. 1-7.
78. Quinn, E.M., et al., Evidence for cis-acting regulation of ANK3 and CACNA1Cgene expression. Bipolar Disord,2010.12(4):p.440-5.
79. Manolio, T.A., et al., Finding the missing heritability of complex diseases. Nature,2009.461(7265):p.747-53.
80. Nejentsev, S., et al., Rare variants of IFIHl, a gene implicated in antiviral responses, protect against type 1 diabetes. Science,2009.324(5925):p.387-9.
81. Cohen, J.C., et al., Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med,2006.354(12):p.1264-72.
82. Abecasis, GR., et al., A map of human genome variation from population-scale sequencing. Nature,2010.467(7319):p.1061-73.
83. Ewing, A.D. and H.H. Kazazian, Jr., High-throughput sequencing reveals extensive variation in human-specific LI content in individual human genomes. Genome Res,2010.20(9):p.1262-70.
84. Dietrich, J., et al., Ligand-induced TCR down-regulation is not dependent on constitutive TCR cycling. J Immunol,2002.168(11):p.5434-40.
85. Pang, M., et al., Defective expression and tyrosine phosphorylation of the T cell receptor zeta chain in peripheral blood T cells from systemic lupus erythematosus patients. Clin Exp Immunol,2002.129(1):p.160-8.
86. Nambiar, M.P., et al., Prevalence of T cell receptor zeta chain deficiency in systemic lupus erythematosus. Lupus,2003.12(1):p.46-51.
87. Gorman, C.L., et al., Polymorphisms in the CD3Z gene influence TCRzeta expression in systemic lupus erythematosus patients and healthy controls. J Immunol,2008.180(2):p.1060-70.
88. Fu, Q., et al., Association of a functional IRF7 variant with systemic lupus erythematosus. Arthritis Rheum,2011.63(3):p.749-54.
89. Li, J., Y. You, and S. Chen, The role of upstream stimulatory factor 1 in the transcriptional regulation of the human TBX21 promoter mediated by the T-1514C polymorphism associated with systemic lupus erythematosus. Immunogenetics,2012.64(5):p.361-70.
90. Hikami, K., et al., Association of a functional polymorphism in the 3'-untranslated region of SPI1 with systemic lupus erythematosus. Arthritis Rheum,2011.63(3):p.755-63.
91. Sakurai, D., et al., Preferential binding to Elk-1 by SLE-associated IL10 risk allele upregulates IL10 expression. PLoS Genet,2013.9(10):p. e1003870.
92. Choi, J.W., et al., A common intronic variant of CXCR3 is functionally associated with gene expression levels and the polymorphic immune cell responses to stimuli. J Allergy Clin Immunol,2008.122(6):p.1119-1126 e7.
93. Su, K., et al., A promoter haplotype of the immunoreceptor tyrosine-based inhibitory motif-bearing FcgammaRIIb alters receptor expression and associates with autoimmunity. I. Regulatory FCGR2B polymorphisms and their association with systemic lupus erythematosus. J Immunol,2004. 172(11):p.7186-91.
94. Maeda, T., et al., Role of the proto-oncogene Pokemon in cellular transformation and ARF repression. Nature,2005.433(7023):p.278-85.
95. Hellqvist, M., et al., The human forkhead protein FREAC-2 contains two functionally redundant activation domains and interacts with TBP and TFIIB. J Biol Chem,1998.273(36):p.23335-43.
96. Berndt, J.A., et al., The transcriptional regulator Yin Yang 1 activates the myelin PLP gene. J Neurochem,2001.77(3):p.935-42.
97. Shi, Y., J.S. Lee, and K.M. Galvin, Everything you have ever wanted to know about Yin Yang 1. Biochim Biophys Acta,1997.1332(2):p. F49-66.
98. Li, J.R., et al., A common promoter variant of TBX21 is associated with allele specific binding to Yin-Yang 1 and reduced gene expression. Scand J Immunol, 2011.73(5):p.449-58.
99. Riveros, C, et al., A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PLoS One,2010.5(12):p. e14176.
100. Simonsen, A., et al., Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci,2004.117(Pt 18): p.4239-51.
101. Clausen, T.H., et al., p62/SQSTMl and ALFY interact to facilitate the formation ofp62 bodies/ALIS and their degradation by autophagy. Autophagy, 2010.6(3):p.330-44.
102. Filimonenko, M., et al., The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell,2010. 38(2):p.265-79.
103. Isakson, P., P. Holland, and A. Simonsen, The role of ALFY in selective autophagy. Cell Death Differ,2013.20(1):p.12-20.
104. Yamamoto, A. and A. Simonsen, Aljy-dependent elimination of aggregated proteins by macroautophagy:can there be too much of a good thing? Autophagy,2011.7(3):p.346-50.
105. Alessandri, C., et al., T lymphocytes from patients with systemic lupus erythematosus are resistant to induction of autophagy. FASEB J,2012.26(11): p.4722-32.
106. Clarke, A.J., et al., Autophagy is activated in systemic lupus erythematosus and required for plasmablast development. Ann Rheum Dis,2014.
107. Furtado, J. and D.A. Isenberg, B cell elimination in systemic lupus erythematosus. Clin Immunol,2013.146(2):p.90-103.
108. Dorner, T., C. Giesecke, and P.E. Lipsky, Mechanisms of B cell autoimmunity in SLE. Arthritis Res Ther,2011.13(5):p.243.
109. Anolik, J.H., B cell biology:implications for treatment of systemic lupus erythematosus. Lupus,2013.22(4):p.342-9.
110. Salmon, J.E. and M.J. Roman, Subclinical atherosclerosis in rheumatoid arthritis and systemic lupus erythematosus. Am J Med,2008.121(10 Suppl 1): p. S3-8.
111. Ren, Y, et al., Increased apoptotic neutrophils and macrophages and impaired macrophage phagocytic clearance of apoptotic neutrophils in systemic lupus erythematosus. Arthritis Rheum,2003.48(10):p.2888-97.
112. Majai, G, et al., Decreased apopto-phagocytic gene expression in the macrophages of systemic lupus erythematosus patients. Lupus,2014.23(2):p. 133-45.
113. Nah, J., et al., BECNl/Beclin 1 is recruited into lipid rafts byprion to activate autophagy in response to amyloid beta 42. Autophagy,2013.9(12):p. 2009-21.
114. Kroemer, G. and B. Levine, Autophagic cell death:the story of a misnomer. Nat Rev Mol Cell Biol,2008.9(12):p.1004-10.
1. Rahman, A. and D.A. Isenberg, Systemic lupus erythematosus. N Engl J Med, 2008.358(9):p.929-39.
2. Niewold, T.B., et al., High serum IFN-alpha activity is a heritable risk factor for systemic lupus erythematosus. Genes Immun,2007.8(6):p.492-502.
3. Alarcon-Segovia, D., et al., Familial aggregation of systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases in 1,177 lupus patients from the GLADEL cohort. Arthritis Rheum,2005.52(4):p.1138-47.
4. Fessel, W.J., Systemic lupus erythematosus in the community. Incidence, prevalence, outcome, and first symptoms; the high prevalence in black women. Arch Intern Med,1974.134(6):p.1027-35.
5. Danchenko, N., J.A. Satia, and M.S. Anthony, Epidemiology of systemic lupus erythematosus:a comparison of worldwide disease burden. Lupus,2006.15(5):p. 308-18.
6. Tikly, M. and S.V. Navarra, Lupus in the developing world--is it any different? Best Pract Res Clin Rheumatol,2008.22(4):p.643-55.
7. Systemic lupus erythematosus-an update. Drug Ther Bull,2011.49(7):p.81-4.
8. Nightingale, A.L., R.D. Farmer, and C.S. de Vries, Incidence of clinically diagnosed systemic lupus erythematosus 1992-1998 using the UK General Practice Research Database. Pharmacoepidemiol Drug Saf,2006.15(9):p.656-61.
9. Somers, E.C., et al., Incidence of systemic lupus erythematosus in the United Kingdom,1990-1999. Arthritis Rheum,2007.57(4):p.612-8.
10. Adebajo, A.O., Low frequency of autoimmune disease in tropical Africa. Lancet, 1997.349(9048):p.361-2.
11. Minaur, N., et al., Rheumatic disease in an Australian Aboriginal community in North Queensland, Australia. A WHO-ILAR COPCORD survey. J Rheumatol, 2004.31(5):p.965-72.
12. Senna, E.R., et al., Prevalence of rheumatic diseases in Brazil:a study using the COPCORD approach. J Rheumatol,2004.31(3):p.594-7.
13. Molokhia, M., et al., Systemic lupus erythematosus in migrants from west Africa compared with Afro-Caribbean people in the UK. Lancet,2001.357(9266):p. 1414-5.
14. Bae, S.C., P. Fraser, and M.H. Liang, The epidemiology of systemic lupus erythematosus in populations of African ancestry:a critical review of the "prevalence gradient hypothesis". Arthritis Rheum,1998.41(12):p.2091-9.
15. Molokhia, M. and P. McKeigue, Systemic lupus erythematosus:genes versus environment in high risk populations. Lupus,2006.15(11):p.827-32.
16. Namjou, B., et al., Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort. Genes Immun,2011.12(4):p.270-9.
17. Brown, E.E., J.C. Edberg, and R.P. Kimberly, Fc receptor genes and the systemic lupus erythematosus diathesis. Autoimmunity,2007.40(8):p.567-81.
18. Yang, J., et al., ELF1 is associated with systemic lupus erythematosus in Asian populations. Hum Mol Genet,2011.20(3):p.601-7.
19. Sheng, Y.J., et al., Follow-up study identifies two novel susceptibility loci PRKCB and 8p 11.21 for systemic lupus erythematosus. Rheumatology (Oxford),2011. 50(4):p.682-8.
20. Zhang, Z., et al., Polymorphisms at 16p13 are associated with systemic lupus erythematosus in the Chinese population. J Med Genet,2011.48(1):p.69-72.
21. Cunninghame Graham, D.S., et al., Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with systemic lupus erythematosus. PLoS Genet,2011.7(10):p. el002341.
22. Zhang, Y., et al., Two missense variants in UHRF1BP1 are independently associated with systemic lupus erythematosus in Hong Kong Chinese. Genes Immun,2011.12(3):p.231-4.
23. Gateva, V., et al., A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1228-33.
24. Han, J.W., et al., Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1234-7.
25. Graham, R.R., et al., Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet,2008.40(9):p.1059-61.
26. Harley, J.B., et al., Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet,2008.40(2):p.204-10.
27. Kozyrev, S.V., et al., Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat Genet,2008.40(2):p.211-6.
28. Connolly, J.J. and H. Hakonarson, Role of cytokines in systemic lupus erythematosus:recent progress from GWAS and sequencing. J Biomed Biotechnol, 2012.2012:p.798924.
29. Cui, Y., Y. Sheng, and X. Zhang, Genetic susceptibility to SLE:recent progress from GWAS. J Autoimmun,2013.41:p.25-33.
30. Deng, Y. and B.P. Tsao, Genetic susceptibility to systemic lupus erythematosus in the genomic era. Nat Rev Rheumatol,2010.6(12):p.683-92.
31. Criswell, L.A., et al., Analysis of families in the multiple autoimmune disease genetics consortium (MADGC) collection:the PTPN22 620W allele associates with multiple autoimmune phenotypes. Am J Hum Genet,2005.76(4):p.561-71.
32. Yang, W., et al., Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet,2010.6(2):p. e1000841.
33. Bottini, N., et al., A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat Genet,2004.36(4):p.337-8.
34. Chung, S.A., et al., Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. PLoS Genet,2011. 7(3):p.e1001323.
35. Cunninghame Graham, D.S., et al., Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nat Genet,2008. 40(1):p.83-9.
36. Farres, M.N., et al., OX40/OX40L in systemic lupus erythematosus:association with disease activity and lupus nephritis. Ann Saudi Med,2011.31(1):p.29-34.
37. Guerra, S.G., T.J. Vyse, and D.S. Cunninghame Graham, The genetics of lupus:a functional perspective. Arthritis Res Ther,2012.14(3):p.211.
38. Kaplan, M.H., STAT4:a critical regulator of inflammation in vivo. Immunol Res, 2005.31(3):p.231-42.
39. Lessard, C.J., et al., Identification of a systemic lupus erythematosus susceptibility locus at 11p 13 between PDHX and CD44 in a multiethnic study. Am J Hum Genet, 2011.88(1):p.83-91.
40. Li, Y., et al., Phosphorylated ERM is responsible for increased T cell polarization, adhesion, and migration in patients with systemic lupus erythematosus. J Immunol, 2007.178(3):p.1938-47.
41. Crispin, J.C., et al., Expression of CD44 variant isoforms CD44v3 and CD44v6 is increased on T cells from patients with systemic lupus erythematosus and is correlated with disease activity. Arthritis Rheum,2010.62(5):p.1431-7.
42. Hom, G., et al., Association of systemic lupus erythematosus with C8orfl3-BLK and ITGAM-ITGAX. N Engl J Med,2008.358(9):p.900-9.
43. Vene, R., et al., Redox remodeling allows and controls B-cell activation and differentiation. Antioxid Redox Signal,2010.13(8):p.1145-55.
44. Barrett, J.C., et al., Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet,2009.41(6):p.703-7.
45. Franke, A., et al., Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet,2008.40(11):p.1319-23.
46. Ramos, P.S., et al., Genetic analyses of interferon pathway-related genes reveal multiple new loci associated with systemic lupus erythematosus. Arthritis Rheum, 2011.63(7):p.2049-57.
47. Yap, W.H., et al., STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cells. FEBS Lett,2005.579(20):p.4470-8.
48. Hu, W., et al., Down-regulated expression of IKZF1 mRNA in peripheral blood mononuclear cells from patients with systemic lupus erythematosus. Rheumatol Int,2011.31(6):p.819-22.
49. Flesher, D.L., et al., Recent advances in the genetics of systemic lupus erythematosus. Expert Rev Clin Immunol,2010.6(3):p.461-79.
50. Robinson, T., et al., Autoimmune disease risk variant of IFIH1 is associated with increased sensitivity to IFN-alpha and serologic autoimmunity in lupus patients. J Immunol,2011.187(3):p.1298-303.
51. Feng, D., et al., Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus. Arthritis Rheum,2010.62(2):p.562-73.
52. Wang, D., et al., Ets-1 deficiency leads to altered B cell differentiation, hyperresponsiveness to TLR9 and autoimmune disease. Int Immunol,2005.17(9): p.1179-91.
53. Ishizaki, M., et al., Involvement of tyrosine kinase-2 in both the IL-12/Thl and IL-23/Th17 axes in vivo. J Immunol,2011.187(1):p.181-9.
54. Jarvinen, T.M., et al., Tyrosine kinase 2 and interferon regulatory factor 5 polymorphisms are associated with discoid and subacute cutaneous lupus erythematosus. Exp Dermatol,2010.19(2):p.123-31.
55. Tao, J.H., et al., Meta-analysis of TYK2 gene polymorphisms association with susceptibility to autoimmune and inflammatory diseases. Mol Biol Rep,2011. 38(7):p.4663-72.
56. Fransen, K., et al., Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet,2010.19(17):p.3482-8.
57. Orozco, G., et al., Study of the common genetic background for rheumatoid arthritis and systemic lupus erythematosus. Ann Rheum Dis,2011.70(3):p. 463-8.
58. Chuang, T.H. and R.J. Ulevitch, Triad3A, an E3 ubiquitin-protein ligase regulating Toll-like receptors. Nat Immunol,2004.5(5):p.495-502.
59. Salloum, R. and T.B. Niewold, Interferon regulatory factors in human lupus pathogenesis. Transl Res,2011.157(6):p.326-31.
60. Shimane, K., et al., The association of a nonsynonymous single-nucleotide polymorphism in TNFAIP3 with systemic lupus erythematosus and rheumatoid arthritis in the Japanese population. Arthritis Rheum,2010.62(2):p.574-9.
61. Beyaert, R., K. Heyninck, and S. Van Huffel, A20 and A20-binding proteins as cellular inhibitors of nuclear factor-kappa B-dependent gene expression and apoptosis. Biochem Pharmacol,2000.60(8):p.1143-51.
62. Coughlin, J.J., et al, RasGRPl and RasGRP3 regulate B cell proliferation by facilitating B cell receptor-Ras signaling. J Immunol,2005.175(11):p.7179-84.
63. Lee, J., et al., pH-dependent internalization of muramyl peptides from early endosomes enables Nod1 and Nod2 signaling. J Biol Chem,2009.284(35):p. 23818-29.
64. Nath, S.K., et al., A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet, 2008.40(2):p.152-4.
65. Han, S., et al., Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Hum Mol Genet,2009.18(6):p.1171-80.
66. Yang, W., et al., ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Hum Mol Genet,2009.18(11):p.2063-70.
67. Luo, B.H., C.V. Carman, and T.A. Springer, Structural basis of integrin regulation and signaling. Annu Rev Immunol,2007.25:p.619-47.
68. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. Hum Mol Genet, 2010.19(5):p.953-62.
69. Varade, J., et al., Replication study of 10 genes showing evidence for association with multiple sclerosis:validation of TMEM39A, IL12B and CBLB [correction of CLBL] genes. Mult Scler,2012.18(7):p.959-65.
70. Zhao, H., et al., An intronic variant associated with systemic lupus erythematosus changes the binding affinity of Yinyangl to downregulate WDFY4. Genes Immun, 2012.13(7):p.536-42.
71. Dai, R. and S.A. Ahmed, MicroRNA, a new paradigm for understanding immunoregulation, inflammation, and autoimmune diseases. Transl Res,2011. 157(4):p.163-79.
72. Thai, T.H., P.A. Christiansen, and G.C. Tsokos, Is there a link between dysregulated miRNA expression and disease? Discov Med,2010.10(52):p. 184-94.
73. Nelson, P., et al., The microRNA world:small is mighty. Trends Biochem Sci, 2003.28(10):p.534-40.
74. Davidson-Moncada, J., F.N. Papavasiliou, and W. Tam, MicroRNAs of the immune system:roles in inflammation and cancer. Ann N Y Acad Sci,2010.1183: p.183-94.
75. Wahid, F., et al., MicroRNAs:synthesis, mechanism, function, and recent clinical trials. Biochim Biophys Acta,2010.1803(11):p.1231-43.
76. Lindsay, M.A., microRNAs and the immune response. Trends Immunol,2008. 29(7):p.343-51.
77. Pauley, K.M., S. Cha, and E.K. Chan, MicroRNA in autoimmunity and autoimmune diseases. J Autoimmun,2009.32(3-4):p.189-94.
78. Dai, Y, et al., Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients. Lupus,2007.16(12):p.939-46.
79. Dai, Y, et al., Comprehensive analysis of microRNA expression patterns in renal biopsies of lupus nephritis patients. Rheumatol Int,2009.29(7):p.749-54.
80. Te, J.L., et al., Identification of unique microRNA signature associated with lupus nephritis. PLoS One,2010.5(5):p. e10344.
81. Pan, W., et al., MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol,2010.184(12):p.6773-81.
82. Stagakis, E., et al., Identification of novel microRNA signatures linked to human lupus disease activity and pathogenesis:miR-21 regulates aberrant T cell responses through regulation of PDCD4 expression. Ann Rheum Dis,2011.70(8): p.1496-506.
83. Zhao, S., et al., MicroRNA-126 regulates DNA methylation in CD4+T cells and contributes to systemic lupus erythematosus by targeting DNA methyltransferase 1. Arthritis Rheum,2011.63(5):p.1376-86.
84. Tang, Y., et al., MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum,2009.60(4):p.1065-75.
85. Hai-yan, W., et al., Expression of MicroRNA-146a in peripheral blood mononuclear cells in patients with systemic lupus erythematosus. Zhongguo Yi Xue Ke Xue Yuan Xue Bao,2011.33(2):p.185-8.
86. Luo, X., et al., A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus. PLoS Genet, 2011.7(6):p.el002128.
87. Wang, G, et al., Serum and urinary cell-free MiR-146a and MiR-155 in patients with systemic lupus erythematosus. J Rheumatol,2010.37(12):p.2516-22.
88. Divekar, A.A., et al., Dicer insufficiency and microRNA-155 overexpression in lupus regulatory T cells:an apparent paradox in the setting of an inflammatory milieu. J Immunol,2011.186(2):p.924-30.
89. Ando, Y, et al., Two-step cleavage of hairpin RNA with 5'overhangs by human DICER. BMC Mol Biol,2011.12:p.6.
2. D'Cruz, D.P., M.A. Khamashta, and G.R. Hughes, Systemic lupus erythematosus. Lancet,2007.369(9561):p.587-96.
3. Tsao, B.P., The genetics of human systemic lupus erythematosus. Trends Immunol,2003.24(11):p.595-602.
4. Kariuki, S.N. and T.B. Niewold, Genetic regulation of serum cytokines in systemic lupus erythematosus. Transl Res,2010.155(3):p.109-17.
5. Cohen-Solal, J.F., et al., Hormonal regulation of B-cell function and systemic lupus erythematosus. Lupus,2008.17(6):p.528-32.
6. Ramos-Casals, M., et al., Acute viral infections in patients with systemic lupus erythematosus:description of 23 cases and review of the literature. Medicine (Baltimore),2008.87(6):p.311-8.
7. Bultink, I.E., Osteoporosis and fractures in systemic lupus erythematosus. Arthritis Care Res (Hoboken),2012.64(1):p.2-8.
8. Ortega, L.M., et al., Review:Lupus nephritis:pathologic features, epidemiology and a guide to therapeutic decisions. Lupus,2010.19(5):p. 557-74.
9. Mok, C.C., Biomarkers for lupus nephritis:a critical appraisal. J Biomed Biotechnol,2010.2010:p.638413.
10. Anaya, J.M., et al., Lupus nephritis in Colombians:contrasts and comparisons with other populations. Clin Rev Allergy Immunol,2011.40(3):p.199-207.
11. de Zubiria Salgado, A. and C. Herrera-Diaz, Lupus nephritis:an overview of recent findings. Autoimmune Dis,2012.2012:p.849684.
12. Varela, D.C., et al., Delayed lupus nephritis. Ann Rheum Dis,2008.67(7):p. 1044-6.
13. Moser, K.L., et al., Recent insights into the genetic basis of systemic lupus erythematosus. Genes Immun,2009.10(5):p.373-9.
14. Selmi, C., Q. Lu, and M.C. Humble, Heritability versus the role of the environment in autoimmunity. J Autoimmun,2012.39(4):p.249-52.
15. Ngalamika, O., et al., Epigenetics, autoimmunity and hematologic malignancies:a comprehensive review. J Autoimmun,2012.39(4):p.451-65.
16. Kaiser, R. and L.A. Criswell, Genetics research in systemic lupus erythematosus for clinicians:methodology, progress, and controversies. Curr Opin Rheumatol,2010.22(2):p.119-25.
17. Zhou, Y. and Q. Lu, DNA methylation in T cells from idiopathic lupus and drug-induced lupus patients. Autoimmun Rev,2008.7(5):p.376-83.
18. Freimer, N. and C. Sabatti, The use of pedigree, sib-pair and association studies of common diseases for genetic mapping and epidemiology. Nat Genet, 2004.36(10):p.1045-51.
19. Lander, E. and L. Kruglyak, Genetic dissection of complex traits:guidelines for interpreting and reporting linkage results. Nat Genet,1995.11(3):p. 241-7.
20. Sabatti, C., S. Service, and N. Freimer, False discovery rate in linkage and association genome screens for complex disorders. Genetics,2003.164(2):p. 829-33.
21. Frazer, K.A., et al., A second generation human haplotype map of over 3.1 million SNPs. Nature,2007.449(7164):p.851-61.
22. Purcell, S., et al., PLINK:a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet,2007.81(3):p.559-75.
23. Klein, R.J., et al., Complement factor H polymorphism in age-related macular degeneration. Science,2005.308(5720):p.385-9.
24. Hindorff, L.A., et al., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A,2009.106(23):p.9362-7.
25. Kingsley, C.B., Identification of causal sequence variants of disease in the next generation sequencing era. Methods Mol Biol,2011.700:p.37-46.
26. Harley, J.B., et al., Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet,2008.40(2):p.204-10.
27. Han, J.W., et al., Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1234-7.
28. Yang, W., et al., Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet,2010.6(2):p. e1000841.
29. Cui, Y., Y. Sheng, and X. Zhang, Genetic susceptibility to SLE:recent progress from GWAS. J Autoimmun,2013.41:p.25-33.
30. Wang, C., et al., Genes identified in Asian SLE GWASs are also associated with SLE in Caucasian populations. Eur J Hum Genet,2013.21(9):p.994-9.
31. Barbosa, M.D., et al., Identification of the homologous beige and Chediak-Higashi syndrome genes. Nature,1996.382(6588):p.262-5.
32. Cullinane, A.R., A.A. Schaffer, and M. Huizing, The BEACH is hot:a LYST of emerging roles for BEACH-domain containing proteins in human disease. Traffic,2013.14(7):p.749-66.
33. Lemmon, M.A., Structural basis for high-affinity phosphoinositide binding by pleckstrin homology domains. Biochem Soc Trans,1999.27(4):p.617-24.
34. Lemmon, M.A., Pleckstrin homology domains:not just for phosphoinositides. Biochem Soc Trans,2004.32(Pt 5):p.707-11.
35. Smith, T.F., et al., The WD repeat:a common architecture for diverse functions. Trends Biochem Sci,1999.24(5):p.181-5.
36. Li, D. and R. Roberts, WD-repeat proteins:structure characteristics, biological function, and their involvement in human diseases. Cell Mol Life Sci,2001.58(14):p.2085-97.
37. Tchernev, V.T., et al., The Chediak-Higashi protein interacts with SNARE complex and signal transduction proteins. Mol Med,2002.8(1):p.56-64.
38. Wang, J.W., et al., Identification of a novel lipopolysaccharide-inducible gene with key features of both A kinase anchor proteins and chsl/beige proteins. J Immunol,2001.166(7):p.4586-95.
39. Lopez-Herrera, G, et al., Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity. Am J Hum Genet,2012. 90(6):p.986-1001.
40. Montfort, A., et al., FAN stimulates TNF(alpha)-induced gene expression, leukocyte recruitment, and humoral response. J Immunol,2009.183(8):p. 5369-78.
41. Segui, B., et al., Involvement of FAN in TNF-induced apoptosis. J Clin Invest, 2001.108(1):p.143-51.
42. Finley, K.D., et al., blue cheese mutations define a novel, conserved gene involved in progressive neural degeneration. J Neurosci,2003.23(4):p. 1254-64.
43. Hocking, L.J., et al., Functional interaction between sequestosome-1/p62 and autophagy-linked FYVE-containing protein WDFY3 in human osteoclasts. Biochem Biophys Res Commun,2010.402(3):p.543-8.
44. Klionsky, D.J., Autophagy revisited:a conversation with Christian de Duve. Autophagy,2008.4(6):p.740-3.
45. Klionsky, D.J., et al., A unified nomenclature for yeast autophagy-related genes. Dev Cell,2003.5(4):p.539-45.
46. Majeski, A.E. and J.F. Dice, Mechanisms of chaperone-mediated autophagy. Int J Biochem Cell Biol,2004.36(12):p.2435-44.
47. Levine, B. and J. Yuan, Autophagy in cell death:an innocent convict? J Clin Invest,2005.115(10):p.2679-88.
48. Lockshin, R.A. and Z. Zakeri, Apoptosis, autophagy, and more. Int J Biochem Cell Biol,2004.36(12):p.2405-19.
49. Bhattacharya, A. and N.T. Eissa, Autophagy and autoimmunity crosstalks. Front Immunol,2013.4:p.88.
50. Pierdominici, M., et al., Role of autophagy in immunity and autoimmunity, with a special focus on systemic lupus erythematosus. FASEB J,2012.26(4): p.1400-12.
51. Zhou, X.J., et al., Genetic association of PRDM1-ATG5 intergenic region and autophagy with systemic lupus erythematosus in a Chinese population. Ann Rheum Dis,2011.70(7):p.1330-7.
52. Parkes, M, et al., Sequence variants in the autophagy gene 1RGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet,2007.39(7):p.830-2.
53. Lichtman, E.I., S.M. Helfgott, and M.A. Kriegel, Emerging therapies for systemic lupus erythematosus--focus on targeting interferon-alpha. Clin Immunol,2012.143(3):p.210-21.
54. Lee, H.K., et al., Autophagy-dependent viral recognition by plasmacytoid dendritic cells. Science,2007.315(5817):p.1398-401.
55. Cao, W., et al., Toll-like receptor-mediated induction of type I interferon in plasmacytoid dendritic cells requires the rapamycin-sensitive PI(3)K-mTOR-p70S6Kpathway. Nat Immunol,2008.9(10):p.1157-64.
56. Wu, T., et al., Metabolic disturbances associated with systemic lupus erythematosus. PLoS One,2012.7(6):p. e37210.
57. Zhou, R., et al., A role for mitochondria in NLRP3 inflammasome activation. Nature,2011.469(7329):p.221-5.
58. Kaspar, J.W., S.K. Niture, and A.K. Jaiswal, Nrf2:INrf2 (Keapl) signaling in oxidative stress. Free Radic Biol Med,2009.47(9):p.1304-9.
59. Komatsu, M., et al., Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell,2007.131(6):p.1149-63.
60. He, Y., et al., Identification of a lysosomal pathway that modulates glucocorticoid signaling and the inflammatory response. Sci Signal,2011. 4(180):p. ra44.
61. Hochberg, M.C., Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum, 1997.40(9):p.1725.
62. Gateva, V., et al., A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1228-33.
63. Plenge, R.M., Recent progress in rheumatoid arthritis genetics:one step towards improved patient care. Curr Opin Rheumatol,2009.21(3):p.262-71.
64. Kochi, Y., et al., Genetics of rheumatoid arthritis:underlying evidence of ethnic differences. J Autoimmun,2009.32(3-4):p.158-62.
65. Tian, C., P.K. Gregersen, and M.F. Seldin, Accounting for ancestry: population substructure and genome-wide association studies. Hum Mol Genet,2008.17(R2):p. R143-50.
66. Greene, C.S., et al., Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One,2009.4(6):p. e5639.
67. Hardy, J. and A. Singleton, Genomewide association studies and human disease. N Engl J Med,2009.360(17):p.1759-68.
68. Graham, R.R., et al., Review of recent genome-wide association scans in lupus. J Intern Med,2009.265(6):p.680-8.
69. Lee, H.S. and S.C. Bae, What can we learn from genetic studies of systemic lupus erythematosus? Implications of genetic heterogeneity among populations in SLE. Lupus,2010.19(12):p.1452-9.
70. Guerra, S.G., T.J. Vyse, and D.S. Cunninghame Graham, The genetics of lupus: a functional perspective. Arthritis Res Ther,2012.14(3):p.211.
71. Kaplan, M.H., STAT4:a critical regulator of inflammation in vivo. Immunol Res,2005.31(3):p.231-42.
72. Nath, S.K., et al., A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet,2008.40(2):p.152-4.
73. Han, S., et al., Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Hum Mol Genet,2009.18(6):p.1171-80.
74. Molineros, J.E., et al., Admixture mapping in lupus identifies multiple functional variants within IFIHl associated with apoptosis, inflammation, and autoantibodyproduction. PLoS Genet,2013.9(2):p. e1003222.
75. Kawasaki, A., et al., Association of IRF5 polymorphisms with systemic lupus erythematosus in a Japanese population:support for a crucial role of intron 1 polymorphisms. Arthritis Rheum,2008.58(3):p.826-34.
76. Barnes, B.J., et al., Global and distinct targets of IRF-5 and IRF-7 during innate response to viral infection. J Biol Chem,2004.279(43):p.45194-207.
77. Novais, R.C. and Y.R. Thorstenson, The evolution of Pyrosequencing(R) for microbiology:From genes to genomes. J Microbiol Methods,2011.86(1):p. 1-7.
78. Quinn, E.M., et al., Evidence for cis-acting regulation of ANK3 and CACNA1Cgene expression. Bipolar Disord,2010.12(4):p.440-5.
79. Manolio, T.A., et al., Finding the missing heritability of complex diseases. Nature,2009.461(7265):p.747-53.
80. Nejentsev, S., et al., Rare variants of IFIHl, a gene implicated in antiviral responses, protect against type 1 diabetes. Science,2009.324(5925):p.387-9.
81. Cohen, J.C., et al., Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med,2006.354(12):p.1264-72.
82. Abecasis, GR., et al., A map of human genome variation from population-scale sequencing. Nature,2010.467(7319):p.1061-73.
83. Ewing, A.D. and H.H. Kazazian, Jr., High-throughput sequencing reveals extensive variation in human-specific LI content in individual human genomes. Genome Res,2010.20(9):p.1262-70.
84. Dietrich, J., et al., Ligand-induced TCR down-regulation is not dependent on constitutive TCR cycling. J Immunol,2002.168(11):p.5434-40.
85. Pang, M., et al., Defective expression and tyrosine phosphorylation of the T cell receptor zeta chain in peripheral blood T cells from systemic lupus erythematosus patients. Clin Exp Immunol,2002.129(1):p.160-8.
86. Nambiar, M.P., et al., Prevalence of T cell receptor zeta chain deficiency in systemic lupus erythematosus. Lupus,2003.12(1):p.46-51.
87. Gorman, C.L., et al., Polymorphisms in the CD3Z gene influence TCRzeta expression in systemic lupus erythematosus patients and healthy controls. J Immunol,2008.180(2):p.1060-70.
88. Fu, Q., et al., Association of a functional IRF7 variant with systemic lupus erythematosus. Arthritis Rheum,2011.63(3):p.749-54.
89. Li, J., Y. You, and S. Chen, The role of upstream stimulatory factor 1 in the transcriptional regulation of the human TBX21 promoter mediated by the T-1514C polymorphism associated with systemic lupus erythematosus. Immunogenetics,2012.64(5):p.361-70.
90. Hikami, K., et al., Association of a functional polymorphism in the 3'-untranslated region of SPI1 with systemic lupus erythematosus. Arthritis Rheum,2011.63(3):p.755-63.
91. Sakurai, D., et al., Preferential binding to Elk-1 by SLE-associated IL10 risk allele upregulates IL10 expression. PLoS Genet,2013.9(10):p. e1003870.
92. Choi, J.W., et al., A common intronic variant of CXCR3 is functionally associated with gene expression levels and the polymorphic immune cell responses to stimuli. J Allergy Clin Immunol,2008.122(6):p.1119-1126 e7.
93. Su, K., et al., A promoter haplotype of the immunoreceptor tyrosine-based inhibitory motif-bearing FcgammaRIIb alters receptor expression and associates with autoimmunity. I. Regulatory FCGR2B polymorphisms and their association with systemic lupus erythematosus. J Immunol,2004. 172(11):p.7186-91.
94. Maeda, T., et al., Role of the proto-oncogene Pokemon in cellular transformation and ARF repression. Nature,2005.433(7023):p.278-85.
95. Hellqvist, M., et al., The human forkhead protein FREAC-2 contains two functionally redundant activation domains and interacts with TBP and TFIIB. J Biol Chem,1998.273(36):p.23335-43.
96. Berndt, J.A., et al., The transcriptional regulator Yin Yang 1 activates the myelin PLP gene. J Neurochem,2001.77(3):p.935-42.
97. Shi, Y., J.S. Lee, and K.M. Galvin, Everything you have ever wanted to know about Yin Yang 1. Biochim Biophys Acta,1997.1332(2):p. F49-66.
98. Li, J.R., et al., A common promoter variant of TBX21 is associated with allele specific binding to Yin-Yang 1 and reduced gene expression. Scand J Immunol, 2011.73(5):p.449-58.
99. Riveros, C, et al., A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PLoS One,2010.5(12):p. e14176.
100. Simonsen, A., et al., Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci,2004.117(Pt 18): p.4239-51.
101. Clausen, T.H., et al., p62/SQSTMl and ALFY interact to facilitate the formation ofp62 bodies/ALIS and their degradation by autophagy. Autophagy, 2010.6(3):p.330-44.
102. Filimonenko, M., et al., The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell,2010. 38(2):p.265-79.
103. Isakson, P., P. Holland, and A. Simonsen, The role of ALFY in selective autophagy. Cell Death Differ,2013.20(1):p.12-20.
104. Yamamoto, A. and A. Simonsen, Aljy-dependent elimination of aggregated proteins by macroautophagy:can there be too much of a good thing? Autophagy,2011.7(3):p.346-50.
105. Alessandri, C., et al., T lymphocytes from patients with systemic lupus erythematosus are resistant to induction of autophagy. FASEB J,2012.26(11): p.4722-32.
106. Clarke, A.J., et al., Autophagy is activated in systemic lupus erythematosus and required for plasmablast development. Ann Rheum Dis,2014.
107. Furtado, J. and D.A. Isenberg, B cell elimination in systemic lupus erythematosus. Clin Immunol,2013.146(2):p.90-103.
108. Dorner, T., C. Giesecke, and P.E. Lipsky, Mechanisms of B cell autoimmunity in SLE. Arthritis Res Ther,2011.13(5):p.243.
109. Anolik, J.H., B cell biology:implications for treatment of systemic lupus erythematosus. Lupus,2013.22(4):p.342-9.
110. Salmon, J.E. and M.J. Roman, Subclinical atherosclerosis in rheumatoid arthritis and systemic lupus erythematosus. Am J Med,2008.121(10 Suppl 1): p. S3-8.
111. Ren, Y, et al., Increased apoptotic neutrophils and macrophages and impaired macrophage phagocytic clearance of apoptotic neutrophils in systemic lupus erythematosus. Arthritis Rheum,2003.48(10):p.2888-97.
112. Majai, G, et al., Decreased apopto-phagocytic gene expression in the macrophages of systemic lupus erythematosus patients. Lupus,2014.23(2):p. 133-45.
113. Nah, J., et al., BECNl/Beclin 1 is recruited into lipid rafts byprion to activate autophagy in response to amyloid beta 42. Autophagy,2013.9(12):p. 2009-21.
114. Kroemer, G. and B. Levine, Autophagic cell death:the story of a misnomer. Nat Rev Mol Cell Biol,2008.9(12):p.1004-10.
1. Rahman, A. and D.A. Isenberg, Systemic lupus erythematosus. N Engl J Med, 2008.358(9):p.929-39.
2. Niewold, T.B., et al., High serum IFN-alpha activity is a heritable risk factor for systemic lupus erythematosus. Genes Immun,2007.8(6):p.492-502.
3. Alarcon-Segovia, D., et al., Familial aggregation of systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases in 1,177 lupus patients from the GLADEL cohort. Arthritis Rheum,2005.52(4):p.1138-47.
4. Fessel, W.J., Systemic lupus erythematosus in the community. Incidence, prevalence, outcome, and first symptoms; the high prevalence in black women. Arch Intern Med,1974.134(6):p.1027-35.
5. Danchenko, N., J.A. Satia, and M.S. Anthony, Epidemiology of systemic lupus erythematosus:a comparison of worldwide disease burden. Lupus,2006.15(5):p. 308-18.
6. Tikly, M. and S.V. Navarra, Lupus in the developing world--is it any different? Best Pract Res Clin Rheumatol,2008.22(4):p.643-55.
7. Systemic lupus erythematosus-an update. Drug Ther Bull,2011.49(7):p.81-4.
8. Nightingale, A.L., R.D. Farmer, and C.S. de Vries, Incidence of clinically diagnosed systemic lupus erythematosus 1992-1998 using the UK General Practice Research Database. Pharmacoepidemiol Drug Saf,2006.15(9):p.656-61.
9. Somers, E.C., et al., Incidence of systemic lupus erythematosus in the United Kingdom,1990-1999. Arthritis Rheum,2007.57(4):p.612-8.
10. Adebajo, A.O., Low frequency of autoimmune disease in tropical Africa. Lancet, 1997.349(9048):p.361-2.
11. Minaur, N., et al., Rheumatic disease in an Australian Aboriginal community in North Queensland, Australia. A WHO-ILAR COPCORD survey. J Rheumatol, 2004.31(5):p.965-72.
12. Senna, E.R., et al., Prevalence of rheumatic diseases in Brazil:a study using the COPCORD approach. J Rheumatol,2004.31(3):p.594-7.
13. Molokhia, M., et al., Systemic lupus erythematosus in migrants from west Africa compared with Afro-Caribbean people in the UK. Lancet,2001.357(9266):p. 1414-5.
14. Bae, S.C., P. Fraser, and M.H. Liang, The epidemiology of systemic lupus erythematosus in populations of African ancestry:a critical review of the "prevalence gradient hypothesis". Arthritis Rheum,1998.41(12):p.2091-9.
15. Molokhia, M. and P. McKeigue, Systemic lupus erythematosus:genes versus environment in high risk populations. Lupus,2006.15(11):p.827-32.
16. Namjou, B., et al., Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort. Genes Immun,2011.12(4):p.270-9.
17. Brown, E.E., J.C. Edberg, and R.P. Kimberly, Fc receptor genes and the systemic lupus erythematosus diathesis. Autoimmunity,2007.40(8):p.567-81.
18. Yang, J., et al., ELF1 is associated with systemic lupus erythematosus in Asian populations. Hum Mol Genet,2011.20(3):p.601-7.
19. Sheng, Y.J., et al., Follow-up study identifies two novel susceptibility loci PRKCB and 8p 11.21 for systemic lupus erythematosus. Rheumatology (Oxford),2011. 50(4):p.682-8.
20. Zhang, Z., et al., Polymorphisms at 16p13 are associated with systemic lupus erythematosus in the Chinese population. J Med Genet,2011.48(1):p.69-72.
21. Cunninghame Graham, D.S., et al., Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with systemic lupus erythematosus. PLoS Genet,2011.7(10):p. el002341.
22. Zhang, Y., et al., Two missense variants in UHRF1BP1 are independently associated with systemic lupus erythematosus in Hong Kong Chinese. Genes Immun,2011.12(3):p.231-4.
23. Gateva, V., et al., A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1228-33.
24. Han, J.W., et al., Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet,2009.41(11):p.1234-7.
25. Graham, R.R., et al., Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet,2008.40(9):p.1059-61.
26. Harley, J.B., et al., Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet,2008.40(2):p.204-10.
27. Kozyrev, S.V., et al., Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat Genet,2008.40(2):p.211-6.
28. Connolly, J.J. and H. Hakonarson, Role of cytokines in systemic lupus erythematosus:recent progress from GWAS and sequencing. J Biomed Biotechnol, 2012.2012:p.798924.
29. Cui, Y., Y. Sheng, and X. Zhang, Genetic susceptibility to SLE:recent progress from GWAS. J Autoimmun,2013.41:p.25-33.
30. Deng, Y. and B.P. Tsao, Genetic susceptibility to systemic lupus erythematosus in the genomic era. Nat Rev Rheumatol,2010.6(12):p.683-92.
31. Criswell, L.A., et al., Analysis of families in the multiple autoimmune disease genetics consortium (MADGC) collection:the PTPN22 620W allele associates with multiple autoimmune phenotypes. Am J Hum Genet,2005.76(4):p.561-71.
32. Yang, W., et al., Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. PLoS Genet,2010.6(2):p. e1000841.
33. Bottini, N., et al., A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat Genet,2004.36(4):p.337-8.
34. Chung, S.A., et al., Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. PLoS Genet,2011. 7(3):p.e1001323.
35. Cunninghame Graham, D.S., et al., Polymorphism at the TNF superfamily gene TNFSF4 confers susceptibility to systemic lupus erythematosus. Nat Genet,2008. 40(1):p.83-9.
36. Farres, M.N., et al., OX40/OX40L in systemic lupus erythematosus:association with disease activity and lupus nephritis. Ann Saudi Med,2011.31(1):p.29-34.
37. Guerra, S.G., T.J. Vyse, and D.S. Cunninghame Graham, The genetics of lupus:a functional perspective. Arthritis Res Ther,2012.14(3):p.211.
38. Kaplan, M.H., STAT4:a critical regulator of inflammation in vivo. Immunol Res, 2005.31(3):p.231-42.
39. Lessard, C.J., et al., Identification of a systemic lupus erythematosus susceptibility locus at 11p 13 between PDHX and CD44 in a multiethnic study. Am J Hum Genet, 2011.88(1):p.83-91.
40. Li, Y., et al., Phosphorylated ERM is responsible for increased T cell polarization, adhesion, and migration in patients with systemic lupus erythematosus. J Immunol, 2007.178(3):p.1938-47.
41. Crispin, J.C., et al., Expression of CD44 variant isoforms CD44v3 and CD44v6 is increased on T cells from patients with systemic lupus erythematosus and is correlated with disease activity. Arthritis Rheum,2010.62(5):p.1431-7.
42. Hom, G., et al., Association of systemic lupus erythematosus with C8orfl3-BLK and ITGAM-ITGAX. N Engl J Med,2008.358(9):p.900-9.
43. Vene, R., et al., Redox remodeling allows and controls B-cell activation and differentiation. Antioxid Redox Signal,2010.13(8):p.1145-55.
44. Barrett, J.C., et al., Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet,2009.41(6):p.703-7.
45. Franke, A., et al., Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nat Genet,2008.40(11):p.1319-23.
46. Ramos, P.S., et al., Genetic analyses of interferon pathway-related genes reveal multiple new loci associated with systemic lupus erythematosus. Arthritis Rheum, 2011.63(7):p.2049-57.
47. Yap, W.H., et al., STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cells. FEBS Lett,2005.579(20):p.4470-8.
48. Hu, W., et al., Down-regulated expression of IKZF1 mRNA in peripheral blood mononuclear cells from patients with systemic lupus erythematosus. Rheumatol Int,2011.31(6):p.819-22.
49. Flesher, D.L., et al., Recent advances in the genetics of systemic lupus erythematosus. Expert Rev Clin Immunol,2010.6(3):p.461-79.
50. Robinson, T., et al., Autoimmune disease risk variant of IFIH1 is associated with increased sensitivity to IFN-alpha and serologic autoimmunity in lupus patients. J Immunol,2011.187(3):p.1298-303.
51. Feng, D., et al., Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus. Arthritis Rheum,2010.62(2):p.562-73.
52. Wang, D., et al., Ets-1 deficiency leads to altered B cell differentiation, hyperresponsiveness to TLR9 and autoimmune disease. Int Immunol,2005.17(9): p.1179-91.
53. Ishizaki, M., et al., Involvement of tyrosine kinase-2 in both the IL-12/Thl and IL-23/Th17 axes in vivo. J Immunol,2011.187(1):p.181-9.
54. Jarvinen, T.M., et al., Tyrosine kinase 2 and interferon regulatory factor 5 polymorphisms are associated with discoid and subacute cutaneous lupus erythematosus. Exp Dermatol,2010.19(2):p.123-31.
55. Tao, J.H., et al., Meta-analysis of TYK2 gene polymorphisms association with susceptibility to autoimmune and inflammatory diseases. Mol Biol Rep,2011. 38(7):p.4663-72.
56. Fransen, K., et al., Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet,2010.19(17):p.3482-8.
57. Orozco, G., et al., Study of the common genetic background for rheumatoid arthritis and systemic lupus erythematosus. Ann Rheum Dis,2011.70(3):p. 463-8.
58. Chuang, T.H. and R.J. Ulevitch, Triad3A, an E3 ubiquitin-protein ligase regulating Toll-like receptors. Nat Immunol,2004.5(5):p.495-502.
59. Salloum, R. and T.B. Niewold, Interferon regulatory factors in human lupus pathogenesis. Transl Res,2011.157(6):p.326-31.
60. Shimane, K., et al., The association of a nonsynonymous single-nucleotide polymorphism in TNFAIP3 with systemic lupus erythematosus and rheumatoid arthritis in the Japanese population. Arthritis Rheum,2010.62(2):p.574-9.
61. Beyaert, R., K. Heyninck, and S. Van Huffel, A20 and A20-binding proteins as cellular inhibitors of nuclear factor-kappa B-dependent gene expression and apoptosis. Biochem Pharmacol,2000.60(8):p.1143-51.
62. Coughlin, J.J., et al, RasGRPl and RasGRP3 regulate B cell proliferation by facilitating B cell receptor-Ras signaling. J Immunol,2005.175(11):p.7179-84.
63. Lee, J., et al., pH-dependent internalization of muramyl peptides from early endosomes enables Nod1 and Nod2 signaling. J Biol Chem,2009.284(35):p. 23818-29.
64. Nath, S.K., et al., A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet, 2008.40(2):p.152-4.
65. Han, S., et al., Evaluation of imputation-based association in and around the integrin-alpha-M (ITGAM) gene and replication of robust association between a non-synonymous functional variant within ITGAM and systemic lupus erythematosus (SLE). Hum Mol Genet,2009.18(6):p.1171-80.
66. Yang, W., et al., ITGAM is associated with disease susceptibility and renal nephritis of systemic lupus erythematosus in Hong Kong Chinese and Thai. Hum Mol Genet,2009.18(11):p.2063-70.
67. Luo, B.H., C.V. Carman, and T.A. Springer, Structural basis of integrin regulation and signaling. Annu Rev Immunol,2007.25:p.619-47.
68. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. Hum Mol Genet, 2010.19(5):p.953-62.
69. Varade, J., et al., Replication study of 10 genes showing evidence for association with multiple sclerosis:validation of TMEM39A, IL12B and CBLB [correction of CLBL] genes. Mult Scler,2012.18(7):p.959-65.
70. Zhao, H., et al., An intronic variant associated with systemic lupus erythematosus changes the binding affinity of Yinyangl to downregulate WDFY4. Genes Immun, 2012.13(7):p.536-42.
71. Dai, R. and S.A. Ahmed, MicroRNA, a new paradigm for understanding immunoregulation, inflammation, and autoimmune diseases. Transl Res,2011. 157(4):p.163-79.
72. Thai, T.H., P.A. Christiansen, and G.C. Tsokos, Is there a link between dysregulated miRNA expression and disease? Discov Med,2010.10(52):p. 184-94.
73. Nelson, P., et al., The microRNA world:small is mighty. Trends Biochem Sci, 2003.28(10):p.534-40.
74. Davidson-Moncada, J., F.N. Papavasiliou, and W. Tam, MicroRNAs of the immune system:roles in inflammation and cancer. Ann N Y Acad Sci,2010.1183: p.183-94.
75. Wahid, F., et al., MicroRNAs:synthesis, mechanism, function, and recent clinical trials. Biochim Biophys Acta,2010.1803(11):p.1231-43.
76. Lindsay, M.A., microRNAs and the immune response. Trends Immunol,2008. 29(7):p.343-51.
77. Pauley, K.M., S. Cha, and E.K. Chan, MicroRNA in autoimmunity and autoimmune diseases. J Autoimmun,2009.32(3-4):p.189-94.
78. Dai, Y, et al., Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients. Lupus,2007.16(12):p.939-46.
79. Dai, Y, et al., Comprehensive analysis of microRNA expression patterns in renal biopsies of lupus nephritis patients. Rheumatol Int,2009.29(7):p.749-54.
80. Te, J.L., et al., Identification of unique microRNA signature associated with lupus nephritis. PLoS One,2010.5(5):p. e10344.
81. Pan, W., et al., MicroRNA-21 and microRNA-148a contribute to DNA hypomethylation in lupus CD4+T cells by directly and indirectly targeting DNA methyltransferase 1. J Immunol,2010.184(12):p.6773-81.
82. Stagakis, E., et al., Identification of novel microRNA signatures linked to human lupus disease activity and pathogenesis:miR-21 regulates aberrant T cell responses through regulation of PDCD4 expression. Ann Rheum Dis,2011.70(8): p.1496-506.
83. Zhao, S., et al., MicroRNA-126 regulates DNA methylation in CD4+T cells and contributes to systemic lupus erythematosus by targeting DNA methyltransferase 1. Arthritis Rheum,2011.63(5):p.1376-86.
84. Tang, Y., et al., MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum,2009.60(4):p.1065-75.
85. Hai-yan, W., et al., Expression of MicroRNA-146a in peripheral blood mononuclear cells in patients with systemic lupus erythematosus. Zhongguo Yi Xue Ke Xue Yuan Xue Bao,2011.33(2):p.185-8.
86. Luo, X., et al., A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus. PLoS Genet, 2011.7(6):p.el002128.
87. Wang, G, et al., Serum and urinary cell-free MiR-146a and MiR-155 in patients with systemic lupus erythematosus. J Rheumatol,2010.37(12):p.2516-22.
88. Divekar, A.A., et al., Dicer insufficiency and microRNA-155 overexpression in lupus regulatory T cells:an apparent paradox in the setting of an inflammatory milieu. J Immunol,2011.186(2):p.924-30.
89. Ando, Y, et al., Two-step cleavage of hairpin RNA with 5'overhangs by human DICER. BMC Mol Biol,2011.12:p.6.
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