Update on human systemic lupus erythematosus genetics

PURPOSE OF REVIEW: Susceptibility to systemic lupus erythematosus (SLE) has a genetic component. In recent years, nine complete genome scans using family collections that differ greatly in ethnic compositions and geographic locations have identified several strong, confirmed SLE susceptibility loci. Evidence implicating individual gene polymorphisms (or haplotypes) within some of the linked intervals has been reported. This review highlights recent findings that may lead to the identification of putative genes and new insights in the pathogenesis of SLE. RECENT FINDINGS: Eight of the best-supported SLE susceptibility loci are 1q23, 1q25-31, 1q41-42, 2q35-37, 4p16-15.2, 6p11-21, 12p24, and 16q12. These are chromosomal regions exhibiting genome-wide significance for linkage in single studies and suggestive evidence for linkage in other samples. Linkage analyses conditioning on pedigrees in which one affected member manifesting a particular clinical condition have also yielded many chromosomal regions linked to SLE. The linked interval on chromosome 6p has been narrowed to 0.5 approximately 1.0 Mb (million basepairs) of 3 MHC class II containing risk haplotypes in white subjects. Cumulative results have shown that hereditary deficiencies of complement component C4A (a MHC class III gene) confer risk for SLE in almost all ethnic groups studied. The FcgammaR genes (located at 1q23) have been convincingly demonstrated to play an important role in susceptibility to SLE (and/or lupus nephritis). The evidence for the intronic single nucleotide polymorphism of program cell death gene 1 (PDCD1 at 2q37) to confer susceptibility is promising but not yet compelling. Within several established susceptibility loci, evidence for association of positional candidate genes is emerging. SUMMARY: Further replications of linkage and association are the immediate task. The respective contribution of each susceptibility gene, relationships between genotypes and phenotypes, and potential interactions between susceptibility gene products need to be elucidated. This line of investigation is now well poised to provide novel insights into how genetic variants can affect functional pathways leading to the development of SLE.     

A two-stage, genome-wide screen for susceptibility loci in primary Raynaud's phenomenon

OBJECTIVE: To identify chromosomal regions containing genes involved in the susceptibility to primary Raynaud's phenomenon (RP). METHODS: Six extended families with multiple individuals affected with primary RP (n = 37) were examined for linkage in a 2-stage, whole-genome screen, using a total of 298 microsatellite markers. RESULTS: Multipoint, nonparametric linkage analysis identified 5 areas of possible linkage, with a nominal level of significance of P < or = 0.05. Analysis of a finer map of markers in these regions defined the regions of linkage as 21.4 cM on 6q13-6q23.3 (D6S261; P = 0.0004), 10.2 cM on 7p22-7p15 (D7S664; P = 0.014), 1.6 cM on 9p23-9p22 (D9S156; P = 0.0075), 5.1 cM on 17p13.1-17p12 (D17S1791; P = 0.036), and 11.8 cM on Xp11.4-Xp11.23 (DXS8054; P = 0.006). Three potential candidate genes map to these regions: the beta subunit of the muscle acetylcholine receptor and the serotonin 1B and 1E receptors. CONCLUSION: These results provide evidence of the presence and location of genes that are involved in the genetic susceptibility to primary RP.     

A C/T single-nucleotide polymorphism in the region of the CD40 gene is associated with Graves' disease.

Graves' disease (GD) develops as a result of an interaction between susceptibility genes and environmental factors. We have previously mapped a susceptibility locus for GD on chromosome 20q11 (GD-2), which has recently been independently replicated. Among the genes mapped to 20q11 was the CD40 gene, an important costimulatory molecule and a good positional candidate gene for GD. We investigated whether the CD40 gene was the GD susceptibility gene on 20q11. Linkage analysis in a subset of Caucasian families showed a maximum multipoint logarithm of odds (LOD) score of 3.3 at the CD40 locus. We then sequenced all 9 exons of the CD40 gene in 8 probands and 10 controls and identified a new C/T single-nucleotide polymorphism (SNP) in the Kozak sequence of the CD40 gene at position -1. Case control association analysis of the CD40 C/T(-1) SNP in 154 Caucasian patients with GD and 118 Caucasian controls showed an association between the CC genotype and GD (p = 0.048, relative risk [RR] = 1.6). Furthermore, the association was stronger when only the probands from the linked families (n = 20) were used (p = 0.009, RR = 4.8). Transmission disequilibrium test (TDT) analysis also showed preferential transmission of the C allele of the CD40 C/T(-1) SNP to affected individuals (p = 0.02). In conclusion, our results suggested that the CD40 gene was a new susceptibility gene for GD within certain families because it was both linked and associated with GD.     

人系统性红斑狼疮遗传易感性研究进展

系统性红斑狼疮(SLE)是一种多因素疾病,其发病机制至今尚未明确.但越来越多的研究证据表明,遗传易感性在疾病发生中起重要作用.人类基因组研究显示约50多个基因座(loci)与SLE有关,独立队列研究证实至少有9个区域有明显相关性,包括lq23、lq31-32、lq41-42、2q35-37、4p16-15.2、6p21-11、11p13、12q24及16q12-13.对具体患者,多个不同位点的基因组合可引起疾病表型的多样性.近期研究进一步证实,遗传因素在决定疾病易感性及临床表型时起作用,不同种族、地域人群中所涉及的相关基因有所差异.     

An update on genetic studies of systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a complex, multifactorial autoimmune disease. Genetic factors are thought to contribute to its pathogenesis. There have been numerous recent advances in the study of murine and human lupus genetics. In well-defined experimental transgenic or gene-knockout mouse models, the development of lupus-like disease has implicated specific genes and pathways in the disease pathogenesis. Linkage analyses have mapped multiple susceptibility loci and disease suppressive loci using inbred strains of mice that spontaneously develop lupus-like disease. Elegant genetic dissection and function studies have led to the recent identification of two murine candidate susceptibility genes, Ifi202 (encoding an interferon-inducible protein) and Cr2 (encoding complement receptors 1 and 2). In human lupus, casecontrol studies have established associations of SLE with certain major histocompatibility class II alleles, complement deficiencies, and polymorphisms of Fcψ receptor genes, a complement-related gene, and cytokine genes. During the past several years, linkage analyses using SLE multiplex families have provided many chromosomal regions for further exploration of susceptibility genes. Six regions exhibiting significant linkage to SLE are promising. Studies are underway to fine map these linked regions and to identify the genes in the susceptibility regions. An understanding of the genes involved in the development of lupus should provide targets for more focused therapy in lupus.     

Genetic mapping of a 17q chromosomal region linked to obesity phenotypes in the IRAS family study

OBJECTIVE: Obesity is widely accepted to be influenced by both environmental and genetic factors. Several recent studies have used the positional cloning approach in an attempt to discover genes contributing to obesity. In the IRAS Family Study a genomewide scan was performed on 1425 individuals of Hispanic descent (90 extended pedigree families) to identify regions of the genome linked to obesity phenotypes. METHODS: Nonparametric QTL linkage analysis was performed using a variance components approach. The genome scan was performed in two phases: an initial genome scan in 45 families and a replication scan in 45 families. Fine mapping and candidate gene analyses were also performed. General estimating equations (GEE1) and quantitative pedigree disequilibrium tests (QPDT) were used for association analysis of single SNP and haplotype data. RESULTS: Evidence for linkage to obesity traits was observed in each scan on the long arm of chromosome 17. When data from both scans was combined, a region on chromosome 17q was identified with evidence of linkage to visceral adipose tissue (VAT; LOD 3.11), waist circumference (WAIST) (LOD 2.5) and body mass index (BMI) (LOD 2.81). Nine additional microsatellite markers were identified and genotyped on all Hispanic individuals, with a mean marker density of approximately 1 marker/3 cM. Evidence of linkage remained significant with LOD 3.05 for VAT, LOD 2.44 for BMI and LOD 1.92 for WAIST. Fine mapping analyses suggest the possibility of two different obesity loci. In addition, the LOD - 1 interval of the major VAT peak decreased from 83-108 to 95-111 cM. Three positional candidate genes under the peak: somatostatin receptor 2 (SSTR2), galanin receptor 2 (GALR2), and growth hormone bound protein receptor 2 (GRB2) were chosen for detailed evaluation. Multiple polymorphisms within each candidate were genotyped and tested for association with the obesity phenotypes. Little evidence of association was detected between polymorphisms and obesity traits. CONCLUSION: In conclusion, replication of linkage and fine mapping suggest that a region on chromosome 17q contains a gene (or genes) that contributes to the genetic etiology of obesity with the strongest evidence for linkage to VAT. Candidate genes in the region do not appear to account for the evidence of linkage. Additional studies are necessary to identify the obesity-related polymorphisms.     

Progress in searching for susceptibility gene for inflammatory bowel disease by positional cloning

Inflammatory bowel disease (IBD) includes two clinical subtypes: Crohn disease (CD) and ulcerative colitis (UC). The general prevalence is about 1.0-2.0 % in Western countries.It is predominantly regarded as a multifactorial disorder involving environmental factors and polygenic defects. The view was confirmed by a lot of evidences from clinical attributions and animal models, espedally from epidemiological investigations. So the etiological study of IBD has been focused on searching for susceptibility genes by positional cloning,which consists of two steps: linkage analysis and association analysis. Linkage analysis has been an important method of searching for susceptibility genes to polygenic diseases as well as single-gene disorders. IBD, as a polygenic disease, has been widely investigat~l by linkage analysis for susceptibility gene since 1996. The paper reviewed 38 artides, which covered almost all original researches in relation to IBD and linkage analysis. So far, several loci, such as 16q, 12q, 6p and 3p,have been identified by the studies. The most striking is 16q12 (IBD1), which linked only with CD not UC in the majority of sbJdies. Assodation analysis, as one essential step for positional doning, is usually carried out by genotyping candidate genes selected by means of linkage analysis or other methods, for figuring out the frequencies of alleles and comparing the frequendes between IBD group and healthy control group to identify the specific allele. It has been established that IBD is implicated in immune disorder. So the studies were centered on the genes of NOD2/CARD15, HLA-Ⅱ, cytokine,receptor and adhesion molecule. This paper reviewed 14 original artides on assodation between NOD2 and IBD that have been published since 2001. All results, with the exception of one report from a Japanese group, provide evidences that the three kinds of variants of NOD2 are susceptibility factors for IBD.This addde also comprehensively analyzed 18 original researches of HLA gene polymorphism in IBD. We found extensive discrepancy among the conclusions and a novel hypothesis was put forward to explain the discordance. Most studies published recently on association between IBD and cytokine gene polymorphism were reviewed.     

Linkage and interaction of loci on 1q23 and 16q12 may contribute to susceptibility to systemic lupus erythematosus

OBJECTIVE: Six recent genome scans of different systemic lupus erythematosus (SLE) multiplex family cohorts showed multiple putative susceptibility loci. In the present study, we examined 4 previously identified loci to replicate findings of significant linkage to 1q23 and 16q12, and to support findings of suggestive linkage to 14q21-23 and 20p12 in a cohort of 115 multiethnic nuclear families containing 145 SLE-affected sibpairs. METHODS: Model-free, multipoint linkage analyses (SIBPAL2, SAGE version 4.0) and exclusion mapping (GeneHunter) were performed. RESULTS: Linkages to 1q23 (peak at D1S2675, mean allele sharing [MAS] 0.56; P = 0.003) and to 16q12 (peaks between D16S753 and D16S757, MAS 0.57; P = 0.003) were confirmed, but linkage evidence at 20p12 was weak and inconsistent (MAS 0.52-0.56; from P = 0.005 to P not significant). Evidence for linkage to 1q23 and 16q12 was stronger in 68 non-Caucasian affected sibpairs than in 77 Caucasian affected sibpairs. Exclusion mapping ruled out linkage at 14q21-23 (lambda(s) [sib recurrence risk or genotypic risk ratio] = 1.8). Because the pericentromeric region of chromosome 16 has been identified by genome scans in several autoimmune diseases, we postulated that it might harbor an autoimmune modifier gene. To explore this possibility, we tested for an interaction between 16q12 and 1q23, and between 16q12 and 20p12. Haplotype sharing at 1q23 increased concomitantly with increased haplotype sharing at 16q12 (P = 0.008 by nonparametric Jonckheere-Terpstra exact statistical test). No evidence supporting an interaction between 16q12 and 20p12 was observed. Analysis of sibpairs sharing 2 alleles at 16q12 also showed increased allele sharing at 1q23 (MAS from 0.56 to 0.65). CONCLUSION: These data support the presence of SLE susceptibility genes at 1q23 and 16q12, particularly in non-Caucasians. The skewed distribution of haplotypes suggests that genetic interaction of these two loci may affect SLE susceptibility.     

Genetic epidemiology of primary osteoarthritis

Primary osteoarthritis (OA) is a late onset disease that fits most accurately into the oligogenic, multifactorial class of genetic diseases. Twin pair and family risk studies have highlighted a surprisingly large genetic component to OA and have prompted the search for predisposing genes. These searches have taken three forms: (1) parametric linkage analysis of rare families in which OA segregates as a Mendelian trait, (2) model-free linkage analysis of affected sibling pairs, and (3) association analysis of known candidate genes. Within the past year linkage analysis studies have highlighted that chromosomes 2, 4, 6, 7, 11, 16, and the X may each harbor an OA susceptibility gene. Chromosomes 2, 4, and 16 were identified in multiple genome scans and are therefore the most likely to encode susceptibility. Association analysis of candidates suggests that the syntenic genes for type II collagen and the vitamin D receptor (12q12--q13.1) may also encode for OA susceptibility.     

Growing evidence for diabetes susceptibility genes from genome scan data

Genome-wide scans for linkage have provided one of the dominant approaches adopted by researchers in their efforts to identify genes responsible for the inherited component of type 2 diabetes susceptibility. Around 20 genome scans have now been completed, in a wide variety of populations. Integration of data from these diverse scans has proven far from trivial, but the contours of genome-wide linkage topography are steadily emerging from the fog of data. Identification of the calpain- 10 gene as the probable basis for the chromosome 2q linkage seen in Mexican Americans has provided validation of this positional cloning approach. This report provides an update on recent type 2 diabetes genome scan data, focusing on several chromosomal regions where the evidence for linkage has considerably strengthened in the past year. The current and future value of genome-wide linkage information in the search for type 2 diabetes susceptibility effects is also discussed.     

Genome-wide association studies for discovery of genes involved in asthma

Asthma is the result of a complex interaction between environmental factors and genetic variants that confer susceptibility. Studies of the genetics of asthma have previously been conducted using linkage designs and candidate gene association studies. Recently, the association study design has been extended from specific candidate genes to an unbiased genome-wide approach: the genome-wide association study (GWAS). To date, there have been 12 GWAS to look for susceptibility loci for asthma and related traits. The first GWAS for asthma discovered a novel associated locus on chromosome 17q21 encompassing the genes ORMDL3, GSDMB and ZPBP2. None of these genes would have been selected in a candidate association study based on current knowledge of the functions of these genes. Nevertheless, this finding has been consistently replicated in independent populations of European ancestry and also in other ethnic groups. Thus, chromosome 17q21 seems to be a true asthma susceptibility locus. Other genes that were identified in more than one GWAS are IL33, RAD50, IL1RL1 and HLA-DQB1. Additional novel susceptibility genes identified in a single study include DENND1BI and IL2RB. Discovering the causal mechanism behind these associations is likely to yield great insights into the development of asthma. It is likely that further meta-analyses of asthma GWAS data from existing international consortia will uncover more novel susceptibility genes and further increase our understanding of this disease.     

Identification of novel susceptibility genes in childhood-onset systemic lupus erythematosus using a uniquely designed candidate gene pathway platform

OBJECTIVE: Childhood-onset systemic lupus erythematosus (SLE) presents a unique subgroup of patients for genetic study. The present study was undertaken to identify susceptibility genes contributing to SLE, using a novel candidate gene pathway microarray platform to investigate gene expression in patients with childhood-onset SLE and both of their parents. METHODS: Utilizing bioinformatic tools, a platform of 9,412 single-nucleotide polymorphisms (SNPs) from 1,204 genes was designed and validated. Molecular inversion probes and high-throughput SNP technologies were used for assay development. Seven hundred fifty three subjects, corresponding to 251 full trios of childhood-onset SLE families, were genotyped and analyzed using transmission disequilibrium testing (TDT) and multitest corrections. RESULTS: Family-based TDT showed a significant association of SLE with a N673S polymorphism in the P-selectin gene (SELP) (P = 5.74 x 10(-6)) and a C203S polymorphism in the interleukin-1 receptor-associated kinase 1 gene (IRAK1) (P = 9.58 x 10(-6)). These 2 SNPs had a false discovery rate for multitest correction of <0.05, and therefore a >95% probability of being considered as proven. Furthermore, 7 additional SNPs showed q values of <0.5, suggesting association with SLE and providing a direction for followup studies. These additional genes notably included TNFRSF6 (Fas) and IRF5, supporting previous findings of their association with SLE pathogenesis. CONCLUSION: SELP and IRAK1 were identified as novel SLE-associated genes with a high degree of significance, suggesting new directions in understanding the pathogenesis of SLE. The overall design and results of this study demonstrate that the candidate gene pathway microarray platform used provides a novel and powerful approach that is generally applicable in identifying genetic foundations of complex diseases.     

The genetic basis of ankylosing spondylitis

PURPOSE OF REVIEW: Genetic factors provide over 90% of the overall susceptibility to ankylosing spondylitis, with about half of the genetic contribution attributed to HLA-B27 and other major histocompatibility complex genes. Recent studies have focused on non-major histocompatibility complex genes. This review is aimed at summarizing the status of major histocompatibility complex and non-major histocompatibility complex genes in ankylosing spondylitis susceptibility, and suggests areas for future studies. RECENT FINDINGS: A recent meta-analysis of published scans of ankylosing spondylitis susceptibility has confirmed sites on chromosomes 3q, 6p (the major histocompatibility complex), 10q, 16q and 19q in ankylosing spondylitis susceptibility. Non-major histocompatibility complex candidate gene analyses have confirmed a role for the IL-1 gene complex. The search for other non-major histocompatibility complex candidate genes, however, has been complicated by inadequate power in most previous studies. Innovations in genetic methodologies will allow thorough genome wide linkage disequilibrium mapping studies in large cohorts of patients that will result in the dissection of the genetic susceptibility to ankylosing spondylitis. SUMMARY: Nearly half of the susceptibility to ankylosing spondylitis is provided by major histocompatibility complex genes. Non-major histocompatibility complex genes, most notably the IL-1 gene complex, have been identified and novel technologies promise that a more thorough examination of the rest of the genome will soon elucidate the genetic basis of this disease.     

弥漫性甲状腺肿伴甲状腺功能亢进症致病易感基因识别鉴定研究的现状

经过半个世纪对弥漫性甲状腺肿伴甲状腺功能亢进症(Graves’disease,GD,甲亢)候选基因在小样本人群中的研究,提供了不少相互矛盾的结果.在这些研究中,仅仅证实主要组织相容性复合物(MHC)是甲亢的一个致病易感位点,因为这个位点对甲亢发生影响较大.应用以低密度的微卫星标志进行全基因组连锁分析,虽然发现了一些甲亢的致病易感区段,但并未能识别真正的甲亢致病易感基因.随后由于大量单核苷酸多态性(SNP)的发现及其标签SNP(Tag SNP)技术的出现,人们对候选基因上的Tag SNP在大样本人群中的分析,发现了一些真正的甲亢致病易感基因,包括免疫相关的基因如MHC、CTLA4、SCGB3A2/UGRP1和FCRL3以及一个甲状腺特异的基因TSHR(促甲状腺素受体基因).同时,也发现了一些还有争议但需要进一步证实的甲亢易感基因如PTPN22和甲状腺球蛋白基因等.在不久的将来,全基因组关联分析和全基因组再测序技术,在甲亢易感基因识别鉴定中的应用,无疑将会促进大量甲亢易感基因的发现,加深人们对甲亢发病机制的理解.     

Conservation of FcepsilonRI gamma chain coding region in normals and in SLE patients

High-frequency single nucleotide polymorphism (SNP) alleles are useful in mapping genes responsible for disease susceptibility. Functionally, Fcgamma receptors (FcgammaR) have been implicated in autoimmune disease, and the gene encoding the signaling element for several FcgammaR, Fc-epsilon-receptor gamma-chain (FcepsilonRIgamma), has several SNPs in the immunoreceptor tyrosine activation motif (ITAM) recorded in GenBank. Direct sequencing of the FcepsilonRIgamma coding region found potentially polymorphic sites in the 5'-->3' direction in control donors, which were not confirmed in the reverse direction (n = 66), and further exploration of 80 SLE patients revealed no non-synonymous SNPs. One normal donor was heterozygous for a non-synonymous SNP at nt 38 which changed the fifth codon from valine (GTG) to methionine (ATG). Although the EST databases suggest candidate SNPs, insertions and deletions, these appear to be artifacts, most probably due to secondary structure. The coding region of FcepsilonRIgamma shows a remarkable absence of nucleotide diversity. Either as yet unidentified regulatory elements of FcepsilonRIgamma or other genes in the region of human chromosome 1q23 are likely to be systemic lupus erythematosus disease susceptibility and severity genes.     

自身免疫性甲状腺病的遗传及易感性研究进展

自身免疫性甲状腺病(AITD)是常见的器官特异性自身免疫性疾病,但其发病机制尚未完全明了,目前认为其发病明显受遗传因素的影响,已发现多种免疫调节基因、甲状腺特异基因、染色体的一些区域与AITD存在一定联系.全基因组扫描发现多个位点与AITD相关,尤其是中国汉族人群的Graves病易感位点定于5q31,它们为AITD遗传易感基因的研究提供了新的方向.本文就该领域研究进展进行综述.     

Use of Tag single nucleotide polymorphisms (SNPs) to screen PTPN21: no association with Graves' disease

OBJECTIVE: The protein-tyrosine-phosphate nonreceptor 22 gene (PTPN22) has recently been identified as a susceptibility locus for a number of autoimmune diseases including Graves' disease (GD). PTPN21 is another member of the PTPN family and its gene PTPN21 maps to the first reported region of genetic linkage to GD, GD-1, on chromosome 14q31. The aim of this study was to determine whether PTPN21 is acting as a GD susceptibility locus in UK Caucasian subjects. DESIGN: A case control association study of seven Tag single nucleotide polymorphisms (SNPs) (rs1469602, rs8007288, rs1998670, rs11622270, rs2274736, rs2295136 and rs366476) selected to predict 51 un-genotyped polymorphisms present within PTPN21. PATIENTS: Unrelated Caucasian patients of UK origin with GD and ethnically and gender matched control subjects with no family history of autoimmune disease were recruited. In total, DNA was obtained from 768 GD patients and 768 control subjects. RESULTS: No association of any of the seven Tag SNPs was detected with GD. Preliminary evidence of association of rs2274736 was found with younger age of GD onset (0-30 years) (OR = 1. 48 [95% CI = 1.11-1.97]). No other correlations with clinical phenotype or previously established susceptibility loci were detected. CONCLUSIONS: Using a Tag SNP approach we screened PTPN21 as a susceptibility locus for GD and found no evidence for association with disease. Preliminary evidence for association of rs2274736 with younger age of GD onset requires replication in similar sized data sets to exclude a false positive result. Methods such as the Tag SNP approach significantly reduce the amount of genotyping required when screening candidate loci, including those within regions of chromosomal linkage.     

Genetic loci linked to pituitary-thyroid axis set points: a genome-wide scan of a large twin cohort

Objective: Previous studies have shown that circulating concentrations of TSH, free T(4), and free T(3) are genetically regulated, but the genes responsible remain largely unknown. The aim of this study was to identify genetic loci associated with these parameters. Design: We performed a multipoint, nonparametric genome-wide linkage scan of 613 female dizygotic twin pairs. All subjects were euthyroid (TSH 0.4-4.0 mU/liter) with negative thyroid peroxidase antibodies and no history of thyroid disease. The genome scan comprised 737 microsatellite markers supplemented with dinucleotide markers. Data were analyzed using residualized thyroid hormone data after adjustment for age, smoking, and body mass index. Results: Multipoint linkage analysis gave linkage peaks for free T(4) on chromosome 14q13 and 18q21 [logarithm of odds (LOD) 2.4-3.2]; TSH on chromosomes 2q36, 4q32, and 9q34 (LOD 2.1-3.2); and free T(3) on chromosomes 7q36, 8q22, and 18q21 (LOD 2.0-2.3). Conclusions: This study has identified eight genomic locations with linkage of LOD of 2.0 or greater. These results should enable targeted positional candidate and positional cloning studies to advance our understanding of genetic control of the pituitary-thyroid axis.