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Genes and Immunity (2008) 9, 187–194 & 2008 Nature Publishing Group All rights reserved 1466-4879/08 $30.00 www.nature.com/gene

ORIGINAL ARTICLE

Interferon regulatory factor-5 is genetically associated with systemic lupus erythematosus in African Americans JA Kelly1,11, JM Kelley2,11, KM Kaufman1,3,4, J Kilpatrick1, GR Bruner1, JT Merrill1, JA James1,4, SG Frank1, E Reams2, EE Brown2, AW Gibson2, MC Marion5, CD Langefeld5, Q-Z Li6, DR Karp6, EK Wakeland6, M Petri7, R Ramsey-Goldman8, JD Reveille9, LM Vila´10, GS Alarco´n2, RP Kimberly2, JB Harley1,3,4 and JC Edberg2 Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; 2University of Alabama at Birmingham, Birmingham, AL, USA; US Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA; 4University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; 5Wake Forest University School of Medicine, Winston-Salem, NC, USA; 6University of Texas Southwestern Medical Center, Dallas, TX, USA; 7Johns Hopkins University, Baltimore, MD, USA; 8Northwestern University Feinberg School of Medicine, Chicago, IL, USA; 9University of Texas-Houston Health Science Center, Houston, TX, USA and 10University of Puerto Rico Medical Sciences Campus, San Juan, PR, USA 1 3

Increased expression of interferon (IFN)-inducible genes is implicated in the pathogenesis of systemic lupus erythematosus (SLE). One transcription factor responsible for regulating IFN, interferon regulatory factor-5 (IRF5), has been associated with SLE in genetic studies of Asian, Caucasian and Hispanic populations. We genotyped up to seven polymorphic loci in or near IRF5 in a total of 4870 African-American and Caucasian subjects (1829 SLE sporadic cases and 3041 controls) from two independent studies. Population-based case–control comparisons were performed using the Pearson’s w2-test statistics and haplotypes were inferred using HaploView. We observed significant novel associations with the IRF5 variants rs2004640 and rs3807306 in African Americans and replicated previously reported associations in Caucasians. While we identified risk haplotypes, the majority of haplotypic effects were accounted for by one SNP (rs3807306) in conditional analyses. We conclude that genetic variants of IRF5 associate with SLE in multiple populations, providing evidence that IRF5 is likely to be a crucial component in SLE pathogenesis among multiple ethnic groups. Genes and Immunity (2008) 9, 187–194; doi:10.1038/gene.2008.4; published online 21 February 2008 Keywords: SLE; African Americans; IRF5; genetic association

Introduction Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by loss of tolerance to nuclear antigens, immune complex deposition and tissue destruction. SLE is present in approximately 1/2500 people and is nine times more prevalent among women.1 It has an earlier onset, more severe disease manifestations and a four times higher prevalence in African Americans compared to Caucasians in the United States.2,3 The diagnosis of SLE requires the presence of 4 of 11 defined criteria of the American College of Rheumatology (ACR), lacking a defined etiology.4,5 Both genetic and environmental factors have been suggested as causative Correspondence: Dr JB Harley, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. E-mail: [email protected] or Dr JC Edberg, University of Alabama at Birmingham, 1530 3rd Avenue South, SHEL 207, Birmingham, AL 35294, USA. E-mail: [email protected] 11 These authors contributed equally to this work. Received 19 November 2007; revised 14 January 2008; accepted 15 January 2008; published online 21 February 2008

agents for the pathogenesis and variable clinical manifestations of SLE. Case–control association studies implicate numerous candidate gene loci.6 In addition, medications, ultraviolet radiation exposure and infectious pathogens are possible environmental contributors to SLE etiology.7,8 Patients with SLE often show increased expression of interferon (IFN)-inducible genes, the presence of which can correlate with more severe disease manifestations such as neurological, renal or hematological involvement.9 Interferon regulatory factor-5 (IRF5), a transcription factor, regulates the expression of IFN-a genes,10,11 thus making it a good candidate gene for SLE susceptibility. Recent publications have reported a significant association between single nucleotide polymorphisms (SNPs) and haplotypes of IRF5 and SLE, both in familyand population-based studies of patients from multiple ethnicities12–21 (including meta-analyses)16; however, these studies have not examined African Americans. Ethnic-specific association studies are necessary to confirm the applicability of previous results to multiple populations because approximately 8% of genetic variation is due to population differences22 and patterns of linkage disequilibrium (LD) can vary markedly by ethnic

IRF5 associates with SLE in African Americans JA Kelly et al

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group.23 Minor allele frequencies of many SNPs differ substantially between populations, allowing alleles, when expanded in frequency within one group, more chances to confer greater genetic susceptibility in that one particular population.24 Examples of ethnic-specific differences in SLE genetic association studies include an association of the p53 gene in Koreans25 that did not replicate in a Spanish Caucasian population,26 an association of the heat-shock-protein-encoding gene, HSP70, in Spaniards and Africans but not in Mexicans27 and the varying levels of significance of CTLA4 associated with SLE in Asians and Europeans.28 There are even differences in levels of significance within association studies of IRF5 and SLE, such as with studies of Caucasian,12,14,17–19 Hispanic (Mexican)15 and Asian subjects.16 In this report, we evaluate genetic associations of IRF5 with SLE in independent studies (Oklahoma Medical Research Foundation (OMRF) and ‘Cases of SLE’ (CASSLE) based at the University of Alabama at Birmingham (UAB)) comprised of African-American and Caucasian patients and controls (n ¼ 4870). We replicate the previous associations of IRF5 with SLE found in multiple Caucasian populations and report novel findings of associations in African Americans. Our results highlight the need to determine ethnic-specific differences in genetic association studies and confirm the importance of IRF5 in the pathogenesis of SLE across multiple ethnic groups.

Results Association of SLE and IRF5 variants To determine if IRF5 variants associate with SLE in African Americans, we genotyped up to seven variants in two independent sporadic SLE case–control studies (Table 1). We detected significant associations with the minor T allele at rs2004640 (P ¼ 0.0008) and the minor A allele at rs3807306 (P ¼ 0.02) in the OMRF participants. We replicated the association at rs3807306 (P ¼ 0.008) in CASSLE and found suggestive associations at rs2070197 (P ¼ 0.02) and rs10954213 (P ¼ 0.03). When combining the two for more power, the most significant associations were observed at rs2004640 (P ¼ 0.0001) and rs3807306 (P ¼ 0.0002). In Caucasians, we replicated the effects previously reported.12,14,17–19 Similar to African Americans, we again found the strongest associations at rs2004640 (P ¼ 2.2 109) and rs3807306 (P ¼ 3.0 109) in both OMRF and CASSLE and in both studies combined. Allele frequencies were similar to Caucasian populations previously reported (Table 2). In the Caucasian populations, the T (rs2004640) and A (rs3807306) risk alleles were the major alleles. IRF5 haplotype analysis The haplotype structure of IRF5 is unknown in African Americans. Accordingly, in samples from the AfricanAmerican CASSLE subjects, we performed haplotype analysis using five variants of IRF5 (rs2004640-rs752637rs3807306-rs10954213-rs2280714). We excluded rs729302 from the haplotype analysis because of its large physical distance and low LD from the other IRF5 SNPs (D0 ¼ 0.16) and rs2070197 because of its low minor allele Genes and Immunity

frequency in African Americans (0.02). We observed a significant haplotype (TGAAA) determined by the minor A risk allele at rs3807306 (haplotype frequencies (HF) ¼ 0.39 cases and 0.32 controls) (Table 3). Using multivariate analysis, it was evident that rs3807306 was responsible for the majority of the observed association with SLE because all other variants individually and the haplotype as a unit lost significance when conditioned on rs3807306 (P ¼ 0.06) (Table 4). In Caucasians, significance was again produced with the same five-marker haplotype (TGAAA) (P ¼ 2.4 107; odds ratio (OR) ¼ 1.5 (1.3–1.8); HF ¼ 0.53 cases and 0.43 controls). After dropping rs752637 from this haplotype analysis due to Hardy–Weinberg disequilibrium in Caucasians, the remaining four markers still demonstrated significant association (P ¼ 1.6 105; OR ¼ 1.4 (1.3–1.7)) (Table 3). We also observed two protective haplotypes, both driven by the non-risk alleles at rs2004640 (G) and rs3807306 (C) that when combined produce (P ¼ 0.0002 (OR ¼ 0.8) (0.7–0.9); HF ¼ 0.39 cases and 0.48 controls). We noticed differences in haplotypes block structure between ethnicities particularly in regard to the highly associated SNP rs3807306 (Figure 1). We also tested the previously identified SLE risk threemarker haplotype (rs2004640-rs2070197-rs10954213) in the CASSLE subjects.13 In African Americans, we observed a marginal protective effect with the GTG haplotype (P ¼ 0.03; HF ¼ 0.39 cases and 0.45 controls). The risk TCA haplotype was observed, but its frequency was extremely low (P ¼ 0.01; OR ¼ 1.9 (1.1–3.5); HF ¼ 0.04 cases and 0.02 controls). Again, when conditioned upon, rs3807306 removed all other associations within the haplotype. In Caucasians, we observed an association with the risk TCA haplotype (P ¼ 0.0004) and the protective GTG haplotype (P ¼ 0.001); however, we did not observe significance with the previously reported GTA protective haplotype13 (Table 5). HF using these loci from a previous study are also provided in Table 5 for comparison.13

Discussion IRF5 association with SLE in Caucasian populations was initially reported when evaluating genes of the type I IFN pathway in participants from Sweden and Finland.18 Since then, several additional studies have evaluated the association between IRF5 and SLE in Caucasian,12–14,17,19 Korean16 and Hispanic (Mexican)15 populations, emphasizing the importance of this gene in SLE etiology. However, no studies have been reported to date in African Americans. In the present study, we evaluated seven variants of IRF5 for genetic association with SLE using populationbased case–control association designs in African Americans and Caucasians. We establish association of IRF5 with SLE in African Americans using independent studies. The most significant associations detected were with rs2004640, which has been associated in every study to date, and with rs3807306, which has been only recently associated in a UK-based study.17 We also identified a five-marker (rs2004640-rs752637-rs3807306rs10954213-rs2280714) risk haplotype (TGAAA) in both ethnic groups and determined that its causative effect is due to rs3807306. While five-marker haplotypes containing

Table 1

Allele frequencies and allelic associations of IRF5 variants with SLE in African Americans and Caucasians

SNP

Risk allele

African Americans

Caucasians

Minor allele

MAF cases

MAF controls

w2

P-value

Odds ratio (95% CI)

Minor allele

MAF cases

MAF controls

w2

P-value

Odds ratio (95% CI)

A T G A A

C T A A G

0.15 0.52 0.49 0.39 0.38

0.19 0.44 0.48 0.34 0.42

4.1 11.4 — 5.8 —

0.04 0.0008 — 0.02 —

1.3 (1.0–1.7) 1.4 (1.2–1.7) — 1.3 (1.0–1.6) —

C G A C G

0.25 0.40 0.32 0.43 0.31

0.32 0.49 0.38 0.51 0.35

12.9 17.9 7.8 18.0 4.7

0.0003 0.00002 0.005 0.00002 0.03

1.4 1.4 1.3 1.4 1.2

(1.2–1.6) (1.2–1.6) (1.1–1.5) (1.2–1.6) (1.0–1.4)

CASSLE rs729302 rs2004640 rs752637 rs3807306 rs2070197 rs10954213 rs2280714

A T G A C A A

C T A A C G G

0.18 0.50 0.43 0.40 0.04 0.43 0.37

0.18 0.46 0.48 0.34 0.02 0.48 0.40

— — — 7.1 5.4 4.5 —

— — — 0.008 0.02 0.03 —

— — — 1.3 (1.1–1.6) 1.9 (1.1–3.3) 1.2 (1.0–1.5) —

C G A C C G G

0.26 0.44 0.32 0.45 0.15 0.34 0.29

0.33 0.51 0.38 0.53 0.10 0.39 0.34

13.1 17.9 10.3 17.9 12.1 7.9 6.4

0.0003 0.00002 0.001 0.00002 0.0005 0.005 0.01

1.4 1.4 1.3 1.4 1.5 1.3 1.3

(1.2–1.7) (1.2–1.7) (1.1–1.5) (1.2–1.7) (1.2–2.0) (1.1–1.5) (1.1–1.5)

OMRF and CASSLE rs729302 A rs2004640 T rs752637 G rs3807306 A rs2070197 C rs10954213 A rs2280714 A

C T A A C G G

0.17 0.51 0.45 0.40 0.04 0.43 0.38

0.19 0.45 0.48 0.34 0.02 0.48 0.41

— 14.6 — 14.1 5.4 4.5 4.9

— 0.0001 — 0.0002 0.02 0.03 0.03

— 1.3 (1.1–1.5) — 1.2 (1.1–1.4) 1.9 (1.1–3.3) 1.2 (1.0–1.5) 1.2 (1.0–1.3)

C G A C C G G

0.26 0.41 0.32 0.44 0.15 0.34 0.30

0.32 0.49 0.38 0.52 0.10 0.39 0.35

25.2 35.8 15.9 35.2 12.1 7.9 13.0

5.2 107 2.2 109 6.7 105 3.0 109 0.0005 0.005 0.004

1.4 1.4 1.3 1.4 1.5 1.3 1.3

(1.2–1.5) (1.2–1.5) (1.1–1.4) (1.2–1.5) (1.2–2.0) (1.1–1.5) (1.1–1.4)


OMRF rs729302 rs2004640 rs752637 rs3807306 rs2280714

Abbreviations: CASSLE, cases of systemic lupus erythematosus; CI, confidence interval; IRF5, interferon regulatory factor-5; MAF, minor allele frequency; OMRF, Oklahoma Medical Research Foundation; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism; w2, Pearson’s w2-statistic. Non-significant results are not indicated.

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Table 2 Alleles of IRF5 variants with SLE in previously reported Caucasian populations SNP

rs729302

rs2004640

rs752637

rs3807306 rs2070197a

rs10954213 rs2280714

Population

MAF

Odds ratio

Confidence intervals

1.4 1.4 1.4

1.2–1.5 1.3–1.7 1.2–1.7

Study reference

SLE

Control

United States Spain Sweden United Kingdom

0.26 0.25 0.27 0.27

0.32 0.31 0.34

United States Argentina Finland Spain Spain Sweden Sweden Sweden United Kingdom United States

0.32 0.46 0.37 0.37 0.36 0.37 0.37 0.38 0.42 0.39

0.38 0.56 0.52 0.46 0.44 0.48 0.44 0.48

1.3 1.5 1.8 1.4 1.4 1.6 1.3 1.5

1.1–1.4 1.2–1.9 1.3–2.7 1.2–1.7 1.3–1.7 1.3–1.9 1.0–1.7 1.2–1.9

0.49

1.5

1.3–1.7

12


0.32 0.29 0.29 0.33

0.38 0.34 0.37

1.3 1.3 1.4

1.1–1.4 1.1–1.6 1.2–1.7

Current

United States Sweden

0.56 0.58

0.48 0.46

1.4 1.6

1.2–1.5 1.3–1.9

Current


0.15 0.19 0.23 0.16

0.10 0.10 0.12

1.5 2.0 2.1

1.2–2.0 1.7–2.4 1.6–2.6

Current

United States Sweden

0.34 0.29

0.39 0.37

1.3 1.5

1.1–1.5 1.2–1.7

Current


0.30 0.27 0.25 0.31

0.35 0.30 0.32

1.3 1.1 1.4

1.1–1.4 1.0–1.3 1.2–1.7

Current

Current 21 20 17

Current 12 18 12 21 20 12 18 17

21 20 17

20

21 20 17

20

21 20 17

Abbreviations: CASSLE, cases of systemic lupus erythematosus; IRF5, interferon regulatory factor-5; MAF, minor allele frequency; OMRF, Oklahoma Medical Research Foundation; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism. Current study reference refers to CASSLE and OMRF combined. a Allele frequencies for rs10488631 are substituted for rs2070197, a marker in strong linkage disequilibrium (LD), in some populations.

the non-risk alleles at rs2004640 (G) and rs3807306 (C) confer a strong protective effect in Caucasians (as is consistent with previous reports12), this effect is not present in African Americans. With the previously identified three-marker haplotype, African American and Caucasians show a similar pattern of association. Since genetic variants in IRF5 have been largely unexplored in African Americans, we set out to determine if genetic association in this population differs significantly from Caucasians. There is precedent for ethnic-specific SLE associations with CRP,29 PDCD130 and TNF.31 However, our data suggest that effects of IRF5 are common to both ethnicities. Similar results have been reported for IRF5 variants in Hispanics (Mexican),15 and we have preliminary data on 459 Hispanic SLE patients and 296 matched controls that agree with significant associations at rs2004640 and rs3807306 similar to both African Americans and Caucasians (data not presented). We note that our findings may be limited by false discovery and the possibility that the observed Genes and Immunity

associations might be due to linkage with other polymorphisms not evaluated. We had between 44 and 98% statistical power to detect an OR of 1.3 given the wide range of allele frequencies among controls and assuming a type I error of 0.05. Confirmatory studies among large African-American populations will be required. To date, three functional IRF5 variants have been identified. The T allele at rs2004640 creates a GT donor splice site for exon 1b,12 the A allele at rs10954213 results in more stable IRF5 transcripts leading to higher IRF5 levels17 and a 30-bp insertion/deletion at exon 6 differentiates the ability of IRF5 to initiate transcription of target genes.13 Genetic associations at these loci may provide clues about which mechanisms cause improper regulation of IFN responses during SLE pathogenesis. In summary, this is the first study to date to report positive genetic associations between SLE and IRF5 SNPs/haplotypes in African Americans, providing evidence of a common genetic contributor to SLE in various


Table 3

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IRF5 haplotype analyses Haplotype

Haplotype frequency

rs2004640 rs752637 rs3807306 rs10954213 rs2280714 African American

T G G T G T

Caucasian

T G G T T G

G A G G A G

Case

Control

A C C C C C

A G A A A G

A G A A A A

0.39 0.36 0.07 0.06 0.03 0.02

0.32 0.38 0.06 0.08 0.03 0.03

A C C C C C

A G A A G

A G A A A

0.54 0.28 0.11 — 0.05 0.39

0.45 0.34 0.14 — 0.05 0.48

w2

P-value

Odds ratio (95% CI)

9.93 0.45 0.88 1.93 0.35 0.56

0.002 — — — — —

1.4 (1.1–1.7) — — — — —

18.58 1.6 105 8.16 0.004 6.13 0.01 — — 0.22 — 13.51 0.0002

1.4 (1.2–1.7) 0.8 (0.7–0.9) 0.7 (0.6–0.9) — — 0.8 (0.7–0.9)

Abbreviations: CI, confidence interval; IRF5, interferon regulatory factor-5. Only haplotypes with minor allele frequencies X0.02 are presented. Non-significant results are not indicated. rs752637 is not included in the Caucasian haplotype analysis because of Hardy–Weinberg disequilibrium among controls (Po0.001). The A allele of rs3807306 was only seen in the TGAAA haplotype. w2: Pearson’s w2-statistic.

Table 4

IRF5 multivariate analysis

Marker

P-value Original rs3807306

rs2070197

rs10954213

0.97 0.11 0.07 0.008 0.02 0.04 0.14

0.511 0.43 0.451 — 0.0683 0.882 0.854

0.908 0.207 0.149 0.031 — 0.0676 0.208

0.549 0.722 0.016 0.077 0.0375 — 0.427

0.0003 3.97 105 0.994 2.72 105 0.0003 0.006 0.996

0.039 0.73 0.97 — 0.0298 0.392 0.827

0.0047 0.002 0.903 0.002 — 0.081 0.945

0.003 0.011 0.999 0.001 0.004 — 0.986

African American rs729302 rs2004640 rs752637 rs3807306 rs2070197 rs10954213 rs2280714 Caucasian rs729302 rs2004640 rs752637 rs3807306 rs2070197 rs10954213 rs2280714

Conditioned on

Abbreviation: IRF5, interferon regulatory factor-5.

populations and demonstrating that IRF5 is a crucial player in SLE pathogenesis in multiple ethnicities.

Participants, materials and methods Participant recruitment and biological sample collection We included 4870 participants (1829 sporadic SLE cases and 3041 controls) enrolled with informed consent into the Lupus Genetics Studies at the OMRF as described previously32 and the CASSLE case–control study collected at UAB (coordinating center), Northwestern

University (Chicago, IL, USA), Johns Hopkins University (Baltimore, MD, USA), University of Texas-Houston Health Sciences Center and the University of Puerto Rico (San Juan, PR, USA) (Table 6). OMRF also included 113 cases (51 Caucasians, 62 African Americans) and 82 controls (39 Caucasians, 13 African Americans) provided by the University of Texas Southwestern (UTSW) Medical Center. Ethnicity was self-reported and verified by ethnicity of the grandparents, when known. Affected individuals were defined as those meeting 4 of the 11 ACR SLE criteria when evaluated by a study physician.4,5 Demographics and selected clinical characteristics of the study populations are presented in Table 6. Blood or mouthwash samples were collected from each participant, and genomic DNA was isolated and stored using standard methods. All protocols were approved by the Institutional Review Boards at each respective institution. Genotyping OMRF data were generated using a GoldenGate custom bead array on the Illumina platform (San Diego, CA, USA) at the UTSWMC Microarray Core Facility (Dallas, TX, USA). CASSLE data were generated using TaqMan allelic discrimination assays (Applied Biosystems, Foster City, CA, USA). TaqMan reactions were performed in a 5 ml volume according to the manufacturer’s instructions on a 384-well-based ABI7900HT at UAB. Five SNPs were genotyped on all subjects (rs729302, rs2004640, rs752637, rs3807306 and rs2280714), and two SNPs (rs2070197 and rs10954213) were additionally genotyped in CASSLE participants to replicate recent haplotype-based findings in Caucasians.13,14,17 Statistical analyses SNPs were found to be in Hardy–Weinberg equilibrium unless noted otherwise. Population-based case–control comparisons (allelic w2-statistics) were calculated using SAS v9.0. Haplotype analyses were conducted using Genes and Immunity


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Figure 1 Linkage disequilibrium (LD) across interferon regulatory factor-5 (IRF5) in African Americans and Caucasians. These figures were drawn with HaploView v4.0 available from the Broad Institute. Darker boxes indicate higher (stronger) LD values. (a) African-American, (b) Caucasion.

Table 5 Three-marker haplotype analyses Haplotype

Frequency

rs2004640

rs2070197

rs10954213

Case

Control

African American

T G G T T

T T T C T

A G A A G

0.43 0.39 0.10 0.04 0.03

0.41 (0.28) 0.45 (0.52) 0.09 (0.20) 0.02 0.03

Caucasian

T G G T T

T T T C T

A G A A G

0.38 0.28 0.13 0.15 0.06

(0.38) (0.29) (0.12) (0.18) (0.04)

0.35 0.34 0.16 0.10 0.05

(0.36) (0.35) (0.14) (0.11) (0.04)

Odds ratio (95% CI)

w2

P-value

0.60 4.97 0.67 5.99 0.12

— 0.03 — 0.01 —

— 0.8 (0.7–1.0) — 1.9 (1.1–3.5) —

— 0.001 — 0.0004 —

— 0.8 (0.6–0.9) — 1.6 (1.2–1.9) —

2.57 10.38 2.80 12.61 0.30

Abbreviation: CI, confidence interval. Non-significant P-values are not indicated. This analysis is based on haplotype associations from a recent study of interferon regulatory factor-5 (IRF5) with systemic lupus erythematosus (SLE) among Caucasians.13 Numbers in brackets indicate haplotypes frequencies in an African (Yoruban) population (n ¼ 50) or in European simplex samples from the United Kingdom and the United States.13

Table 6 Composition of OMRF and CASSLE SLE and control subjects

Controls (total) African American Caucasian Cases (total) African American % Female Age at onset % ANA-positive % Renal Involvement Caucasian % Female Age at onset % ANA-positive % Renal Involvement

OMRF

CASSLE

OMRF and CASSLE

2009 701 (476:225) 1308 (936:372)

1032 428 (353:75) 604 (439:165)

3041 1129 (829:300) 1912 (1375:537)

712 268 (252:16) 92.2 36.7±12.0 98.8 56.2 444 (386:58) 91.2 35.3±14.2 98.0 34.9

1117 491 (457:34) 92.9 32.3±11.1 93.5 54.8 626 (559:67) 89.3 35.2±13.5 88.4 28.8

1829 759 (709:50) 92.7 33.8±11.4 95.3 55.3 1070 (945:125) 90.1 35.2±13.7 91.6 30.8

LUMINA

221 89 35.4±12.0 97.7 62 176 85 41.2±13.0 91.4 25

Abbreviations: ANA, antinuclear antibody; CASSLE, cases of systemic lupus erythematosus; OMRF, Oklahoma Medical Research Foundation; SLE, systemic lupus erythematosus. (Ratios in parentheses) indicate number of female and male participants, respectively. Percentage of ANA-positive patients represents one point in time determination (at study enrollment) and is not a cumulative measure. LUMINA indicates data from the LUpus in MInorities, NAture versus nurture cohort3 to provide comparisons of demographics and clinical characteristics to other studies. Genes and Immunity


HaploView v3.2 (Broad Institute). The WHAP software package (Harvard University) was used to calculate ORs and 95% CIs using unconditional logistic regression analyses of SNP and haplotype effects.

Acknowledgements We thank Debbie McDuffie, Lifeng Zhang and Julius Tate (UAB) for technical assistance. We also acknowledge our study participants without whom this study would not have been possible. This work was supported by the NIH (AI24717, AI31584, AI53747, AI62629, AR12253, AR33062, AR42460, AR42476, AR43727, DE15223, P01AR49084, K24-AR02138, MO1-RR00032, MO1-RR00048, M01-RR00052, P60-AR48098, RR15577, RR20143 and T32-AR07450), the Alliance for Lupus Research, the American College of Rheumatology Research and Education Foundation, Mary Kirland Scholar, Program for Research Experience in Pathology (UAB), University of Alabama Health Sciences Foundation, and the US Department of Veterans Affairs.

Disclosure The authors declare no conflict of interests.

References 1 Hochberg MC. The epidemiology of systemic lupus erythematosus. In: Wallace DJ, Hahn BH (eds). Dubois’ Lupus Erythematosus. Williams and Wilkins: Baltimore, 1997, pp 49–65. 2 Lawrence RC, Helmick CG, Arnett FC, Deyo RA, Felson DT, Giannini EH et al. Estimates of the prevalence of arthritis and selected musculoskeletal disorders in the United States. Arthritis Rheum 1998; 41: 778–799. 3 Alarcon GS, Friedman AW, Straaton KV, Moulds JM, Lisse J, Bastian HM et al. Systemic lupus erythematosus in three ethnic groups: III. A comparison of characteristics early in the natural history of the LUMINA cohort. LUpus in MInority populations: NAture vs. Nurture. Lupus 1999; 8: 197–209. 4 Hochberg MC. Updating the American college of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1997; 40: 1725. 5 Tan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1982; 25: 1271–1277. 6 Harley JB, Kelly JA, Kaufman KM. Unraveling the genetics of systemic lupus erythematosus. Springer Semin Immunopathol 2006; 28: 119–130. 7 Sarzi-Puttini P, Atzeni F, Iaccarino L, Doria A. Environment and systemic lupus erythematosus: an overview. Autoimmunity 2005; 38: 465–472. 8 James JA, Harley JB, Scofield RH. Role of viruses in systemic lupus erythematosus and Sjogren syndrome. Curr Opin Rheumatol 2001; 13: 370–376. 9 Baechler EC, Gregersen PK, Behrens TW. The emerging role of interferon in human systemic lupus erythematosus. Curr Opin Immunol 2004; 16: 801–807. 10 Taniguchi T, Ogasawara K, Takaoka A, Tanaka N. IRF family of transcription factors as regulators of host defense. Annu Rev Immunol 2001; 19: 623–655. 11 Takaoka A, Yanai H, Kondo S, Duncan G, Negishi H, Mizutani T et al. Integral role of IRF-5 in the gene induction programme activated by Toll-like receptors. Nature 2005; 434: 243–249.

193 12 Graham RR, Kozyrev SV, Baechler EC, Reddy MV, Plenge RM, Bauer JW et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006; 38: 550–555. 13 Graham RR, Kyogoku C, Sigurdsson S, Vlasova IA, Davies LR, Baechler EC et al. Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci USA 2007; 104: 6758–6763. 14 Kozyrev SV, Lewen S, Reddy PM, Pons-Estel B, Witte T, Junker P et al. Structural insertion/deletion variation in IRF5 is associated with a risk haplotype and defines the precise IRF5 isoforms expressed in systemic lupus erythematosus. Arthritis Rheum 2007; 56: 1234–1241. 15 Reddy MV, Velazquez-Cruz R, Baca V, Lima G, Granados J, Orozco L et al. Genetic association of IRF5 with SLE in Mexicans: higher frequency of the risk haplotype and its homozygozity than Europeans. Hum Genet 2007; 121: 721–727. 16 Shin HD, Sung YK, Choi CB, Lee SO, Lee HW, Bae SC. Replication of the genetic effects of IFN regulatory factor 5 (IRF5) on systemic lupus erythematosus in a Korean population. Arthritis Res Ther 2007; 9: R32. 17 Cunninghame Graham DS, Manku H, Wagner S, Reid J, Timms K, Gutin A et al. Association of IRF5 in UK SLE families identifies a variant involved in polyadenylation. Hum Mol Genet 2007; 16: 579–591. 18 Sigurdsson S, Nordmark G, Goring HH, Lindroos K, Wiman AC, Sturfelt G et al. Polymorphisms in the tyrosine kinase 2 and interferon regulatory factor 5 genes are associated with systemic lupus erythematosus. Am J Hum Genet 2005; 76: 528–537. 19 Demirci FY, Manzi S, Ramsey-Goldman R, Minster RL, Kenney M, Shaw PS et al. Association of a common interferon regulatory factor 5 (IRF5) variant with increased risk of systemic lupus erythematosus (SLE). Ann Hum Genet 2007; 71 (Part 3): 308–311. 20 Sigurdsson S, Goring HH, Kristjansdottir G, Milani L, Nordmark G, Sandling J et al. Comprehensive evaluation of the genetic variants of interferon regulatory factor 5 reveals a novel 5bp length polymorphism as strong risk factor for systemic lupus erythematosus. Hum Mol Genet 2007 (doi:10.1093/hmg/ddm359). 21 Ferreiro-Neira I, Calaza M, Alonso-Perez E, Marchini M, Scorza R, Sebastiani GD et al. Opposed independent effects and epistasis in the complex association of IRF5 to SLE. Genes Immun 2007; 8: 429–438. 22 Ioannidis JP, Ntzani EE, Trikalinos TA. ‘Racial’ differences in genetic effects for complex diseases. Nat Genet 2004; 36: 1312–1318. 23 Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA et al. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet 2006; 38: 1251–1260. 24 Ioannidis JP, Trikalinos TA, Ntzani EE, Contopoulos-Ioannidis DG. Genetic associations in large versus small studies: an empirical assessment. Lancet 2003; 361: 567–571. 25 Lee YH, Rho YH, Choi SJ, Ji JD, Song GG. The functional p53 codon 72 polymorphism is associated with systemic lupus erythematosus. Lupus 2005; 14: 842–845. 26 Sanchez E, Sabio JM, Callejas JL, de Ramon E, de Haro M, Jimenez-Alonso J et al. Study of a functional polymorphism in the p53 gene in systemic lupus erythematosus: lack of replication in a Spanish population. Lupus 2006; 15: 658–661. 27 Vargas-Alarcon G, Granados J, Martinez-Laso J, GomezCasado E, Zuniga J, Salgado N et al. Lack of association between the polymorphism at the heat-shock protein (HSP702) gene and systemic lupus erythematosus (SLE) in the Mexican mestizo population. Genes Immun 2000; 1: 367–370. 28 Lee YH, Harley JB, Nath SK. CTLA-4 polymorphisms and systemic lupus erythematosus (SLE): a meta-analysis. Hum Genet 2005; 116: 361–367. Genes and Immunity


194 29 Szalai AJ, Alarcon GS, Calvo-Alen J, Toloza SM, McCrory MA, Edberg JC et al. Systemic lupus erythematosus in a multiethnic US Cohort (LUMINA). XXX: association between C-reactive protein (CRP) gene polymorphisms and vascular events. Rheumatology (Oxford) 2005; 44: 864–868. 30 Thorburn CM, Prokunina-Olsson L, Sterba KA, Lum RF, Seldin MF, Alarcon-Riquelme ME et al. Association of PDCD1 genetic variation with risk and clinical manifestations of systemic lupus erythematosus in a multiethnic cohort. Genes Immun 2007; 8: 279–287.

Genes and Immunity

31 Parks CG, Pandey JP, Dooley MA, Treadwell EL, St Clair EW, Gilkeson GS et al. Genetic polymorphisms in tumor necrosis factor (TNF)-alpha and TNF-beta in a population-based study of systemic lupus erythematosus: associations and interaction with the interleukin-1alpha-889 C/T polymorphism. Hum Immunol 2004; 65: 622–631. 32 Kaufman KM, Kelly JA, Herring BJ, Adler AJ, Glenn SB, Namjou B et al. Evaluation of the genetic association of the PTPN22 R620W polymorphism in familial and sporadic systemic lupus erythematosus. Arthritis Rheum 2006; 54: 2533–2540.