Systemic lupus erythematosus susceptibility loci defined by genome scan meta-analysis

Platelet Activation Mechanisms and Consequences of Immune Thrombocytopenia

Autoimmune disorders are often associated with low platelet count or thrombocytopenia. In immune-induced thrombocytopenia (IIT), a common mechanism is increased platelet activity, which can have an increased risk of thrombosis. In addition, or alternatively, auto-antibodies suppress platelet formation or augment platelet clearance. Effects of the auto-antibodies are linked to the unique structural and functional characteristics of platelets. Conversely, prior platelet activation may contribute to the innate and adaptive immune responses. Extensive interplay between platelets, coagulation and complement activation processes may aggravate the pathology. Here, we present an overview of the reported molecular causes and consequences of IIT in the most common forms of autoimmune disorders. These include idiopathic thrombocytopenic purpura (ITP), systemic lupus erythematosus (SLE), antiphospholipid syndrome (APS), drug-induced thrombocytopenia (DITP), heparin-induced thrombocytopenia (HIT), COVID-19 vaccine-induced thrombosis with thrombocytopenia (VITT), thrombotic thrombocytopenia purpura (TTP), and hemolysis, the elevated liver enzymes and low platelet (HELLP) syndrome. We focus on the platelet receptors that bind auto-antibodies, the immune complexes, damage-associated molecular patterns (DAMPs) and complement factors. In addition, we review how circulating platelets serve as a reservoir of immunomodulatory molecules. By this update on the molecular mechanisms and the roles of platelets in the pathogenesis of autoimmune diseases, we highlight platelet-based pathways that can predispose for thrombocytopenia and are linked thrombotic or bleeding events.

Role of serum leptin levels and leptin receptor gene polymorphisms in systemic lupus erythematosus

BACKGROUND

Serum leptin and leptin receptor gene polymorphisms may play a role in the etiopathogenesis of SLE.

OBJECTIVE

This study was undertaken to explore the relationship between serum leptin levels and leptin receptor (LEPR) gene polymorphisms with susceptibility to SLE in Egyptian population and to study their relationships with clinical, laboratory, radiographic findings, and disease activity of SLE (SLEDAI).

MATERIALS AND METHODS

A total of 50 unrelated female patients, who met the SLICC classification criteria for SLE and fifty healthy blood donors, matched for age, sex, and BMI with SLE patients, serving as a control group, were included in this study. All participants had completed preliminary questionnaires and clinical, laboratory, and radiographic examinations. Serum leptin levels were measured by ELISA assays. LEPR genotyping was done by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. We compared serum leptin levels and LEPR gene polymorphisms in SLE patients and controls, and we tested their relationships with clinical, laboratory, and radiographic findings and SLEDAI in SLE patients.

RESULTS

The present study showed significant differences of serum leptin levels between SLE patients and controls (p < 0.001). Moreover, higher frequencies of variant genotype (AA) and (A) allele were found in SLE patients compared to controls (p = 0.008 and 0.001, respectively). No associations were observed between the serum leptin, various LEPR genotypes, and gene alleles and the development of clinical, laboratory, and radiological manifestations. Furthermore, no associations were observed between the various LEPR genotypes or gene alleles and leptin levels (p = 0.633 and 0.337 respectively) in SLE patients. Additionally, no correlations were observed between leptin levels, various genotypes, and alleles with SLEDAI (p = 0.244, 0.741, and 0.838 respectively) in SLE patients.

CONCLUSION

Serum leptin and LEPR gene polymorphism increase risk of SLE in Egyptian population; however, they are not associated with the development of clinical, lab, and radiological findings. Disease activity is neither correlated with serum leptin level nor associated with LEPR gene polymorphism. Serum levels of leptin are not associated with LEPR gene polymorphism. Key Points • Serum leptin and LEPR gene polymorphism increase risk of SLE in Egyptian patients. • Serum leptin is not associated with SLE disease activity.

Circulating pentraxin-3 levels in patients with systemic lupus erythematosus: a meta-analysis

Aim: An existing meta-analysis have investigated the PTX3 levels in systemic lupus erythematosus (SLE) patients, but the number of studies has increased since 2015. We performed an updated meta-analysis to derive a more accurate estimation. Methods: The related literature was systematically searched in PubMed, Embase and The Cochrane Library database (up to 28 February, 2019). Results: SLE patients had significantly higher PTX3 levels than controls (pooled SMD = 0.48; 95% CI: 0.11-0.84). Subgroup analyses indicated SLE patients from non-Caucasian population, with age ≥45 years, SLE disease activity index (SLEDAI) ≥10 and plasma samples had higher PTX3 levels. Conclusion: Circulating PTX3 levels are increased in SLE patients, and affected by age, ethnicity, SLEDAI and sample type.

Potential therapeutic drugs for ischemic stroke based on bioinformatics analysis

Ischemic stroke (IS) is a complex disease affected by various environmental factors, genetic factors and their interactions. Because genetic factors occupy an irreplaceable place in the pathogenesis of IS, the identification of genetic factors has become one of the hot spots in the current research. In the present study, we aimed to identify possible gene targets and relevant drug molecules in the pathogenesis of IS. Microarray dataset of GSE16561 was downloaded from Gene Expression Omnibus database. The differentially expressed genes (DEGs) between IS group and control group were obtained using limma package in R. Ground-Operation Simulation package in R language was used to cluster DEGs according to their biological process, cellular components and molecular functions with respect to the GO annotation. The DEGs were analyzed by Search Tool for the Retrieval of Interacting Genes online database and Cytoscape software to predict their interaction relationship. Finally, the DEGs were submitted to DGIdb dataset and related drug molecules were retrieved. 20 DEGs were identified from IS group including 1 downregulated and 19 upregulated genes. The function enrichment analysis revealed that the DEGs were enriched in three GO terms, mainly including inflammatory response, positive regulation of protein kinase activity and innate immune response. Finally, 10 drug molecules were identified from the DEGs. Our study identified some potential biological targets and drug molecules for the treatment of IS.

Copy number variations and polymorphisms in HSP90AB1 and risk of systemic lupus erythematosus and efficacy of glucocorticoids

The aim of our study was to assess the associations of HSP90AB1 copy number variations (CNVs) with systemic lupus erythematosus (SLE) risk and glucocorticoids (GCs) efficacy, as well as the relationship between HSP90AB1 single‐nucleotide polymorphisms (SNPs) and GCs efficacy. HSP90AB1 CNVs and SLE risk were analysed in 519 patients and 538 controls. Patients treated with GCs were followed up for 12 weeks and were divided into sensitive and insensitive groups to investigate the effects of CNVs (419 patients) and SNPs (457 patients) on the efficacy of GCs. Health‐related quality of life (HRQoL) was also measured by SF‐36 at baseline and week 12 to explore the relationship between CNVs/SNPs and HRQoL improvements in Chinese SLE patients. Our results indicated a statistically significant association between HSP90AB1 CNVs and SLE (P_BH = 0.039), and this association was more pronounced in the female subgroup (P_BH = 0.039). However, we did not detect association of HSP90AB1 CNVs/SNPs with efficacy of GCs. But we found a marginal association between SNP rs13296 and improvement in Role‐emotional, while this association was not strong enough to survive in the multiple testing corrections. Collectively, our findings suggest that the copy number of HSP90AB1 is associated with SLE susceptibility. But copy number and polymorphisms of HSP90AB1 may not be associated with efficacy of GCs.

Distinct gene expression characteristics in epithelial cell-Porphyromonas gingivalis interactions by integrating transcriptome analyses

Porphyromonas gingivalis is a pivotal periodontal pathogen, and the epithelial cells serve as the first physical barrier to defend the host from bacterial attack. Within this host-bacteria interaction, P. gingivalis can modify the host immune reaction and adjust the gene expression, which is associated with periodontitis pathogenesis and developing strategies. Herein, a meta-analysis was made to get the differential gene expression profiles in epithelial cells with or without P. gingivalis infection. The network-based meta-analysis program for gene expression profiling was used. Both the gene ontology analysis and the pathway enrichment analysis of the differentially expressed genes were conducted. Our results determined that 290 genes were consistently up-regulated in P. gingivalis infected epithelial cells. 229 gene ontology biological process terms of up-regulated genes were discovered, including "negative regulation of apoptotic process" and "positive regulation of cell proliferation/migration/angiogenesis". In addition to the well-known inflammatory signaling pathways, the pathway associated with a transcriptional misregulation in cancer has also been increased. Our findings indicated that P. gingivalis benefited from the survival of epithelial cells, and got its success as a colonizer in oral epithelium. The results also suggested that infection of P. gingivalis might contribute to oral cancer through chronic inflammation. Negative regulation of the apoptotic process and transcriptional misregulation in cancer pathway are important contributors to the cellular physiology changes during infection development, which have particular relevance to the pathogenesis and progressions of periodontitis, even to the occurrence of oral cancer.

An overview of meta-analysis for clinicians

The number of medical studies being published is increasing exponentially, and clinicians must routinely process large amounts of new information. Moreover, the results of individual studies are often insufficient to provide confident answers, as their results are not consistently reproducible. A meta-analysis is a statistical method for combining the results of different studies on the same topic and it may resolve conflicts among studies. Meta-analysis is being used increasingly and plays an important role in medical research. This review introduces the basic concepts, steps, advantages, and caveats of meta-analysis, to help clinicians understand it in clinical practice and research. A major advantage of a meta-analysis is that it produces a precise estimate of the effect size, with considerably increased statistical power, which is important when the power of the primary study is limited because of a small sample size. A meta-analysis may yield conclusive results when individual studies are inconclusive. Furthermore, meta-analyses investigate the source of variation and different effects among subgroups. In summary, a meta-analysis is an objective, quantitative method that provides less biased estimates on a specific topic. Understanding how to conduct a meta-analysis aids clinicians in the process of making clinical decisions.

Vitamin D receptor FokI, TaqI, and ApaI polymorphisms and susceptibility to systemic lupus erythematosus: an updated meta-analysis

This study aimed to explore whether vitamin D receptor (VDR) polymorphisms are associated with susceptibility to systemic lupus erythematosus (SLE). Meta-analyses were conducted to determine the associations between the VDR FokI, TaqI, and ApaI polymorphisms and SLE in all subjects and each ethnic group. A total of 12 studies were considered in the meta-analysis, which involved 1974 patients and 2506 controls. Meta-analysis of the VDR FokI polymorphism showed no association between SLE and the FokI F allele in all study subjects (OR = 1.047, 95% CI = 0.781-1.403, p = 0.758). However, the meta-analysis showed a significant association between SLE and the VDR FokI F allele in the Arab population (OR = 1.721, 95% CI = 1.417-2.088, p < 0.001). Analysis using the recessive and dominant models and homozygote contrast showed the same pattern for the VDR FokI F allele in Europeans, Asians, and Arabs. This meta-analysis showed that polymorphisms in VDR FokI, TaqI, and ApaI are not associated with SLE susceptibility in overall, European and Asian populations. However, the VDR FokI polymorphism is associated with SLE susceptibility in the Arab population.

Association between circulating leptin levels and systemic lupus erythematosus: an updated meta-analysis

Objective We aimed to evaluate the relationship between circulating leptin levels and systemic lupus erythematosus (SLE). Methods MEDLINE, EMBASE, and Cochrane library databases were searched. Meta-analyses were performed comparing serum/plasma leptin levels in patients with SLE and healthy controls, and on patients with SLE in subgroups based on ethnicity, sample size, data type, and matched variables (age, sex, and/or body mass index (BMI)). Results Eighteen studies including 1333 patients with SLE and 1048 controls were ultimately selected, which showed that leptin levels were significantly higher in the SLE group than in the control group (SMD = 0.611, 95% CI = 0.275-0.947, p < 0.001). When we excluded two outlier studies because of high heterogeneity, leptin levels were also significantly higher in the SLE group than in the control group (SMD = 0.619, 95% CI = 0.431-0.807, p < 0.001). Stratification by ethnicity showed significantly elevated leptin levels in the SLE group in European, Asian, Arab, Latin American, and mixed populations. Subgroup analysis by sample size showed significantly higher leptin levels in the SLE group by small ( n ≤ 100) and large sample numbers ( n > 100) (SMD = 0.780, 95% CI = 0.445-1.115, p < 0.001; SMD = 0.495, 95% CI = 0.275-0.715, p < 0.001). Stratification by data type revealed significantly higher leptin levels in the original data and imputed data groups. Subgroup analysis adjustment revealed significantly higher leptin levels in the SLE group, regardless of adjustment for variables. Conclusions Our meta-analysis demonstrated that leptin levels were significantly higher in patients with SLE, regardless of ethnicity, sample size, data type, and matched variables.

Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets

Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC. Our results showed that PI3K, EGFR, STAT1, and CPBP are important contributors to the changes in cellular physiology that occur during the development of OSCC. Therefore, these genes represent potential diagnostic biomarkers and therapeutic targets for OSCC.

Association between shortened telomere length and systemic lupus erythematosus: a meta-analysis

Objective We aimed to evaluate the relationship between telomere length and systemic lupus erythematosus (SLE). Methods PUBMED and EMBASE databases were searched; meta-analyses were performed comparing telomere length in SLE patients and healthy controls, and on SLE patients in subgroups based on ethnicity, sample type, assay method and data type. Results Eight studies including 472 SLE patients and 365 controls were ultimately selected which showed that telomere length was significantly shorter in the SLE group than in the control group (standardized mean difference (SMD) = -0.835, 95% confidence interval (CI) = -1.291 to -0.380, p = 3.3 × 10^-4). Stratification by ethnicity showed significantly shortened telomere length in the SLE group in Caucasian, Asian and mixed populations (SMD = -0.455, 95% CI = -0.763 to -0.147, p = 0.004; SMD = -0.887, 95% CI = -1.261 to -0.513, p = 3.4 × 10^-4; SMD = -0.535, 95% CI = -0.923 to -0.147, p = 0.007; respectively). Furthermore, telomere length was significantly shorter in the SLE group than in the control group in whole blood and peripheral blood mononuclear cell groups (SMD = -0.361, 95% CI = -0.553 to -0.169, p = 2.3 × 10^-4; SMD = -1.546, 95% CI = -2.583 to -0.510, p = 0.003; respectively); a similar trend was observed in leukocyte groups (SMD = -0.699, 95% CI = -1.511 to -0.114, p = 0.092). Meta-analyses based on assay method or data type revealed similar associations. Conclusions Our meta-analysis demonstrated that telomere length was significantly shorter in patients with SLE, regardless of ethnicity, sample type or assay method evaluated.

Association between TYK2 polymorphisms and susceptibility to autoimmune rheumatic diseases: a meta-analysis

Objective

This study aimed to explore whether TYK2 polymorphisms are associated with susceptibility to autoimmune rheumatic diseases.

Methods

We conducted a meta-analysis on the association between TYK2 polymorphisms and autoimmune rheumatic diseases.

Results

Twelve studies with a total of 16,335 patients and 30,065 controls were included in the meta-analysis. Meta-analysis revealed an association between rheumatic diseases and the 2 allele of the TYK2 rs2304256 (OR = 0.885, 95% CI = 0.802–0.978, p = 0.016). Furthermore, stratification by ethnicity identified a significant association between this polymorphism and rheumatic diseases in Caucasians (OR = 0.822, 95% CI = 0.706–0.889, p = 9.5 × 10−7), but not in Asians (OR = 1.127, 95% CI = 0.835–1.522, p = 0.434). Meta-analysis by rheumatic disease type revealed a significant association between the 2 allele of the TYK2 rs2304256 and SLE in Caucasians (OR = 0.737, 95% CI = 0.673–0.808, p < 1.0 × 10−8) but not in Asians (OR = 1.211, 95% CI = 0.813–1.804, p = 0.347). Meta-analysis revealed that the rs12720356 polymorphism was associated with susceptibility to rheumatic diseases in Caucasians (OR = 0.812, 95% CI = 0.661–0.997, p = 0.046) but not in Asians. Interestingly, the rs280519 polymorphism was significantly associated with susceptibility to SLE both in Caucasians and Asians. However, no associations were found between the rs12720270, rs280500, rs280523 and rs8108236 polymorphisms and susceptibility to rheumatic diseases.

Conclusions

This meta-analysis demonstrates that the TYK2 rs2304256 and rs12720356 polymorphisms are associated with susceptibility to rheumatic diseases, rs2304256 polymorphism is associated with SLE in Caucasians, and rs280519 polymorphism is associated with SLE in Caucasians and Asians.

Association between toll-like receptor polymorphisms and systemic lupus erythematosus: a meta-analysis update

OBJECTIVE

The aim of this study was to determine whether polymorphisms of the Toll-like receptor (TLR) genes are associated with susceptibility to systemic lupus erythematosus (SLE).

METHODS

The authors conducted a meta-analysis of the relationship between 12 TLR polymorphisms and SLE susceptibility.

RESULTS

In total, 26 studies that involved 11,984 patients and 14,572 controls were included in the meta-analysis. The meta-analysis showed no association between the two alleles of the rs352140, rs5743836, and rs352139 polymorphisms of TLR9 and SLE, but indicated an association between the two alleles of the rs187084 polymorphism (TLR9) and SLE in the overall population (OR = 0.869, 95% CI = 0.762-0.992, P = 0.038). No association was detected between rs3764880 (TLR8) and SLE; however, our meta-analysis indicated an association between rs3764879 (TLR8) and SLE in Caucasians (OR = 1.414, 95% CI = 1.139-1.756, P = 0.002). An association between rs179008 (TLR7) and SLE was found in the African (OR = 0.430, 95% CI = 0.238-0.775, P = 0.005), but not in the Caucasian population (OR = 1.206, 95% CI = 0.932-1.614, P = 0.145). Furthermore, our meta-analysis indicated a significant association between rs3853839 (TLR7) and SLE in the Asian population (OR = 0.773, 95% CI = 0.735, 0.823, P < 1.0 × 10(-9)). No associations were found between rs5744168 (TLR5), rs4986791 (TLR4), rs4986790 (TLR4), and rs3775291 (TLR3) polymorphisms and SLE susceptibility.

CONCLUSIONS

Our meta-analysis suggests that TLR7, TLR8, and TLR9 polymorphisms are associated with the development of SLE in Caucasian, Asian, and African populations.

Meta-analysis of the association between functional MICA-TM polymorphisms and systemic lupus erythematosus, rheumatoid arthritis and ankylosing spondylitis

OBJECTIVE

The aim of this study was to determine whether the major histocompatibility complex class I chain-related gene A transmembrane (MICA-TM) polymorphism is associated with susceptibility to systemic lupus erythematous (SLE), rheumatoid arthritis (RA) and ankylosing spondylitis (AS).

METHODS

A meta-analysis was conducted to establish the association between MICA-TM polymorphisms and SLE, RA and AS in the overall study population, as well as in each ethnic group.

RESULTS

A total of 13 comparison studies, including five SLE (1601 patients; 1846 controls), four RA (701 patients; 887 controls) and four AS (346 patients; 356 controls) studies were considered in the meta-analysis. An association between the MICA-TM A5.1 allele and SLE was demonstrated in Europeans but not in Asians: odds ratio (OR) = 1.699, 95 % confidence interval (CI) = 1.123-2.569, p = 0.012 and OR = 0.949, 95 % CI = 0.502-1.793, p = 0.871, respectively. However, no association was found in Europeans after Bonferroni correction (pcorrected = 0.060). An association was found between the MICA-TM A9 allele and RA in Asians (OR = 0.527, 95 % CI = 0.408-0.681, p = 8.9 × 10(-7)) but not in Europeans; the association in Asians remained significant after Bonferroni correction (pcorrected = 4.5 × 10(-6)). An association between the MICA-TM A4 phenotype and AS was observed in European and Asian populations (OR = 12.87, 95 % CI = 6.747-24.58, p < 1.0 × 10(-9) and OR = 9.461, 95 % CI = 5.754-15.55, p < 1.0 × 10(-9), respectively). Meta-analysis stratified by human leukocyte antigen (HLA)-B27 status revealed an association between the MICA-TM A4 phenotype and HLA-B27 positivity AS in Asians, but not in Europeans (OR = 0.318, 95 % CI = 0.102-0.995, p = 0.049 and OR = 2.080, 95 % CI = 0.422-10.25, p = 0.368, respectively). However, the association in Asians was not significant after Bonferroni correction (pcorrected = 0.245).

CONCLUSION

This meta-analysis demonstrated that there was no association between MICA-TM polymorphisms and SLE susceptibility, but that the MICA-TM A9 allele was associated with an RA risk in Asians. Moreover, the association between the MICA-TM A4 phenotype and AS was HLA-B27-dependent.

Genetic associations of leptin-related polymorphisms with systemic lupus erythematosus

Leptin is abnormally elevated in the plasma of patients with systemic lupus erythematosus (SLE), where it is thought to promote and/or sustain pro-inflammatory responses. Whether this association could reflect an increased genetic susceptibility to develop SLE is not known, and studies of genetic associations with leptin-related polymorphisms in SLE patients have been so far inconclusive. Here we genotyped DNA samples from 15,706 SLE patients and healthy matched controls from four different ancestral groups, to correlate polymorphisms of genes of the leptin pathway to risk for SLE. It was found that although several SNPs showed weak associations, those associations did not remain significant after correction for multiple testing. These data do not support associations between defined leptin-related polymorphisms and increased susceptibility to develop SLE.

Association between FCGR3B copy number variations and susceptibility to autoimmune diseases: a meta-analysis

OBJECTIVE

This study determined whether FCGR3B copy number variations (CNVs) were associated with susceptibility to autoimmune diseases.

METHODS

A meta-analysis was conducted to determine the association between FCGR3B CNVs and susceptibility to autoimmune diseases by comparing low FCGR3B CN (<2 to ≥2) and high FCGR3B CN (>2 to ≤2).

RESULTS

In all, 28 comparative studies from 15 reports involving 12,160 patients and 11,103 controls were included in this meta-analysis. The meta-analysis showed a significant association between low FCGR3B CN and autoimmune diseases (OR=1.496, 95% CI=1.301-1.716, p=1.0×10(-9)). Subgroup analysis according to ethnicity indicated an association between low FCGR3B CN and autoimmune diseases in Caucasians (OR=1.482, 95% CI=1.219-1.801, p=7.7×10(-6)) and Asians (OR=1.498, 95% CI=1.306-1.717, p=1.0×10(-9)). Meta-analysis according to the type of autoimmune disease indicated a significant association of low FCGR3B CN with systemic lupus erythematosus (SLE; OR=1.797, 95% CI=1.562-2.068, p<1.0×10(-9)), primary Sjogren's syndrome (pSS; OR=2.263, 95% CI=1.316-3.892, p=0.003), and Wegener's granulomatosis (WG; OR=1.973, 95% CI=1.178-3.302, p=0.010), but not with rheumatoid arthritis (RA; OR=1.333, 95% CI=0.947-1.877, p=0.099). However, the meta-analysis showed no association between high FCGR3B CN and SLE, RA, pSS, and WG.

CONCLUSIONS

Thus, the results of this meta-analysis indicated that low FCGR3B CN increased susceptibility to autoimmune diseases, especially SLE, pSS, and WG.

Chemokine receptor 5 Δ32 polymorphism and systemic lupus erythematosus, vasculitis, and primary Sjogren's syndrome. Meta-analysis of possible associations

OBJECTIVE

The aim of this study was to determine whether the functional chemokine receptor 5 delta32 (CCR5-Δ32) polymorphism is associated with susceptibility to systemic lupus erythematosus (SLE), vasculitis, and primary Sjogren's syndrome (pSS).

RESULTS

A total of 12 studies were analyzed, including 5 on SLE, 5 on vasculitis, and 2 on pSS, encompassing 1881 patients and 2391 controls. Meta-analysis indicated no association between SLE and the CCR5-Δ32 allele (OR 0.842, 95 % CI 0.793-1.804, p = 0.657), and no association between the CCR5-Δ32 allele and SLE in Europeans (OR 0.647, 95 % CI 0.306-1.368, p = 0.255). Meta-analysis of the CCR5-Δ32 allele and the Δ32Δ32 + Δ32 W genotype showed no association with lupus nephritis (LN; OR 1.771, 95 % CI 0.475-6.595, p = 0.395; OR 2.192, 95 % CI 0.182-26.42, p = 0.537, respectively). In addition, meta-analysis revealed no association between the CCR5-Δ32 allele and vasculitis in all study subjects and in Europeans (OR 1.241, 95 % CI 0.951-1.620, p = 0.111; OR 1.359, 95 % CI 0.803-2.303, p = 0.254, respectively). However, the overall OR for the CCR5-Δ32 allele was significantly higher in Kawasaki disease (KD; OR 1.746, 95 % CI 1.003-2.955, p = 0.038) and the meta-analysis of the Δ32Δ32 + Δ32 W genotype showed a trend indicating an association with KD (OR 1.683, 95 % CI 0.921-3.077, p = 0.091). No association was found between the CCR5-Δ32 polymorphism and pSS.

CONCLUSION

This meta-analysis demonstrates that the CCR5-Δ32 polymorphism is associated with KD, but does not facilitate susceptibility to SLE, LN, or pSS.

Interleukin-18 promoter -607 C/A and -137 G/C polymorphisms and susceptibility to type 1 diabetes: A meta-analysis

OBJECTIVE

The aim of this study was to determine whether the functional interleukin-18 (IL-18) promoter -607 C/A (rs1946518) and -137 G/C (rs187238) polymorphisms are associated with susceptibility to type 1 diabetes (TID).

METHODS

A meta-analysis was conducted to assess the associations between the IL-18 -607 C/A and -137 G/C polymorphisms and T1D in overall and by ethnic group.

RESULTS

A total of 6075 cases and 5744 controls from ten studies were considered in this meta-analysis. In all study subjects, the meta-analysis showed no association between T1D and the IL-18 -607 C allele (OR=1.083, 95% CI=0.930-1.260, p=0.307). However, stratification by ethnicity indicated an association between the IL-18 -607 C allele and T1D in Asians (OR=1.506, 95% CI=1.172-1.936, p=0.001), but not in Europeans (OR=0.988, 95% CI=0.808-1.209, p=0.907). Analysis using recessive and dominant models and homozygote contrast showed the same -607 C allele pattern in Asians and Europeans. Meta-analysis of the IL-18 -137 G/C polymorphism showed no association between T1D and the IL-18 -137 G allele in all study subjects (OR=1.066, 95% CI=0.926-1.2289, p=0.375). Stratification by ethnicity indicated no association between the IL-18 -137 G allele and T1D in Europeans and Asians (OR=1.021, 95% CI=0.961-1.085, p=0.504; OR=0.851, 95% CI=0.5821-1.245, p=0.406).

CONCLUSIONS

Our meta-analysis demonstrates that the IL-18 -607 C/A polymorphism may be associated with susceptibility to T1D in Asians, but not in Europeans.

Integrative meta-analysis of differentially expressed genes in osteoarthritis using microarray technology

The aim of the present study was to identify differentially expressed (DE) genes in patients with osteoarthritis (OA), and biological processes associated with changes in gene expression that occur in this disease. Using the INMEX (integrative meta-analysis of expression data) software tool, a meta-analysis of publicly available microarray Gene Expression Omnibus (GEO) datasets of OA was performed. Gene ontology (GO) enrichment analysis was performed in order to detect enriched functional attributes based on gene-associated GO terms. Three GEO datasets, containing 137 patients with OA and 52 healthy controls, were included in the meta-analysis. The analysis identified 85 genes that were consistently differentially expressed in OA (30 genes were upregulated and 55 genes were downregulated). The upregulated gene with the lowest P-value (P=5.36E-07) was S-phase kinase-associated protein 2, E3 ubiquitin protein ligase (SKP2). The downregulated gene with the lowest P-value (P=4.42E-09) was Proline rich 5 like (PRR5L). Among the 210 GO terms that were associated with the set of DE genes, the most significant two enrichments were observed in the GO categories of 'Immune response', with a P-value of 0.000129438, and 'Immune effectors process', with a P-value of 0.000288619. The current meta-analysis identified genes that were consistently DE in OA, in addition to biological pathways associated with changes in gene expression that occur during OA, which may provide insight into the molecular mechanisms underlying the pathogenesis of this disease.

Associations between the functional CD40 rs4810485 G/T polymorphism and susceptibility to rheumatoid arthritis and systemic lupus erythematosus: a meta-analysis

Objective

The aim of this study was to determine whether the functional CD40 rs4810485 G/T polymorphism is associated with susceptibility to rheumatoid arthritis (RA) or with susceptibility to systemic lupus erythematosus (SLE).

Methods

A series of meta-analyses were conducted to test for association between the CD40 rs4810485 G/T polymorphism and RA or SLE.

Results

A total of 21 comparisons involving 15,095 patients and 27,050 controls for RA, and 1353 patients and 2342 controls for SLE were considered. Meta-analysis showed a significant association between the CD40 rs4810485 T allele and RA in all subjects (odds ratio (OR) 0.890, 95% confidence interval (CI) 0.846–0.936, p = 5.5 × 10−7). After stratification by ethnicity, the CD40 T allele was found to be significantly associated with RA in Europeans (OR 0.879, 95% CI 0.848–0.901, p = 3.0 × 10−9). A similar pattern of association was observed between the CD40 T allele and RA when the analysis was performed using the recessive, dominant, and additive models. Meta-analysis also showed a significant association between the CD40 polymorphism and SLE in Europeans (OR for the T allele 0.715, 95% CI 0.641–0.832, p = 1.4 × 10−6).

Conclusions

Our meta-analyses confirm that the CD40 rs4810485 G/T polymorphism is associated with susceptibility to RA and SLE in Europeans.

Genome-wide association pathway analysis to identify candidate single nucleotide polymorphisms and molecular pathways for gastric adenocarcinoma

To demonstrate candidate single nucleotide polymorphisms that might affect susceptibility to gastric adenocarcinoma as well as their potential mechanisms and pathway hypotheses, we performed a genome-wide association study dataset of gastric adenocarcinoma. Our study included 472,342 single nucleotide polymorphisms from 2766 cases of gastric cardia adenocarcinoma cases and 11,013 subjects from north central China as control groups. The identify candidate causal SNPs and pathways (ICSNPathway) analysis was employed to identify 13 candidate single nucleotide polymorphisms, nine genes, and 15 pathways. The top three candidate SNPs were rs3765524 (-log10(p) = 8.556), rs2274223 (-log10(p) = 8.633), and rs2076472 (-log10(p) = 3.205). The strongest mechanism involved the modulation of rs4745 and rs12904, thereby affecting their regulatory roles in ephrin receptor binding (p = 0.001; FDR = 0.005). The second strongest hypothetical biological mechanism was that rs932972 and rs1052177 alters the regulatory role of the glycolysis pathway (p < 0.001; FDR = 0.013). The most significant pathway was the regulation of the ephrin receptor binding pathway, which involved EFNA1, TIAM1, EFNA5, EFNB2, and EFNB3.

Association between the functional ITGAM rs1143679 G/A polymorphism and systemic lupus erythematosus/lupus nephritis or rheumatoid arthritis: an update meta-analysis

The aim of this study was to determine whether the functional integrin-α-M (ITGAM) rs1143679 polymorphism is associated with susceptibility to systemic lupus erythematosus (SLE), lupus nephritis (LN), and rheumatoid arthritis (RA). A series of meta-analyses were conducted to test for associations between the ITGAM rs1143679 polymorphism and SLE, LN, or RA. A total of 24 comparisons involving 7,738 patients and 8,309 controls for SLE, and 2,663 patients and 2,694 controls in RA were considered. Meta-analysis showed a significant association between the ITGAM rs1143679 A allele and SLE in all subjects (OR 1.773, 95 % CI 1.656, 1.901, p < 1.0 × 10(-9)). After stratification by ethnicity, the A allele was found to be significantly associated with SLE in European, Latin American, and Asian. A significant association was also found between the ITGAM A allele and lupus nephritis in Europeans (OR 2.131, 95 % CI 1.565, 2.903, p = 1.6 × 10(-7)). However, no association was found between RA and the ITGAM rs1143679 polymorphism. Our meta-analyses confirm that the ITGAM rs1143679 polymorphism is associated with SLE susceptibility in different ethnic groups and demonstrate that the polymorphism is associated with LN in European.

The insertion/deletion polymorphism in the angiotensin-converting enzyme and susceptibility to schizophrenia or Parkinson's disease: A meta-analysis

INTRODUCTION

The purpose of this study was to examine whether the insertion (I) and deletion (D) polymorphism of the angiotensin-converting enzyme (ACE) confers susceptibility to schizophrenia and Parkinson's disease (PD).

MATERIALS AND METHODS

A meta-analysis was performed of the associations between the ACE I/D polymorphism and schizophrenia and PD.

RESULTS

Thirteen studies with 2024 cases and 2230 controls comprising eight studies on schizophrenia and five on PD were included in the meta-analysis. The meta-analysis revealed no association between the ACE D allele and schizophrenia (OR = 0.990, 95% CI = 0.889-1.102, p = 0.856) or PD (OR = 1.067, 95% CI = 0.907-1.255, p = 0.433). Stratification by ethnicity indicated no association between the ACE D allele and schizophrenia in European, Asian, or Turkish ethnic groups (OR = 0.896, 95% CI = 0.566-1.419, p = 0.640; OR = 1.057, 95% CI = 0.903-1.238, p = 0.492; OR = 1.111, 95% CI = 0.889-1.389, p = 0.354, respectively). Ethnicity-specific meta-analysis was not conducted for PD because only one ethnic PD study was available.

CONCLUSIONS

This meta-analysis found no association between the ACE I/D polymorphism and schizophrenia or PD.

Genome-wide pathway analysis of breast cancer

The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might affect susceptibility to breast cancer and then elucidate their potential mechanisms and generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of breast cancer that included 453,852 SNPs from 1,145 breast cancer patients and 1,142 control subjects of European descent was used in this study. The identify candidate causal SNPs and pathways (ICSNPathway) method was applied to the GWAS dataset. ICSNPathway analysis identified 16 candidate SNPs, 13 genes, and 7 pathways, which together revealed 7 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was that rs3168891 and rs2899849 alter the role of MBIP in the inactivation of mitogen-activated protein kinase (MAPK) (p < 0.001; false discovery rate (FDR) = 0.038). The second strongest mechanism was that rs2229714 modulates RPS6KA1 to affect its role in growth hormone signaling (p = 0.001; FDR = 0.039). The third strongest mechanism was that rs2230394 modulates ITGB1 to regulate the PTEN pathway and hsa04360 (axon guidance pathway) (p < 0.001; FDR = 0.039, 0.041). Use of the ICSNPathway to analyze breast cancer GWAS data identified 16 candidate SNPs, 13 genes (including MBIP, RPS6KA1, and ITGB1), and 7 pathways that might contribute to the susceptibility of patients to breast cancer.

Functional FCGR3A 158 V/F and IL-6 -174 C/G polymorphisms predict response to biologic therapy in patients with rheumatoid arthritis: a meta-analysis

The aim of this study was to investigate whether the Fc gamma receptor 3A (FCGR3A) 158 V/F and interleukin-6 (IL-6) promoter -174 G/C polymorphisms can predict the response to biologic-based therapy in patients with rheumatoid arthritis (RA). We conducted a meta-analysis of studies on the association between the FCGR3A V/F polymorphism or the IL-6 -174 C/G polymorphism and non-responsiveness to biologic therapy in RA patients. A total of 10 studies involving 1,427 patients were considered. These studies consisted of seven studies on the FCGR3A polymorphism and three studies on the IL-6 polymorphism. Meta-analysis showed no association between the FCGR3A VV+VF genotype and non-responders to biologic therapy [odds ratio (OR) 0.881, 95 % confidence interval (CI) 0.505-1.537, p = 0.655]. However, stratification by biologic type indicated an association between the FCGR3A VV+VF genotype and non-responders to rituximab (OR 0.566, 95 % CI 0.373-0.857, p = 0.007), but no association was found in non-responders to tumor necrosis factor (TNF)-blockers (OR 1.337, 95 % CI 0.869-2.056, p = 0.186). Meta-analysis revealed no association between the IL-6 CC+CG genotype and non-responders to the biologics (OR 3.233, 95 % CI 0.766-13.64, p = 0.110). However, an association was found between the IL-6 CC+CG genotype and non-responders to anti-TNF therapy (OR 8.030, 95 % CI 1.807-33.68, p = 0.006). This meta-analysis demonstrates that FCGR3A V allele carriers show a better response to rituximab, and individuals carrying the IL-6 -174 C allele show a poorer response to anti-TNF therapy for RA. Genotyping for these polymorphisms may be a useful tool for predicting the response to biologics with respect to personalized medicine.

Gene-environmental interaction between smoking and shared epitope on the development of anti-cyclic citrullinated peptide antibodies in rheumatoid arthritis: a meta-analysis

OBJECTIVE

The aim of this study was to determine the gene-environment interactions of smoking and shared epitope (SE) both separately and combined on anti-cyclic citrullinated peptide (CCP) antibodies in patients with rheumatoid arthritis (RA).

METHODS

The literature was searched using the MEDLINE, EMBASE and Cochrane databases. A meta-analysis on the associations between tobacco exposure (TE) and/or SE and the development of anti-CCP antibodies in patients with RA was performed.

RESULTS

Eight comparison studies with 5317 RA patients were considered in this meta-analysis. The odds ratio (OR) for positive anti-CCP antibodies in TE+/SE- patients with RA was increased compared with TE-/SE- patients (OR = 1.373, 95% CI = 1.111-1.698, P = 0.003). The ORs for positive anti-CCP antibodies in TE-/SE+ patients and TE+/SE+ patients with RA were also increased compared with TE-/SE- patients (OR = 2.678, 95% CI = 2.031-3.532, P < 1.0 × 1(0-9) in TE-/SE+; OR = 4.233, 95% CI = 2.458-7.291, P = 1.9 × 10(-8) in TE+/SE+). Stratification by ethnicity indicated the same pattern as that shown in the overall group. The OR for positive anti-CCP antibodies in TE+/SE+ patients with RA was much higher than in TE-/SE- patients in Europeans and Asians (OR = 3.879, 95% CI = 2.203-6.830, P = 2.6 × 10(-7); OR = 10.504, 95% CI = 3.182-34.67, P = 1.1 × 10(-4)).

CONCLUSIONS

This meta-analysis suggests a gene-environmental interaction between smoking and SE for the development of anti-CCP antibodies.

Genome-wide pathway analysis in neuroblastoma

The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might play a role in susceptibility to neuroblastoma, elucidate their potential mechanisms, and generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of neuroblastoma that included 442,976 SNPs from 1,627 neuroblastoma patients and 3,254 control subjects of European descent was used in this study. The identify candidate causal SNPs and pathways (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 15 candidate SNPs, 10 genes, and 31 pathways, which revealed 10 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was one wherein SNPrs40401 modulates the role of IL3 in several pathways and conditions, including the stem pathway, asthma (hsa05310), the dendritic cell pathway, and development (0.001 < p < 0.004; 0.001 < FDR < 0.033). The second strongest mechanism identified was that in which rs1048108 and rs16852600 alter the function of BARD1, which negatively regulates developmental process and modulates processes including cell development and programmed cell death (0.001 < p < 0.004; 0.001 < FDR < 0.033). The third mechanism identified was one wherein rs1939212 modulated CFL1, resulting in negative regulation of development, cell death, neural crest cell migration, and apoptosis (0.001 < p < 0.004; 0.001 < FDR < 0.033). By using the ICSNPathway to analyze neuroblastoma GWAS data, 15 candidate SNPs, 10 genes including IL3, BARD1, and CFL, and 31 pathways were identified that might contribute to the susceptibility of patients to neuroblastoma.

Associations between TRAF1-C5 gene polymorphisms and rheumatoid arthritis: a meta-analysis

OBJECTIVE

The aim of this study is to determine whether tumor necrosis factor receptor-associated factor 1-complement 5 (TRAF1-C5) polymorphisms are associated with susceptibility to rheumatoid arthritis (RA) in different populations.

METHODS

We conducted a meta-analysis of associations between the TRAF1-C5 polymorphisms and RA susceptibility.

RESULTS

A total of 24 comparative studies were included in this meta-analysis, including 22,682 patients with RA and 23,493 controls. The meta-analysis showed an association between the second allele of rs10818488 and RA in Europeans, but not in Asians (OR 1.229, 95% CI 1.094-1.381, p = 0.001; OR 1.060, 95% CI 0.930-1.335, p = 0.092). The meta-analysis also indicated an association between the second allele of rs3761847 and RA in Europeans, but not in Asians (OR 1.156, 95% CI 1.006-1.327, p = 0.041; OR 1.049, 95% CI 0.952-1.156, p = 0.333). The meta-analysis revealed an association between the second allele of the rs2900180 and rs10760130 polymorphisms and RA risk in Europeans (OR 1.224, 95% CI 1.065-1.405, p = 0.004; OR 1.072, 95% CI 1.002-1.147, p = 0.042).

CONCLUSIONS

This meta-analysis confirms that the TRAF1-C5 rs10818488, rs3761847, rs2900180 and rs10760130 polymorphisms are associated with RA susceptibility in Europeans.

Meta-analysis of differentially expressed genes in primary Sjogren's syndrome by using microarray

INTRODUCTION

The purpose of this study was to identify differentially expressed (DE) genes and biological processes associated with changes in gene expression in primary Sjogren's syndrome (pSS).

METHODS

We performed a meta-analysis using the INMEX program (integrative meta-analysis of expression data) of publicly available microarray GEO datasets of pSS. We performed Gene Ontology (GO) enrichment analyses and pathway analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG).

RESULTS

Three GEO datasets including 37 cases and 33 controls were available for the meta-analysis. We identified 179 genes across the studies which were consistently DE in pSS (146 up-regulated and 33 down-regulated). The up-regulated gene with the largest effect size (ES) (ES = -2.4228) was SELL (selectin L), whose product is required for the binding and subsequent rolling of leucocytes on endothelial cells to facilitate their migration into secondary lymphoid organs and inflammation sites. The most significant enrichment was in the immune response GO category (P = 2.52 × 10(-25)). The most significant pathway in our KEGG analysis was Epstein-Barr virus infection (P = 9.91 × 10(-06)).

CONCLUSIONS

Our meta-analysis demonstrated genes that were consistently DE and biological pathways associated with gene expression changes with pSS.

Associations between interleukin 1 polymorphisms and susceptibility to systemic lupus erythematosus: a meta-analysis

OBJECTIVE

This study determined whether interleukin 1 (IL1) polymorphisms are associated with susceptibility to systemic lupus erythematosus (SLE).

METHODS

A meta-analysis was conducted on the associations between the IL1A, IL1B, and IL1 receptor antagonist (IL1RN) polymorphisms and SLE.

RESULTS

A total of 15 studies involving 1956 SLE cases and 2347 controls were included in the meta-analysis. The meta-analysis showed an association between SLE and the IL1A -889 T allele in the overall population and Europeans (OR = 0.858, 95% CI = 0.737-0.986, p = 0.032; OR = 0.827, 95% CI = 0.687-0.994, p = 0.043). Meta-analysis of the IL1RN polymorphism revealed an association with SLE in all study subjects (OR for IL1RN*2 = 1.539, 95% CI = 1.266-1.871, p = 1.5 × 10(-2)) and in Europeans and Asians (OR = 1.483, 95% CI = 1.187-1.852, p = 0.001; OR = 1.787, 95% CI = 1.167-2.736, p=0.008). No associations were found between SLE and the IL1B -511 C/T, 3953 C/T, and IL1A +4845 G/T polymorphisms.

CONCLUSIONS

This meta-analysis suggests IL1A -889 C/T polymorphism is associated with susceptibility to SLE in Europeans, and that the IL1RN*2 allele is associated with susceptibility to SLE in Europeans and Asians.

Association between the LCE3C_LCE3B deletion polymorphism and susceptibility to psoriasis: a meta-analysis of published studies

OBJECTIVE

To determine whether a deletion comprising the LCE3C and LCE3B genes (LCE3C_LCE3B-del) confers susceptibility to psoriasis.

METHODS

A meta-analysis was conducted to assess the association between the LCE3C_LCE3B-del polymorphism and psoriasis.

RESULTS

A total of 12,196 patients with psoriasis and 13,092 controls from 19 comparative studies were included in this meta-analysis. The meta-analysis showed a significant association between psoriasis and the LCE3C_LCE3B-del allele (odds ratio [OR], 1.220; 95% confidence interval [CI], 1.152-1.292; p<1.0×10(-9)). Stratification by ethnicity indicated an association between the LCE3C_LCE3B-del allele and psoriasis in Europeans and Asians (OR, 1.213; 95% CI, 1.130-1.302; p=8.0×10(-9) and OR, 1.260; 95% CI, 1.135-1.398; p=1.4×10(-6), respectively). Analysis using a recessive model, dominant model, and homozygote contrast showed the same pattern for the LCE3C_LCE3B-del allele. The analysis performed in a single Tunisian study showed no association between the LCE3C_LCE3B-del allele and psoriasis. Meta-analysis of the LCE3C_LCE3B-del allele showed no association between psoriatic arthritis and the LCE3C_LCE3B-del polymorphism (OR, 1.087; 95% CI, 0.870-1.359; p=0.464).

CONCLUSION

Our meta-analysis demonstrates a significant association between psoriasis and the LCE3C_LCE3B-del polymorphism in Europeans and Asians, but no association with psoriatic arthritis.

Fc receptor-like 3 (FCRL3) -169 C/T polymorphism and systemic lupus erythematosus: a meta-analysis

Our aim was to determine whether the Fc receptor-like 3 (FCRL3) -169 C/T (rs7528684) polymorphism confers susceptibility to systemic lupus erythematosus (SLE). A meta-analysis was conducted on the associations between the FCRL3 -169 C/T polymorphism and the SLE. A total of nine sets of comparisons containing 3,628 patients and 6,490 controls were considered. The meta-analysis showed no association between the SLE and the FCRL3 -169 C allele in all study patients (odds ratio [OR] = 0.999, 95 % confidence interval [CI] = 0.925-1.080, p = 0.986). Stratification by ethnicity indicated no association between the C allele and the SLE in neither Europeans nor Asians (OR = 1.058, 95 % CI = 0.925-1.250, p = 0.414; OR = 0.981, 95 % CI = 0.884-1.088, p = 0.715). Furthermore, analysis using the recessive model, the dominant model, and the homozygote contrast showed the same pattern for the C allele in European and Asian groups, showing no association between the FCRL3 -169 C/T polymorphism and the SLE. Even after excluding studies whose controls were not in Hardy-Weinberg equilibrium, we found that this did not materially affect the meta-analysis results. However, the single Latin American study did show an association between the FCRL3 polymorphism and the SLE under homozygote contrast (OR for CC vs. TT = 2.689, 95 % CI = 1.152-1.277, p = 0.022). This meta-analysis of published studies including 2,544 patients and 3,913 controls demonstrates that the FCRL3 -169 C/T polymorphism does not confer susceptibility to SLE in Europeans or Asians.

Interleukin-10 promoter gene polymorphisms and susceptibility to asthma: a meta-analysis

Objective

The aim of this study was to explore whether the interleukin (IL)-10 polymorphisms and their haplotypes contribute to asthma susceptibility.

Methods

MEDLINE, EMBASE and the COCHRANE library databases were utilized to identify available articles. A meta-analysis was conducted on IL-10 -1082 G/A, -819 C/T, -592 C/A polymorphisms, and their haplotypes and asthma.

Results

Eleven studies involving 2,215 asthma patients and 2,170 controls were considered in the meta-analysis. The meta-analysis revealed no association between asthma and the IL-10 -1082 G allele [Odds ratio (OR) = 0.87, 95% Confidence interval (CI) = 0.68–1.12, p = 0.28]. However, meta-analysis of the five studies in Hardy-Weinburg equilibrium produced the relationship between the IL-10 -1082 G allele and asthma (OR = 0.71, 95% CI = 0.60–0.83, p<0.0001). Stratification by ethnicity indicated an association between the IL-10 -1082 G allele and asthma in East Asians (OR = 0.74, 95% CI = 0.57–0.96, p = 0.02), but not in West Asians. Furthermore, stratification by age indicated an association between the IL-10 -1082 G allele and asthma in adults and mixed groups (OR = 0.77, 95% CI = 0.62–0.96, p = 0.02; OR = 0.67, 95% CI = 0.49–0.92, p = 0.01). No association was found between asthma and IL-10 -819 C/T and IL-10 -592 C/A polymorphisms and their haplotypes.

Conclusion

The IL-10 -1082 G/A polymorphism confers susceptibility to asthma in East Asians and in adults. However, the IL-10 -819 C/T, -592 C/A polymorphisms and their haplotypes are not associated with asthma.

Associations between interleukin-10 polymorphisms and susceptibility to systemic lupus erythematosus: a meta-analysis

OBJECTIVE

The study determined whether interleukin-10 (IL-10) polymorphisms confer susceptibility to systemic lupus erythematosus (SLE).

METHODS

A meta-analysis was conducted on the associations between the IL-10-1082 G/A, -819 C/T, -592 C/A polymorphisms and the haplotype of the IL-10-1082 G/A, -819 C/T, -592 C/A polymorphisms and SLE.

RESULTS

A total of 19 studies involving 2828 SLE patients and 4008 controls were considered in the meta-analysis. Meta-analysis of the IL-10-1082 G/A polymorphism revealed an association between SLE and the IL-10-1082 G allele (odds ratio [OR] = 1.158, 95% confidence interval [CI] = 1.051-1.276, p = 0.003). Stratification by ethnicity indicated an association between the IL-10-1082 G allele and SLE in Europeans (OR=1.160, 95% CI = 1.039-1.296, p = 0.008). Meta-analysis stratified by ethnicity produced an association between the IL-10-819 C allele and SLE in Asians (OR = 1.308, 95% CI = 1.030-1.619, p = 0.027). Meta-analysis of the homozygous GCC/GCC haplotype failed to show a significant association with SLE in Europeans (OR = 1.223, 95% CI=0.981-1.526, p = 0.074). However, meta-analysis of the GCC haplotype revealed a significant association with RA in all study subjects (OR = 1.402, 95% CI = 1.001-1.964, p = 0.049). Stratification by ethnicity indicated an association between the GCC haplotype and SLE in Europeans (OR = 1.656, 95% CI = 1.087-2.523, p = 0.019), but not in Asians (OR = 1.100, 95% CI = 0.703-1.721, p = 0.677). Meta-analysis of homozygous ATA/ATA haplotype failed to show a significant association with SLE in overall and European groups. However, meta-analysis of the ATA haplotype revealed a significant association with SLE in all study subjects (OR = 1.516, 95% CI = 1.039-2.213, p = 0.031) and Asians (OR = 2.580, 95% CI = 2.086-3.192, p < 1 × 10(-9)), but not in Europeans (OR = 1.233, 95% CI = 0.816-1.862, p = 0.320).

CONCLUSIONS

This meta-analysis suggests that the IL-10 polymorphisms confer susceptibility to SLE in Europeans and in Asians.

Pathway analysis of genome-wide association study on asthma

OBJECTIVE

The aims of this study were to identify the candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms of asthma and to generate SNP to gene to pathway hypotheses.

METHODS

SNPs that met a threshold of p ≤ 0.001 in a genome-wide association study (GWAS) dataset of asthma, which included 292,443 SNPs in 473 asthma cases and 1892 controls, were used in the present study. Identify candidate causal SNPs and pathway (ICSNPathway) analysis was applied to this dataset.

RESULTS

ICSNPathway analysis identified four candidate causal SNPs, four genes, and 21 candidate causal pathways, which in total provided four hypothetical biologic mechanisms: (1) rs7192 (nonsynonymous coding) to HLA-DRA to 21 pathways, such as, the role of eosinophils in the chemokine network of allergy, Th1/Th2 differentiation, and asthma (nominal p ≤ 0.001, FDR p ≤ 0.01); (2) rs20541 (nonsynonymous coding) to IL13 to asthma and cytokines and inflammatory response (nominal p<0.001, FDR p ≤ 0.008); (3) rs1058808 (frameshift coding) to ERBB2 to transmembrane receptor activity (nominal p=0.001, FDR p=0.01); (4) rs17350764 (nonsynonymous coding (deleterious)) to OR52J3 to transmembrane receptor activity (nominal p=0.001, FDR p=0.01).

CONCLUSION

By applying ICSNPathway analysis to asthma GWAS data, we found four candidate causal SNPs, four genes involving HLA-DRA and IL-13, and four hypotheses, which may contribute to asthma susceptibility.