A common missense variant rs874881 of PADI4 gene and rheumatoid arthritis: Genetic association study and in-silico analysis

The peptidylarginine-deiminase 4 (PADI4) is involved in the post-translational catalytic conversion of arginine into citrulline. The autoantibodies including anti-citrullinated protein antibodies (ACPAs) produced in response to hypercitrullinated proteins are a hallmark of rheumatoid arthritis (RA) autoimmunity. Therefore, the role of a missense variant rs874881 (Gly112Ala) of PADI4 in RA susceptibility was analyzed, along with in-silico analysis of structural and functional impacts of this substitution. We did a case-control association study and in-silico analysis. For the case-control study, confirmed RA cases and healthy controls were recruited. Genotyping for rs874881 (n = 750) was performed through polymerase chain reaction-restriction fragment length polymorphism. Multivariate logistic regression analysis was employed to determine association. The in-silico analysis was carried out through HOPE, VarMap, MutationAssessor, MutPred2, SIFT, PolyPhen, CADD, REVEL and MetaLR. In the case-control study, the rs874881 exhibited a strong association with increased RA susceptibility (G vs C odds ratio = 3.85, 95 % confidence interval = 2.81-5.27). Interaction analysis revealed significant interaction of genotype with smoking and gender (p < 0.05). Significant results (p < 0.05) were also obtained in stratified analysis by presence/absence of comorbidities and radiographic damage. According to in-silico pathogenicity prediction analysis, this Gly112Ala substitution does not exert a major effect on protein structure and function including its enzymatic activity. We report a significant association of PADI4 rs874881 with overall RA susceptibility. To our knowledge, this is the first study to do the interaction and stratified analyses on the PADI4 rs874881 in RA. Similar detailed studies should also be performed in other populations.

Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes

Background

Circadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons.

Methods

Genotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects.

Results

No significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis.

Discussion

The findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex.

Association between angiotensin-converting enzyme gene insertion/deletion polymorphism and susceptibility to preterm birth: A case-control study and meta-analysis

BACKGROUND

Preterm birth is the largest contributor to newborn mortality, morbidity, and hospitalization in the first year of life worldwide. Previous studies have suggested the importance of genetic variation in the angiotensin-converting enzyme gene, including the angiotensin-converting enzyme gene insertion/deletion polymorphism, in association with preterm birth. The angiotensin-converting enzyme is a key component of the renin-angiotensin system that is involved in blood pressure homeostasis during pregnancy and also affects risk factors of preterm birth, including the regulation of fibrinolytic system, uteroplacental circulation, vascularization of the placenta, and inflammation.

OBJECTIVE

The results of previous studies investigating the association between the insertion/deletion polymorphism and susceptibility to preterm birth have been inconsistent, therefore, we have performed a case-control study and conducted a meta-analysis of related studies to clarify this association.

STUDY DESIGN

In a case-control genetic association study, performed on 217 women with a history of preterm birth and 158 women who experienced full-term pregnancy, the significances of associations between allelic and genotype frequencies and preterm birth were determined using Chi-square tests. Following the case-control study, PubMed, Scopus, Google Scholar, and HugeNavigator databases were systematically searched to identify relevant studies. Altogether, four eligible studies involving 369 cases and 559 controls were included in the meta-analysis. The strength of the association between the angiotensin-converting enzyme gene insertion/deletion polymorphism for preterm birth was estimated by odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs), using a fixed-effects model (Mantel-Haenszel method).

RESULTS

In our case-control study we did not detect a significant association of angiotensin-converting enzyme insertion/deletion alleles and genotypes with preterm birth. The results of the meta-analysis showed a significant association between the angiotensin-converting enzyme gene insertion/deletion and the risk of preterm birth under allelic, dominant, and recessive comparison genetic models (D vs. I: OR = 1.35, 95% CI = 1.11-1.65, p = 0.0033; DD + ID vs. II: OR = 1.52, 95% CI = 1.08-2.15, p = 0.0161; DD vs. ID + II: OR = 1.48, 95% CI = 1.07-2.04, p = 0.0184).

CONCLUSIONS

The present meta-analysis suggests that the insertion/deletion polymorphism of the angiotensin-converting enzyme gene in mothers might be associated with preterm birth, however, further well-designed large replication studies involving various ethnicities are needed to confirm this association.

Polymorphism of the ADRB2 Rs1042713 Gene is not Associated with Spontaneous Preterm Birth: Analyses in a Slovenian Sample and Meta Analysis

The β-2-adrenergic receptor (ADRB2) gene has an important impact on smooth muscle relaxation, including the smooth muscles of the uterus. The results of previously published studies of the association between the ADRB2 rs1042713 polymorphism and spontaneous preterm birth (SPTB) were inconsistent. We evaluated the association between ADRB2 and SPTB in a case-control association study in a Slovenian sample population and performed a meta analysis of previously published studies. No association was found between the polymorphism in the ADRB2 gene and SPTB in the Slovenian sample of 98 SPTB patients and 135 controls under dominant [χ² = 0.01, p = 0.92, odds ratio (OR) = 1.03, 95% confidence interval (95% CI) = 0.52-2.04), recessive (χ² = 0.01, p = 0.92, OR = 0.98, 95% CI = 0.57-1.70) and codominant genetic models (χ² = 0.01, p = 0.92, OR = 0.99, 95% CI = 0.59-1.68). The meta analysis of a pooled sample of 404 SPTB patients and 878 controls suggested no association of ADRB2 polymorphism and SPTB under dominant (OR = 1.12, 95% CI = 0.81-1.54) and recessive genetic models (OR = 0.84, 95% CI = 0.64-1.12). These findings suggest no association between the ADRB2 rs1042713 gene polymorphism and SPTB. Further association studies with larger sample sizes are needed.

MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients

Background/Aim

Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene.

Methods

From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance.

Results

The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis.

Conclusions

This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.

Cumulative effect of the plasma total homocysteine-related genetic variants on schizophrenia risk

Previous studies suggest that elevated total homocysteine levels and the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, which correlates with plasma total homocysteine levels, are risk factors for schizophrenia (SCZ). Recently, a large genome-wide association study (GWAS) of plasma total homocysteine levels in individuals of European ancestry identified many single-nucleotide polymorphisms (SNPs) (n=13,974). The primary purpose of this study was to examine the association between these plasma total homocysteine-related SNPs and SCZ in the Japanese population. First, we investigated associations between six SNPs and plasma total homocysteine levels in non-psychiatric subjects in the Japanese population (n=1030). Then, we evaluated the cumulative effects of three SNPs on SCZ risk by calculating the Genotype Risk Score (GRS) (1120 cases, 2643 controls). Of the six SNPs examined, we replicated similar associations with the European GWAS at four loci (CENPQ, CPS1, MTHFR, and MUT). GRS based on three SNPs (CENPQ, CPS1, and MTHFR) was significantly associated with SCZ. Our findings suggest that common polygenic variations, which are associated with the plasma total homocysteine levels, may contribute to the risk of SCZ.

Association of aldose reductase gene (AKR1B1) polymorphism with diabetic retinopathy

AIMS

Present study aimed to investigate the association of aldose reductase (AKR1B1) gene polymorphism (-106C>T; rs759853) with diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) patients from north India.

METHODS

The present case-control association study recruited 926 subjects, including 487 DR patients and 439 individuals with confirmed T2DM as controls (CDR). AKR1B1 -106C>T polymorphism analysis in these 926 subjects was performed by polymerase chain reaction and direct DNA sequence analysis. Statistical analysis was performed using SPSS package.

RESULTS

Statistically significant differences were observed between the two analyzed groups in the age of onset of diabetes (p=0.000) and duration of diabetes (p=0.000). Genotype distribution of AKR1B1 -106C>T polymorphism differed significantly between DR and CDR groups (p=0.02), however, distribution of allele frequency did not differ significantly (p=0.19). Binary logistic regression analyses showed an association of homozygous recessive TT genotype with diabetic retinopathy (OR: 1.61%, 95% CI, 1.39-2.284, p<0.01) in comparison to wild type CC genotype.

CONCLUSIONS

These findings suggest a statistically significant association of AKR1B1 -106C>T polymorphism with retinopathy in North Indian patients. To our knowledge, this is the first report of association of -106C>T polymorphism in AKR1B1 in DR patients from India.

Association analysis of PPARγ (p.Pro12Ala) polymorphism with type 2 diabetic retinopathy in patients from north India

BACKGROUND

The present study aimed to examine the association of PPARγ (p.Pro12Ala) polymorphism with type 2 diabetic retinopathy (DR) in patients from north India.

MATERIAL AND METHODS

In this case-control association study a total of 1325 subjects (717 DR patients and 608 individuals with confirmed type 2 diabetes mellitus (T2DM) without retinopathy taken as controls (CDR)), were recruited. Genotyping for PPARγ (p.Pro12Ala) polymorphism was performed by Taqman SNP Genotyping Assays using Real time PCR.

RESULTS

Statistically significant differences were observed between the two analyzed groups in the duration of diabetes and random blood glucose levels (p = 0.000 and p = 0.011, respectively). However, genotype and allele frequency distribution of PPARγ (p.Pro12Ala) polymorphism did not differ significantly between DR and CDR groups (p = 0.507 and 0.625, respectively).

CONCLUSIONS

These findings suggest no significant association of p.Pro12Ala polymorphism with retinopathy in tested type 2 diabetic retinopathy patients as compared to T2DM individuals take as controls. To our knowledge, this is the first report of association analysis of p.Pro12Ala polymorphism in PPARγ in DR patients from India.

Association of RAGE (p.Gly82Ser) and MnSOD (p.Val16Ala) polymorphisms with diabetic retinopathy in T2DM patients from north India

AIMS

The present study aimed to examine the association of RAGE (p.Gly82Ser) and MnSOD (p.Val16Ala) polymorphisms with diabetic retinopathy (DR) in north Indian T2DM patients.

METHODS

In this case-control association study, 758 T2DM patients were recruited. 446 with retinal neovascularization, microneurysms and hemorrhages were considered as cases (DR) and 312 patients with T2DM and no clinical signs of retinopathy (DNR), were recruited as controls. Genotypes for RAGE (p.Gly82Ser) and MnSOD (p.Val16Ala) polymorphisms were generated by direct sequencing of amplified products.

RESULTS

Genotype distribution of p.Gly82Ser (RAGE) and p.Val16Ala (MnSOD) polymorphisms were significantly different between DR and DNR (p<0.05) whereas distribution of allele frequency did not differ significantly (p>0.05). A significantly higher frequency of homozygous Ser82 genotype in DR patients was detected compared with DNR (2.4% vs 0.64%) for p.Gly82Ser (RAGE) polymorphism whereas there was a higher frequency of homozygous Ala16 genotype for p.Val16Ala (MnSOD) polymorphism in DR patients compared with DNR (22.6% vs 19.3%). Binary logistic analyses showed an association of homozygous recessive genotype Ser82 with DR (OR: 2.63%, 95% CI: 0.16-15.88, p<0.033) for p.Gly82Ser (RAGE) polymorphism. However, we did not find a significant association of p.Val16Ala polymorphism in MnSOD with retinopathy.

CONCLUSIONS

The findings indicate a statistically significant association of p.Gly82Ser polymorphism in RAGE with DR in T2DM patients.

Evaluation of single nucleotide polymorphisms in the miR-183-96-182 cluster in adulthood attention-deficit and hyperactivity disorder (ADHD) and substance use disorders (SUDs)

Attention deficit-hyperactivity disorder (ADHD) is a neuropsychiatric disorder characterized by inappropriate and impaired levels of hyperactivity, impulsivity and inattention. Around 75% of adults with ADHD show comorbidity with other psychiatric disorders such as disruptive behavior disorders or substance use disorders (SUDs). Recently, there has been growing interest in studying the role of microRNAs (miRNAs) in the susceptibility to complex disorders. Interestingly, converging evidence suggests that single nucleotide polymorphisms (SNPs) within miRNAs or miRNA target sites may modulate the miRNA-mediated regulation of gene expression through the alteration of the miRNA maturation, structure or expression pattern as well as the silencing mechanisms of target genes. Genetic studies and animal models support the involvement of the serotonin receptor (HTR1B) in ADHD. We evaluated the contribution of one SNP in the miR-96 target site at HTR1B and eight tagSNPs within the genomic region containing this miRNA in 695 adults with ADHD (266 and 396 subjects with and without comorbid SUD, respectively), 403 subjects with SUD without life-time diagnosis of ADHD and 485 sex-matched controls from Spain. Single and multiple marker analyses revealed association between two SNPs located at the 3' region of miR-96 (rs2402959 and rs6965643) and ADHD without SUD. Our results provide preliminary evidence for the contribution of two sequence variants at the miR-183-96-182 cluster to ADHD without comorbid SUD, and emphasize the need to take comorbidities into account in genetic studies to minimize the effect of heterogeneity and to clarify these complex phenotypes.