Role of rs2366152 single-nucleotide variant located in the long noncoding RNA HOTAIR gene in the cervical cancer susceptibility in a Polish population

Previous studies have demonstrated an association of the NC_000012.12:g.53962605A > G, (rs2366152) single-nucleotide variant (SNV) situated in the long noncoding homeobox transcript antisense intergenic RNA (HOTAIR) gene with HPV16-related cervical cancer pathogenesis. However, little is known about the role of rs2366152 in cervical cancer progression and how oral birth control pills use, parity, menopausal status, and cigarette smoking influence the role of rs2366152 in cervical carcinogenesis. HRM analysis was used to determine the rs2366152 SNV prevalence in patients with cervical squamous cell carcinoma (SCC) (n = 470) and control group (n = 499) in a Polish Caucasian population. Logistic regression analyses were adjusted for age, using birth control pills, parity, menopausal status, and cigarette smoking. Our genetic studies revealed that the G/A vs. A/A (p = 0.031, p = 0.002) and G/A + G/G vs. A/A (p = 0.035, p = 0.003) genotypes of rs2366152 SNV were significantly related to the grade of differentiation G3 and tumor stage III, respectively. Moreover, cervical cancer risk increased among patients with rs2366152 SNV who smoked cigarettes and used birth control pills. We conclude that rs2366152 may promote the invasion and rapid growth of cervical SCC. Moreover, rs2366152 with cigarette smoking and using birth control pills can also be a risk factor for cervical cancerogenesis.

Dissecting the genetic heterogeneity of gastric cancer

BACKGROUND

Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture.

METHODS

We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO.

FINDINGS

Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level.

INTERPRETATION

Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO.

FUNDING

German Research Foundation (DFG).

Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing

Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.

Associations of ANGPTL6, DOCK6, FABP1, and PCSK9 single-nucleotide variants with hypercholesterolemia in the Polish population: a cross-sectional study

INTRODUCTION

Hypercholesterolemia is a chronic noncommunicable disease predisposing to cardiovascular diseases. Genome‑wide association studies have shown that more than 500 common nucleotide variants are associated with dyslipidemia.

OBJECTIVES

We evaluated associations between selected nucleotide variants in ANGPTL6, DOCK6, FABP1, and PCSK9 genes and hypercholesterolemia in the Polish adult population sample.

PATIENTS AND METHODS

The study included 109 patients with hypercholesterolemia and 251 individuals with no diagnosed lipid disorder. Genotyping of ANGPTL6 rs8112063, DOCK6 rs737337 and rs17699089, FABP1 rs2241883 and rs2919872, and PCSK9 rs562556 and rs11206510 was carried out using highresolution melting curve analysis. Serum concentrations of FABP1, PCSK9, ANGPTL6, and ANGPTL8 were determined in 51 individuals by enzyme‑linked immunosorbent assay.

RESULTS

Carriers of the FABP1 rs2919872 CC genotype were over 2.5‑fold less likely to be diagnosed with hypercholesterolemia than carriers of the T allele (odds ratio [OR], 0.386; 95% CI, 0.203-0.735; P = 0.003; Pcorr = 0.006). There were no associations between rs2919872 and serum lipid concentrations. Carriers of the ANGPTL6 rs8112063 C allele had an almost 2‑fold higher risk of developing hypercholesterolemia than carriers of the T allele (OR, 1.820; 95% CI, 1.053-3.144; P = 0.03; Pcorr = 0.046). Moreover, the carriers of the ANGPTL6 rs8112063 C allele had higher serum concentrations of high-density lipoprotein cholesterol than those with TT genotype (P = 0.009). There were no significant associations between the other tested variants and hypercholesterolemia.

CONCLUSIONS

FABP1 rs2919872 and ANGPTL6 rs8112063 are associated with a risk of hypercholesterolemia in the Polish population.

Identification of a new familial case of 3q29 deletion syndrome associated with cleft lip and palate via whole-exome sequencing

Many unbalanced large copy number variants reviewed in the paper are associated with syndromic orofacial clefts, including a 1.6 Mb deletion on chromosome 3q29. The current report presents a new family with this recurrent deletion identified via whole-exome sequencing and confirmed by array comparative genomic hybridization. The proband exhibited a more severe clinical phenotype than his affected mother, comprising right-sided cleft lip/alveolus and cleft palate, advanced dental caries, heart defect, hypospadias, psychomotor, and speech delay, and an intellectual disability. Data analysis from the 3q29 registry revealed that the 3q29 deletion increases the risk of clefting by nearly 30-fold. No additional rare and pathogenic nucleotide variants were identified that could explain the clefting phenotype and observed intrafamilial phenotypic heterogeneity. These data suggest that the 3q29 deletion may be the primary risk factor for clefting, with additional genomic variants located outside the coding sequences, methylation changes, or environmental exposure serving as modifiers of this risk. Additional studies, including whole-genome sequencing or methylation analyses, should be performed to identify genetic factors underlying the phenotypic variation associated with the recurrent 3q29 deletion.

Vascular Ehlers-Danlos Syndrome: Pathological Variants, Recent Discoveries, and Theoretical Approaches

Vascular Ehlers-Danlos syndrome (vEDS) is a rare autosomal dominant genetic disorder. It is the most fatal among all types of EDS. In addition to typical EDS characteristics, vEDS patients are at risk of blood vessel rupture due to possession of pathogenic variants of the COL3A1 gene, which encodes type III collagen. Type III collagen is a major component of humans' vascular walls. The management of this disease is possible; however, there is no cure as of present. Recently, discoveries with potential impact on the management of vEDS have been elucidated. Mice with vEDS traits treated with a beta-blocker celiprolol showed significant improvements in their thoracic aorta biomechanical strength. Moreover, it has been demonstrated that the specifically designed small interference RNAs (siRNA) can effectively silence the pathogenic variant allele. To enhance the normal allele expression, an intracellularly expressed lysyl oxidase is shown to regulate the transcription rate of the COL3A1 promoter. Similarly, an embryonic homeobox transcription factor Nanog upregulates the wild-type COL3A1 expression through activation of the transforming growth factor-beta pathway, which increases type III collagen synthesis. Despite numerous advancements, more studies are to be performed to incorporate these discoveries into clinical settings, and eventually, more personalized treatments can be created.

The Link between Three Single Nucleotide Variants of the GIPR Gene and Metabolic Health

Single nucleotide variants (SNVs) of the GIPR gene have been associated with BMI and type 2 diabetes (T2D), suggesting the role of the variation in this gene in metabolic health. To increase our understanding of this relationship, we investigated the association of three GIPR SNVs, rs11672660, rs2334255 and rs10423928, with anthropometric measurements, selected metabolic parameters, and the risk of excessive body mass and metabolic syndrome (MS) in the Polish population. Normal-weight subjects (n = 340, control group) and subjects with excessive body mass (n = 600, study group) participated in this study. For all participants, anthropometric measurements and metabolic parameters were collected, and genotyping was performed using the high-resolution melting curve analysis. We did not find a significant association between rs11672660, rs2334255 and rs10423928 variants with the risk of being overweight. Differences in metabolic and anthropometric parameters were found for investigated subgroups. An association between rs11672660 and rs10423928 with MS was identified. Heterozygous CT genotype of rs11672660 and AT genotype of rs10423928 were significantly more frequent in the group with MS (OR = 1.38, 95%CI: 1.03–1.85; p = 0.0304 and OR = 1.4, 95%CI: 1.05–1.87; p = 0.0222, respectively). Moreover, TT genotype of rs10423928 was less frequent in the MS group (OR = 0.72, 95%CI: 0.54–0.95; p = 0.0221).

Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing

For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.

Publication ethics of human studies in the light of the Declaration of Helsinki – a mini-review

The Declaration of Helsinki is a set of ethical principles to be followed by scientists involved in medical research with humans or human cells and tissues. This Declaration defines how scientific research should be planned, carried out, documented, analysed, and published. We summarise and discuss some ethical issues related to publishing original articles, including clinical trials, review papers, and case reports based on the seventh revision of the Declaration of Helsinki. The principles of the Declaration of Helsinki refer most strongly to the publication of medical research results, in particular clinical trials, as original articles. Such papers must meet several ethical requirements, especially the study protocol transparency and the presentation of the results. For case reports, the bioethical aspects related to their publication are twofold - they must include informed and voluntary consent and the confidentiality of study participants. The review papers are of the least bioethical concern. However, whether patients' agreements with specific studies are valid if the data are used in meta-analyses is uncertain. Adherence to ethical policies and standards helps to ensure the highest possible quality of scientific publications. Responsibility for compliance with the Declaration of Helsinki lies not only with the authors preparing their manuscripts but also with the editorial board and reviewers, who must evaluate the ethical soundness of the submitted papers. The additional guidelines for the different types of studies facilitate the implementation of the Declaration principles.

Association of GLP1R variants rs2268641 and rs6923761 with obesity and other metabolic parameters in a Polish cohort

INTRODUCTION

Obesity is a complex disease associated with excessive fat accumulation and numerous metabolic complications. So far, many factors leading to the development of this disorder have been identified, including genetic susceptibility. Various studies linked GLP1R variants with anthropometric and metabolic parameters, suggesting the role of the variation in this gene in metabolic health.

OBJECTIVE

The aim of this study is to investigate the association of two single nucleotide variants of GLP1R gene, rs2268641 and rs6923761, with excessive weight, metabolic syndrome, anthropometric measurements and selected metabolic parameters.

METHODS

Normal-weight subjects (n= 340, control group) and subjects with excessive body mass (n = 600, study group) participated in this study. For all participants, anthropometric measurements and metabolic parameters were collected, and genotyping of the two single nucleotide variants of GLP1R gene, rs2268641 and rs6923761, was performed using the high-resolution melting curve analysis.

RESULTS

Significant differences in the genotype distribution of rs2268641 were found, where homozygous TT genotype was significantly less frequent in the study group with excessive body mass (OR=0.66; p=0.0298). For rs6923761, A allele and homozygous AA genotype were significantly more frequent in the study group with excessive weight than in the control group (OR=1.27; p=0.0239 and OR=1.69; p=0.0205, respectively). The association of studied variants with metabolic parameters was found for rs6923761. For this variant, AA carriers had higher body mass in comparison to GG carriers (p=0.0246), and AA carriers had higher glucose concentration in comparison to AG carriers (p=0.0498). We did not find an association of rs2268641 and rs6923761 with metabolic syndrome.

CONCLUSION

In our study, AA carriers of rs6923761 had higher risk of excessive body mass, whereas TT carriers of rs2268641 had lower risk of being overweight. Moreover, homozygous carriers of the minor allele of rs6923761 had higher glucose concentration in comparison to heterozygous subjects. None of the studied variants were associated with metabolic syndrome in the studied population.

Alpha-1 Antitrypsin Z Variant (AAT PI*Z) as a Risk Factor for Intrahepatic Cholestasis of Pregnancy

Background: Intrahepatic cholestasis of pregnancy (ICP; prevalence 0.2–15.6%) is the most common pregnancy-related liver disorder. It may have serious consequences for a pregnancy, including increased risk of preterm delivery, meconium staining of amniotic fluid, fetal bradycardia, distress, and fetal demise. In cases of high bile acids (>100μmol/L), patients have 10-fold increase in the risk of stillbirth. Biophysical methods of fetal monitoring, such as cardiotocography, ultrasonography, or Doppler have been proven unreliable for risk prediction in the course of intrahepatic cholestasis. Therefore, we believe extensive research for more specific, especially early, markers should be carried out. By analogy with cholestasis in children with inherited alpha-1 antitrypsin deficiency (AATD), we hypothesized the SERPINA1 Z pathogenic variant might be related to a higher risk of cholestasis in pregnancy. This study aimed to investigate the most common AATD variants (Z and S SERPINA1 alleles) in a group of cholestatic pregnant women.

Results: The Z carrier frequency was calculated to be 6.8%, which is much higher compared to the general population [2.3%; the Chi-squared test with Yates correction is 6.8774 (p=0.008)].

Conclusion: Increased prevalence of SERPINA1 PI*Z variant in a group of women with intrahepatic cholestasis may suggest a possible genetic origin of a higher risk of intrahepatic cholestasis in pregnancy.

MiRNA-149 as a Candidate for Facial Clefting and Neural Crest Cell Migration

Nonsyndromic cleft lip with or without palate (nsCL/P) ranks among the most common human birth defects and has a multifactorial etiology. Human neural crest cells (hNCC) make a substantial contribution to the formation of facial bone and cartilage and are a key cell type in terms of nsCL/P etiology. Based on increasing evidence for the role of noncoding regulatory mechanisms in nsCL/P, we investigated the role of hNCC-expressed microRNAs (miRNA) in cleft development. First, we conducted a systematic analysis of miRNAs expressed in human-induced pluripotent stem cell-derived hNCC using Affymetrix microarrays on cell lines established from 4 unaffected donors. These analyses identified 152 candidate miRNAs. Based on the hypothesis that candidate miRNA loci harbor genetic variation associated with nsCL/P risk, the genomic locations of these candidates were cross-referenced with data from a previous genome-wide association study of nsCL/P. Associated variants were reanalyzed in independent nsCL/P study populations. Jointly, the results suggest that miR-149 is implicated in nsCL/P etiology. Second, functional follow-up included in vitro overexpression and inhibition of miR-149 in hNCC and subsequent analyses at the molecular and phenotypic level. Using 3'RNA-Seq, we identified 604 differentially expressed (DE) genes in hNCC overexpressing miR-149 compared with untreated cells. These included TLR4 and JUNB, which are established targets of miR-149, and NOG, BMP4, and PAX6, which are reported nsCL/P candidate genes. Pathway analyses revealed that DE genes were enriched in pathways including regulation of cartilage development and NCC differentiation. At the cellular level, distinct hNCC migration patterns were observed in response to miR-149 overexpression. Our data suggest that miR-149 is involved in the etiology of nsCL/P via its role in hNCC migration.

Paraoxonase 1 gene (PON1) variants concerning hepatitis C virus (HCV) spontaneous clearance in hemodialysis individuals: a case-control study

BACKGROUND

To explore associations between PON1 rs854560, rs662, 705,379, HCV clearance, and interactions between tested PON1 single nucleotide variants (SNVs) and interferon-λ4 gene (IFNL4) rs368234815 variant in hemodialyzed individuals.

METHODS

The study included 83 HD individuals who spontaneously resolved HCV infection (all had known IFNL4 rs368234815 variant) and 104 individuals with persistently positive blood tests for HCV RNA (102 were IFNL4 rs368234815 variant successfully genotyped). We genotyped PON1 by high-resolution melt analysis (rs662) or predesigned TaqMan SNV Genotyping Assay (rs854560, rs705379). We used a logistic regression model to assess the association between genetic data and HCV outcome while adjusting for clinical confounding variables. Epistatic interactions between tested PON1 SNVs and IFNL4 rs368234815 were analyzed by the multifactor dimensionality reduction method.

RESULTS

In the recessive inheritance model, PON1 rs662 GG (OR 9.94, 95% CI 1.20-82.7, P = 0.022) and rs854560 TT (OR 4.31, 95% CI 1.62-11.5, P = 0.003) genotypes were associated with a higher probability for HCV clearance. The haplotype composed of rs662A_rs854560A_rs705379 was not associated with spontaneous HCV clearance. The IFNL4 rs368234815 TT/TT variant was equally distributed among individuals bearing different PON1 SNVs. The epistatic gene-gene analysis did not reveal the interaction between tested PON1 SNVs and IFNL4 rs368234815 (P = 0.094). Regression model, including the PON1 rs662 GG genotype, the PON1 rs854560 genotype, the IFNL4 rs368234815 TT/TT genotype, age at RRT onset, RRT duration, and chronic glomerulonephritis as possible explanatory variables for spontaneous HCV clearance, showed that significant predictors of spontaneous HCV clearance were the IFNL4 rs368234815 TT/TT genotype (OR 2.607, 95% CI 1.298-5.235, P = 0.007), PON1 rs854560 TT (OR 6.208, 1.962-19.644, P = 0.002), PON1 rs662 GG (OR 10.762, 1.222-94.796, P = 0.032), and RRT duration (OR 0.930, 95% CI 0.879-0.984, P = 0.011).

CONCLUSION

In HD individuals, PON1 rs662 GG and rs854560 TT are associated with a higher frequency of spontaneous HCV clearance.

The Prevalence and Morphology of Supernumerary Teeth in Children With Nonsyndromic Cleft Lip and Palate

INTRODUCTION

Cleft lip with or without cleft palate (CL/P) is congenital deformity associated with hyperdontia.

OBJECTIVE

To determine the prevalence and characteristics of supernumerary teeth in patients with CL/P.

DESIGN

Retrospective descriptive and correlation clinical study.

PATIENTS

One hundred thirteen children with cleft (age ranged 9.3-19.2; 67 males and 46 females) treated in Clinic of Congenital Facial Deformities Medical University of Lublin were included in the study.

METHODS

Records evaluation was conducted regarding age, gender, cleft type (Q36, Q37-International Classification of Diseases 10th revision), cleft side, and incidence of supernumeraries. In all supernumerary teeth, size, shape, and developmental degree were analyzed and correlation between the incidence of hyperdontia with different variables was checked. Correlations were detected using chi-square and the Yates correction.

RESULTS

The majority of the examined group were males-59.29% with Q37 (67.26%) and the cleft on the left side (62.83%). Hyperdontia was noted in 26.55%. Only upper lateral incisors were affected. They usually had atypical shape (56.67%), reduced size (83.33%), and delayed development (56.67%).

CONCLUSIONS

The prevalence of supernumerary permanent teeth in patients with cleft was higher than in the general population. Anomaly was more frequent in male patients and occurred mainly on the cleft side. The severity of the cleft did not influenced the frequency of supernumerary teeth, their shape, size, and developmental degree. Supernumerary teeth were characterized by reduced crown size, abnormal structure, incorrect inclination, and delayed development phase.

MO838PARAOXONASE 1 GENE POLYMORPHISMS CONCERNING CARDIOVASCULAR MORTALITY IN CIGARETTE SMOKERS AND NON-SMOKERS TREATED WITH HEMODIALYSIS

Background and Aims

Paraoxonase 1 gene (PON1) single nucleotide variants (SNVs), known as associated with lipoprotein peroxidation, are related to atherosclerotic diseases, including coronary heart disease (CHD). Cigarette smoking, causing increased susceptibility to lipoprotein oxidation, contributes to cardiovascular events, and its effects are linked with PON1 SNVs. We investigated the association of PON1 rs705379 (-108C>T), rs854560 (163A>T), and rs662 (575A>G) SNVs with cardiovascular mortality in maintenance hemodialysis (HD) patients concerning cigarette smoking status.

Method

In the HD group, there were 206 smokers and 659 non-smokers. Among all patients who died (n = 542), cardiovascular mortality was similar in smokers and non-smokers (59.0% vs. 59.3%, respectively). Deceased smokers were burning 20 (5 - 25) cigarettes daily. We obtained PON1 polymorphisms by HRM analysis (rs662) or predesigned TaqMan SNV Genotyping Assay (rs854560, rs705379). All cardiovascular, cardiac, CHD- and non-CHD-related deaths were analyzed in smokers and non-smokers concerning PON1 SNVs and DM status. The Kaplan-Meier method with the log-rank test and the Cox regression analyses were applied for the estimation of survival. If computed P-values were below 0.05, the adjustment for sex, age, and HDL-cholesterol was applied. We have shown only adjusted P-values for survival analyses.

Results

HD cigarette smokers, who died from cardiovascular diseases, were younger (63.5, 31.1 – 86.3 vs. 74.0, 26.8 – 95.9 years, P = 2.992e-10), predominantly men (70, 85.3% vs. 91, 38.1%, P = 1.5e-13), had more atherogenic serum lipid profile (atherogenic index estimated as the TG/HDL cholesterol ratio 4.90, 0.72 – 25.6 vs. 3.79, 0.66 – 49.7, P = 0.003; HDL-cholesterol level 34.8, 17.3 – 103 vs. 40.0, 7 – 103 mg/dL, P = 0.0004; TG 167.0, 48.8 – 652 vs. 149.8, 40.0 – 856 mg/dL, P = 0.034), but similar RRT duration compared to deceased HD non-smokers. Cigarette smoking status did not influence cardiovascular mortality either in DM or non-DM group. DM smokers showed similar cardiovascular mortality to non-DM smokers, but among HD non-smokers, DM patients demonstrated higher cardiovascular mortality than non-DM subjects (P = 0.029). Among all smokers, the rs705379 TT genotype was associated with all cardiovascular (P = 0.028), all cardiac (P = 0.046), and cardiac non-related with CHD (P = 0.001) mortality. The rs705379 TT genotype smokers, who died from cardiac reasons, showed a higher frequency of myocardial infarction than CC+CT bearers (66.7% vs. 29.2%, P = 0.047). Non-DM smokers showed similar qualitative significance to all smokers concerning all cardiovascular, all cardiac, and cardiac non-related with CHD death rates (P-values 0.011, 0.044, and 0.009, respectively). In DM non-smokers, the rs705379 T allele correlated with CHD related deaths (P = 0.020). The rs854560 T allele, compared to the AA genotype, was associated with lower cardiovascular mortality in non-DM smokers (P = 0.008). The rs854560 TT genotype showed a negative correlation with cardiac death non-related to CHD in all non-smokers (P = 0.079). In DM smokers, the rs662 G allele was associated with a higher risk of cardiac mortality (P = 0.005). In all non-smokers and non-DM non-smokers, the rs662 G allele correlated with cardiovascular deaths (P = 0.020 and P = 0.018, respectively).

Conclusion

The variant alleles of PON1 rs705379 (T) and rs662 (G) are associated with cardiac mortality in HD patients. The rs854560 variant allele (T) possessors present better cardiovascular survival than the AA genotype subjects. Cardiovascular mortality is not merely related to polymorphic variants known as associated with lower serum activity or concentration of paraoxonase, a PON1 protein product. Assessing PON1 SNVs enables the prediction of cardiovascular mortality risk in HD smokers and non-smokers and may help select patients for advanced prevention against cardiovascular diseases.

Paraoxonase 1 concerning dyslipidaemia, cardiovascular diseases, and mortality in haemodialysis patients

Paraoxonase 1 (PON1) is known for preventing atherosclerosis through lipid-modifying features, antioxidant activity, anti-inflammatory, anti-apoptosis, anti-thrombosis, and anti-adhesion properties. Uremic patients requiring haemodialysis (HD) are especially prone to atherosclerosis and its complications. We analysed the PON1 gene (PON1) polymorphisms and serum PON1 (paraoxonase) activity concerning dyslipidaemia and related cardiovascular diseases and mortality to show how they associate under uremic conditions modified by maintenance HD treatment. The rs662 AA + AG (OR 1.76, 95%CI 1.10-2.80, P = 0.018), rs854560 TT (OR 1.48, 95%CI 1.04-2.11, P = 0.031), and rs854560 AT + TT (OR 1.28, 95%CI 1.01-1.63, P = 0.040) contributed to the prevalence of atherogenic dyslipidaemia diagnosed by the triglyceride (TG)/HDL-cholesterol ratio ≥ 3.8. The normalized serum PON1 activity positively correlated with atherogenic dyslipidaemia (ẞ 0.67 ± 0.25, P = 0.008). The PON1 rs854560 allele T was involved in the higher prevalence of ischemic cerebral stroke (OR 1.38, 1.02-1.85, P = 0.034). The PON1 rs705379 TT genotype contributed to cardiovascular (HR 1.27, 95% CI 1.03-1.57, P = 0.025) and cardiac (HR 1.34, 95% CI 1.05-1.71, P = 0.018) mortality. All P-values were obtained in multiple regression analyses, including clinical variables. Multifaceted associations of PON1 with dyslipidaemia, ischemic cerebral stroke, and cardiovascular mortality in HD patients provide arguments for the consideration of PON1 and its protein product as therapeutic targets in the prevention of atherosclerosis and its complications in uremic patients.

Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study

BACKGROUND

In non-uremic subjects, IFNL4 rs368234815 predicts HCV clearance. We investigated whether rs368234815 is associated with spontaneous HCV clearance in haemodialysis patients and whether it is a stronger predictor of HCV resolution than the IFNL polymorphisms already associated with HCV clearance in dialysis subjects. We also evaluated an association of rs368234815 with patients` survival and alterations in transcription factor binding sites (TFBS) caused by IFNL polymorphisms.

METHODS

Among 161 haemodialysis patients with positive anti-HCV antibodies, 68 (42.2%) spontaneously resolved HCV infection, whereas 93 remained HCV RNA positive. Patients were tested for near IFNL3 rs12980275, IFNL3 rs4803217, IFNL4 rs12979860, IFNL4 rs368234815, and near IFNL4 rs8099917. IFNL4 rs368234815 polymorphism (TT/TT, ΔG/TT, ΔG/ΔG) was genotyped by restriction fragment length polymorphism analysis; other IFNL polymorphisms - by high resolution melting curve analysis. We used the Kaplan-Meier method with the log-rank test for survival analysis. In silico analysis included the use of ENCODE TFBS ChIP-seq data, HOCOMOCO, JASPAR CORE, and CIS-BP databases, and FIMO software.

RESULTS

The probability (OR, 95%CI, P) of spontaneous HCV clearance for rs368234815 TT/TT patients was higher than for the ΔG allele carriers (2.63, 1.38-5.04, 0.003). This probability for other major homozygotes varied between 2.80, 1.45-5.43, 0.002 for rs12980275 and 2.44, 1.27-4.69, 0.007 for rs12979860. In the additive model, rs368234815 TT/TT was the strongest predictor of HCV clearance (6.38, 1.69-24.2, 0.003). Survival analysis suggested an association of the ΔG allele with mortality due to neoplasms (log-rank P = 0.005). The rs368234815 ∆G allele caused TFBS removal for PLAGL1.

CONCLUSIONS

In haemodialysis patients, the association of rs368234815 with the spontaneous HCV clearance is better than that documented for other IFNL3/IFNL4 polymorphisms only in the additive mode of inheritance. However, identifying the homozygosity in the variant ∆G allele of rs368234815 means a more potent prediction of persistent HCV infection in haemodialysis subjects that we observe in the case of the variant homozygosity of other tested IFNL3/IFNL4 polymorphisms. Removal of PLAGL1 TFBS in subjects harbouring the rs368234815 ∆G allele may contribute to cancer susceptibility. The association of rs368234815 with cancer-related mortality needs further studies in HCV-exposed subjects.

Paraoxonase 1 gene polymorphisms concerning non-insulin-dependent diabetes mellitus nephropathy in hemodialysis patients

AIMS

Data on involvement of paraoxonase 1 gene (PON1) in non-insulin-dependent diabetes mellitus (NIDDM) nephropathy are scarce. We investigated PON1 polymorphisms concerning end-stage NIDDM nephropathy and atherosclerotic complications in NIDDM nephropathy patients treated with hemodialysis (HD).

METHODS

In NIDDM nephropathy (n = 402) and non-diabetic (n = 998) HD subjects, we obtained PON1 polymorphisms by HRM analysis (rs662) or predesigned TaqMan SNV Genotyping Assay (rs854560, rs705379).

RESULTS

Only PON1 rs705379 was associated with end-stage NIDDM nephropathy in the recessive (OR 1.451, 95% CI 1.104-1.906, P = 0.009) and additive (OR 1.398, 95%CI 1.009-1.936, P = 0.046) inheritance modes. NIDDM nephropathy patients bearing the rs854560 T allele were at higher risk for ischemic cerebral stroke (OR 2.087, 95%CI 1.145-3.801, P = 0.016). In non-diabetic patients but not NIDDM nephropathy subjects, atherogenic dyslipidemia corresponded with PON1 rs662 A allele and PON1 rs854560 TT homozygosity.

CONCLUSIONS

In HD patients, NIDDM nephropathy correlates with the TT genotype of PON1 rs705379. The rs854560 T allele indicates a higher risk for atherosclerotic diseases in NIDDM nephropathy subjects. The T alleles of both PON1 SNVs are known as low expression variants downregulated serum PON1 activity. An increase of diminished PON1 activity may be a target in the prevention of NIDDM nephropathy and NIDDM atherosclerotic complications.

Role of ARHGAP29 nucleotide variants in the etiology of non-syndromic cleft lip with or without cleft palate

Aim. Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common birth defect of complex and heterogeneous aetiology. Genome-wide association studies (GWAS) of nsCL/P have identified an association for the 1p22.1 chromosomal region, in which ARHGAP29 was suggested as a candidate gene. Thus, the current study aimed to determine the contribution of the common and rare ARHGAP29 nucleotide variants to the risk of nsCL/P in the Polish population. Material and Methods. In total,197 common nucleotide variants (SNVs) and 22 missense variants located within the ARHGAP29 locus at chromosome 1p22.1 were genotyped by SNV microarray. The study was conducted in 269 individuals with nsCL/P and 569 healthy individuals. Results. Statistical analysis revealed that 31 common nucleotide variants located at the ARHGAP29 locus were significantly associated with the increased risk of nsCL/P. The strongest individual SNV was rs2391467 with a p-value = 2.49E-06 (OR = 1.64, 95%CI: 1.34–2.02). Besides, one potentially deleterious missense variant (rs140877322, p. Arg348Leu) was identified in a single patient with nsCLP. Conclusion. These findings confirm ARHGAP29 as a strong candidate gene for nsCL/P, with both common and rare nucleotide variants of this gene involved in the aetiology of nsCL/P in the Polish population.

P1275PARAOXONASE 1 (PON1) GENE POLYMORPHISMS, PON1 EXPRESSION IN PBMCS, AND SERUM PON1 ACTIVITY CONCERNING DYSLIPIDEMIA AND RELATED COMORBIDITIES IN HEMODIALYSIS (HD) PATIENTS

Background and Aims

PON1 may prevent atherosclerosis influencing lipid metabolism and exerting antioxidant and anti-inflammatory activities. We focused on serum PON1 activity in HD patients concerning dyslipidemia, coronary heart disease (CHD), myocardial infarction (MI), and cerebral stroke (CS). PON1 activity was related to PON1 polymorphisms, PON1 expression in PBMCs, and demographic, clinical, and laboratory data.

Method

In 93 HD patients (men 55, age 66.7, 18.3 – 86.2 years, renal replacement therapy duration 3.9, 0.2 – 22.3 years, CHD 25, MI 15, CS 9), dyslipidemia was diagnosed by K/DOQI guidelines. The TG/HDL-cholesterol ratio of ≥3.8 indicated atherogenic dyslipidemia. Standard diagnostic rules were applied for CHD, MI, and CS recognition. PON1 activity was measured in serum using an automated PON1 assay kit. PON1 polymorphisms were genotyped by high-resolution melting curve analysis (rs662) or using predesigned TaqMan SNV Genotyping Assay (rs854560 and rs705379). In 46 subjects, the relative PON1 transcript level was determined in PBMCs using reverse transcription-quantitative polymerase chain reaction analysis.

Results

In univariate analyses, the lower serum PON1 activity the higher frequency of mixed dyslipidemia (LDL ≥ 100 mg/dL, TG ≥ 200 mg/dL, non-HDL ≥ 130 mg/dl; β ± SE: -21.4 ± 10.0, P = 0.035) and the higher serum TG levels (β ± SE: -1.06 ± 0.49, P = 0.034). Normalized serum PON1 activity (the PON1/HDL ratio) correlated positively with male sex (β ± SE: 0.56 ± 0.25, P = 0.029), atherogenic dyslipidemia (β ± SE: 0.67 ± 0.25, P = 0.008), and cigarette smoking (β ± SE: 0.86 ± 0.42, P = 0.043). After adjustment for gender, cigarette smoking, urine output, living in rural area, and serum phosphorus, significance was maintained between normalized serum PON1 activity and atherogenic dyslipidemia (β ± SE: 0.54 ± 0.24, P = 0.028), male sex (β ± SE: 0.51 ± 0.24, P = 0.037) and cigarette smoking (β ± SE: 0.93±0.41, P = 0.024) as well as revealed for living in rural area (β ± SE: 0.55 ± 0.26, P = 0.039), urine output (β ± SE: -0.14 ± 0.07, P = 0.046), and zinc supplementation (β ± SE: 1.5 ± 0.67, P = 0.029). PON1 activity (101, 27.7 – 213 U/L) and normalized PON1 activity (2.27, 0.57 – 7.10) were not influenced by PON1 polymorphisms and did not yield differences in patients stratified by CHD, MI, CS, and dyslipidemic patterns except atherogenic dyslipidemia. The latter relationship was caused by a correlation between serum PON1 activity and TG (r = -0.220, P = 0.034). PON1 transcript was detected in PBMCs of 9 subjects. They showed a higher prevalence of the AG + GG genotypes of PON1 rs662 (77.8% vs. 34.3%, P = 0.027), a higher serum CRP level (7.8, 2.8 – 46.8 mg/L vs. 3.9, 0.4 – 23.0 mg/L, P = 0.042), and a lower albumin (3.9, 2.6 – 4.5 g/dL vs. 4.2, 3.2 – 4.6 g/dL, P = 0.025) compared with the results of 37 subjects without the PON1 expression. The relative PON1 transcript level did not correlate with serum PON1 activity (r = 0.042, P = 0.915).

Conclusion

In HD patients, serum PON1 activity is associated with atherogenic dyslipidemia but not with already developed CHD and history of MI or CS, even after adjustment for several confounding variables. Illegitimate PON1 transcription occurs in uremic PBMCs at very low level and is influenced by PON1 rs662 polymorphism and upregulated by inflammation. PON1 could be considered as a therapeutic target in prevention of atherosclerosis and its complications in uremic patients.

Polymorphism rs368234815 of interferon-λ4 gene and generation of antibodies to hepatitis B virus surface antigen in extracorporeal dialysis patients

Background: The rs368234815 polymorphism of interferon-λ4 (IFN-λ4) gene (IFNL4) is involved in HBV surface antigen (HBsAg) clearance in non-uremic subjects. The rs368234815 ΔG/ΔG genotype can express IFN-λ4 while the TT/TT genotype cannot. We investigated whether rs368234815 is associated with the development of HBsAg antibodies (anti-HBs) in response to vaccination or infection, and HBsAg loss after infection in uremic patients on extracorporeal dialysis.Research design and methods: Dialyzed patients (n = 467) were genotyped for rs368234815 by the polymerase chain reaction-restriction fragment length polymorphism method. Non-responders to HBV vaccination we compared with responders. HBsAg positive patients not able to develop anti-HBs we compared with individuals who eliminated HBsAg and generated anti-HBs. HBsAg positive patients we compared with subjects who eliminated HBsAg.Results: The ∆G allele was associated with the 1.6-fold higher risk not to develop anti-HBs titers ≥10 IU/L in response to HBV vaccination and infection (P = 0.016 adjusted for gender, age at dialysis onset, HCV RNA). The ∆G/∆G genotype indicated a higher probability of non-responsiveness to HBV vaccination than the TT/TT genotype (OR 2.64, 95%CI 1.01-6.87, adjusted P = 0.048).Conclusions: In extracorporeal dialysis patients, IFNL4 rs368234815 is associated with the capacity to produce protective anti-HBs titers in response to HBV vaccination.

Association of ABCB4 and ABCB11 nucleotide variants with intrahepatic cholestasis of pregnancy

Background: Intrahepatic cholestasis of pregnancy (ICP) is the most common liver disorder during gestation. The exact pathogenesis of ICP is multifactorial and still unclear. Therefore, our study aimed to check whether the selected ABCB4and ABCB11nucleotide variants are associated with an increased risk of ICP. Methods:ICP was diagnosed based on clinical symptoms characteristic of this disease and confirmed by increase in serum bile acids and transaminases, spontaneous resolution of clinical symptoms and normalization of laboratory tests after delivery. The total of 86 pregnant women meeting the criteria were included into the study. Healthy pregnant women with uncomplicated pregnancy served as control group (n=310). Sixcommon nucleotide variants in theABCB11and ABCB4genes were genotypedwith the use of high-resolution melting curve analysis. Conclusion:Our study did not show any significant association of analysed ABCB4and ABCB11nucleotide variants with the increased risk of intrahepatic cholestasis of pregnancy.

Calcium-sensing receptor gene (CASR) polymorphisms and CASR transcript level concerning dyslipidemia in hemodialysis patients: a cross-sectional study

BACKGROUND

There is scarce data on CASR associations with dyslipidemia. We investigated in hemodialysis (HD) patients whether CASR single nucleotide polymorphisms (SNPs) rs7652589 and rs1801725 have associations with dyslipidemia and show epistatic interactions with SNPs of the energy homeostasis-associated gene (ENHO), retinoid X receptor α gene (RXRA), and liver X receptor α gene (LXRA).

METHODS

The study included 1208 HD subjects. For diagnosis of dyslipidemia, both K/DOQI criteria and atherogenic index ≥3.8 were used. CASR rs1801725 was genotyped by TaqMan SNP Genotyping Assay, other SNPs - by high-resolution melting curve analysis or polymerase chain reaction-restriction fragment length polymorphism, as appropriate. Relative transcript levels of CASR, ENHO, RXRA, and LXRA were measured in peripheral blood mononuclear cells. The occurrence of dyslipidemic phenotypes concerning tested polymorphisms was compared using models of inheritance. Haplotypes were estimated using the Haploview 4.2 software. Epistatic interactions between tested SNPs were analyzed using the logistic regression and epistasis option in the PLINK software.

RESULTS

Rs7652589 indicated a greater probability of atherogenic dyslipidemia in the dominant inheritance model (OR 1.4, 95%CI 1.0-2.0, P = 0.026), principally because of increased triglyceride (TG) levels. The rs1801725 variant allele was associated with a decreased probability of dyslipidemia characterized by non-HDL-cholesterol ≥130 mg/dL and TG ≥200 mg/dL (OR 0.6, 0.4-0.9, P = 0.012). There were no epistatic interactions between CASR and RXRA, LXRA, and ENHO regarding dyslipidemia. Both rs7652589 and rs1801725 SNPs were not in linkage disequilibrium (D' = 0.091, r² = 0.003 for the entire HD group) and their haplotypes did not correlate with dyslipidemia. Relative CASR transcript was lower at a borderline significance level in patients harboring the rs1801725 variant allele compared with homozygotes of the major allele (0.20, 0.06-7.80 vs. 0.43, 0.04-5.06, P = 0.058). CASR transcript correlated positively with RXRA transcript (adjusted P = 0.001), LXRA transcript (adjusted P = 0.0009), ENHO transcript (borderline significance, adjusted P = 0.055), dry body weight (adjusted P = 0.035), and renal replacement therapy duration (adjusted P = 0.013).

CONCLUSIONS

CASR polymorphisms (rs7652589, rs1801725) are associated with dyslipidemia in HD patients. CASR correlates with RXRA, LXRA, and ENHO at the transcript level. Further investigations may elucidate whether other CASR SNPs contribute to associations shown in this study.

PAX7 nucleotide variants and the risk of non-syndromic orofacial clefts in the Polish population

OBJECTIVE

The etiology of non-syndromic cleft lip with or without cleft palate (nsCL/P) is multifactorial, heterogeneous, and still not completely understood. The aim of the present study was to examine the associations between common and rare PAX7 nucleotide variants and the risk of this common congenital anomaly in a Polish population.

SUBJECTS AND METHODS

Eight top nsCL/P-associated PAX7 variants identified in our cleft genome-wide association study (GWAS) were selected for replication analysis in an independent group of patients and controls (n = 247 and n = 445, respectively). In addition, mutation screening of the PAX7 protein-coding region was conducted.

RESULTS

Analysis of the pooled data from the GWAS and replication study confirmed that common PAX7 nucleotide variants are significantly associated with the increased risk of nsCL/P. The strongest individual variant was rs1339062 (c.586 + 15617T > C) with a p-value = 2.47E-05 (OR = 1.4, 95%CI: 1.20-1.64). Sequencing analysis identified a novel synonymous PAX7 substitution (c.87G > A, p.Val29Val) in a single patient with nsCLP. This transition located in the early exonic position was predicted to disrupt potential splice enhancer elements.

CONCLUSION

Our study confirmed that PAX7 is a strong candidate gene for nsCL/P. Nucleotide variants of this gene contribute to the etiology of nsCL/P in the homogenous Polish population.

The assessment of GWAS - identified polymorphisms associated with infertility risk in Polish women with endometriosis

OBJECTIVES

Genome-wide association studies in patients with endometriosis revealed ten significant single nucleo-tide polymorphisms (SNPs) in the Caucasian population, which include rs12700667 near NFE2L3, rs12037376 in WNT4, rs7521902 near WNT4, rs13394619 in GREB1, rs10859871 near VEZT, rs1537377 near CDKN2B-AS1, rs4141819 near ETAA1, rs7739264 near ID4, rs1519761 near RND3 and rs6542095 near IL1A.

MATERIAL AND METHODS

We replicated ten polymorphisms among infertile women with endometriosis (n = 315) and healthy fertile women (n = 406) in the Polish Caucasian population. Genotyping was conducted either by high-resolution melting curve analysis or by a pre-designed TaqMan probe.

RESULTS

For all infertile women with endometriosis, the p values of the Cochran-Armitage trend test for the rs12700667 SNP was ptrend = 0.038 and the odds ratio (OR) for the risk allele frequency (RAF) of rs12700667 was 1.304 (95% CI = 1.009-1.685; p = 0.042). In patients with endometriosis with severity stages III/IV, ptrend for rs12700667 SNP was 0.036 and OR for the RAF was 1.394 (95% CI = 1.010-1.923; p = 0.043). In infertile women with endometriosis with severity stages III/IV for rs4141819 SNP, we observed ptrend = 0.026 and for RAF the OR = 1.350 (95% CI = 1.032-1.766; p = 0.029).

CONCLUSIONS

Our results demonstrate association of RAF of rs12700667 and rs4141819 SNPs with infertility in Polish women with advanced endometriosis.

ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients

BACKGROUND

The energy homeostasis-associated gene (ENHO), retinoid X receptor alpha gene (RXRA), and liver X receptor alpha gene (LXRA) are involved in adipogenic/lipogenic regulation. We investigated whether single-nucleotide polymorphisms in these genes (ENHO rs2281997, rs72735260; RXRA rs749759, rs10776909, rs10881578; LXRA rs2279238, rs7120118, rs11039155) are associated with dyslipidaemia, related comorbidities and survival of haemodialysis (HD) patients also tested for T-helper (Th) cell interleukin genes (IL).

METHODS

The study was carried out in 873 HD patients. Dyslipidaemia was diagnosed by the recommendations of the Kidney Disease Outcomes Quality Initiative (K/DOQI) guidelines (2003); atherogenic dyslipidaemia was referred to if the TG/HDL cholesterol ratio was equal to or higher than 3.8. Genotyping of ENHO SNPs, LXRA SNPs, and IL12A rs568408 was carried out using HRM analysis. RXRA SNPs, IL12B rs3212227, and IL18 rs360719 were genotyped using PCR-RFLP analysis. The circulating adropin concentration was determined in 126 patients by enzyme-linked immunosorbent assay. Survival probability was analysed using the Kaplan-Meier method in 440 patients followed through 7.5 years.

RESULTS

Dyslipidaemia by K/DOQI was diagnosed in 459 patients (91% revealed hyper-LDL- cholesterolaemia), atherogenic dyslipidaemia was diagnosed in 454 patients, and 231 patients were free of dyslipidaemia by both criteria. The variant allele (T) of ENHO rs2281997 was associated with the hyper-LDL cholesterolaemic pattern of dyslipidaemia by K/DOQI. The frequency of atherogenic dyslipidaemia was lower in T-allele bearers than in CC-genotype patients. The rs2281997 T allele was associated with lower cardiovascular mortality in HD patients showing atherogenic dyslipidaemia. ENHO, RXRA, and LXRA showed epistatic interactions in dyslipidaemia. Circulating adropin was lower in atherogenic dyslipidaemia than in non-atherogenic conditions. RXRA rs10776909 was associated with myocardial infarction. Bearers of LXRA rs2279238, rs7120118 or rs11039155 minor alleles showed higher mortality. ENHO SNP positions fell within the same DNase 1 hypersensitivity site expressed in the Th1 cell line. Epistatic interactions occurred between rs2281997 and Th1 IL SNPs (rs360719, rs568408).

CONCLUSIONS

Atherogenic dyslipidaemia occurs in HD patients in whom ENHO encodes less adropin. ENHO, RXRA, and LXRA SNPs, separately or jointly, are associated with dyslipidaemia, myocardial infarction, and survival in HD patients. Differences in the availability of transcription binding sites may contribute to these associations.

Further Evidence of the Association of the Diacylglycerol Kinase Kappa (DGKK) Gene With Hypospadias

PURPOSE

Hypospadias is a common developmental anomaly of the male external genitalia. In previous studies conducted on West European, Californian, and Han Chinese populations the relationship between polymorphic variants of the diacylglycerol kinase kappa (DGKK) gene and hypospadias have been reported. The aim was to study the possible associations between polymorphic variants of the DGKK gene and hypospadias using an independent sample of the Polish population.

MATERIALS AND METHODS

Ten single nucleotide polymorphisms in DGKK, which were reported to have an impact on the risk of hypospadias in other populations, were genotyped using high-resolution melting curve analysis in a group of 166 boys with isolated anterior (66%) and middle (34%) forms of hypospadias and 285 properly matched controls without congenital anomalies.

RESULTS

Two DGKK variants rs11091748 and rs12171755 were associated with increased risk of hypospadias in the Polish population. These results were statistically significant, even after applying the Bonferroni correction for multiple comparisons (P < .005). All the tested nucleotide variants were involved in haplotype combinations associated with hypospadias. The global p-values for haplotypes comprising of rs4143304-rs11091748, rs11091748-rs17328236, rs1934179-rs4554617, rs1934183-rs1934179-rs4554617 and rs12171755-rs1934183-rs1934179-rs4554617 were statistically significant, even after the permutation test correction.

CONCLUSION

Our study provides strong evidence of an association between DGKK nucleotide variants, haplotypes and hypospadias susceptibility.

Interferon‑λ4 gene polymorphisms, circulating interferon λ3, and clinical variables in hemodialysis patients exposed to hepatitis E virus

Introduction Factors associated with hepatitis E virus (HEV) infection are rarely recognized in patients on renal replacement therapy (RRT), and the results of studies are inconsistent. Objectives We aimed to search for determinants of HEV seroprevalence among polymorphisms of the interferon‑λ4 gene (IFNL4) associated with seroclearance of hepatotropic viruses (IFNL4 rs12979860, rs8099917 near IFNL4), circulating interferon λ3 (IFN‑λ3), and clinical variables of patients treated with hemodialysis (HD) in a HEV‑endemic region. Patients and methods The study was carried out in 90 HD patients. HEV open reading frame 2 antigen (HEV Ag), immunoglobulin M and G antibodies to HEV (anti‑HEV IgM and anti‑HEV IgG, respectively) and IFN‑λ3 were tested, and IFNL4 polymorphic variants (rs8099917, rs12979860) were genotyped. Survival analysis was conducted concerning anti‑HEV IgG positivity. Results In the study group, there were 37.8% anti‑HEV IgG‑positive subjects. None was HEV Ag or anti‑HEV IgM positive. HD modalities utilizing high‑flux dialyzers (adjusted odds ratio [OR], 3.586; 95% confidence interval [CI], 1.142-11.263; P = 0.03) as well as major homozygosity in rs8099917 (adjusted OR, 4.933; 95% CI, 1.516-16.054; P = 0.008) and rs12979860 (adjusted OR, 3.537; 95% CI, 1.136-11.014, P = 0.03), but not circulating IFN‑λ3 levels, were positive determinants of anti‑HEV IgG positivity. Liver enzyme activities and C‑reactive protein levels tested as response variables to HEV exposure, as well as survival probability, were not different between patients stratified by anti‑HEV IgG positivity. Conclusions Among HD patients, IFNL4 polymorphisms and treatment with high‑flux HD are explanatory variables for isolated anti‑HEV IgG positivity indicating spontaneous HEV resolution.

The Calcium-Sensing Receptor Gene Polymorphism rs1801725 and Calcium-Related Phenotypes in Hemodialysis Patients

BACKGROUND/AIMS

The calcium-sensing receptor gene (CASR) rs1801725 variant is responsible for a non-conservative amino-acid change (A986S) in the calcium-sensing receptor cytoplasmic tail. We hypothesized that rs1801725 polymorphism might be helpful in understanding Ca-related abnormalities in HD patients.

METHODS

In 1215 subjects (245 on cinacalcet), we determined the associations of rs1801725 with secondary hyperparathyroidism (sHPT)-related laboratory parameters, PTH-decreasing effect of cinacalcet hydrochloride, coronary artery disease (CAD), myocardial infarction (MI), nephrolithiasis-related ESRD, and mortality. CASR rs7652589(AT) haplotypes and rs1801725 epistatic interactions with vitamin D signaling pathway genes were examined for associations with selected phenotypes.

RESULTS

The rs1801725 variant allele showed an increasing independent effect on plasma PTH (Pcorrected = 0.009). CASR rs7652589_rs1801725 AT haplotype was associated with 1.7-fold higher frequency of PTH levels over 437 pg/mL than the reference haplotype GG (P = 0.001). CASR rs7652589_rs1801725 AG haplotype was 1.5-fold more frequent in nephrolithiasis-related ESRD than the GG haplotype (P = 0.004). There were no significant associations between rs1801725, CAD, MI, and response to cinacalcet. Variant homozygosity of rs1801725 correlated independently with higher infection-related mortality compared with heterozygosity (HR 7.95, 95%CI 2.15 - 29.37, P = 0.003) and major homozygosity (HR 5.89, 95%CI 1.69 - 20.55, P = 0.040). CASR rs1801725 did not show epistatic interactions with vitamin D signaling pathway genes concerning tested associations.

CONCLUSION

The variant allele of CASR rs1801725 solely and together with the variant allele of rs7652589 increases risk of more advanced sHPT. Homozygosity of the rs1801725 variant allele contributes to infection-related mortality in HD patients.

The molecular basis of non-syndromic orofacial clefts and tooth agenesis

Non-syndromic orofacial clefts and tooth agenesis are two of the most common craniofacial birth defects. Both of them have a complex etiology, with genetic and environmental factors involved. Additionally, the epigenetic modifications have been implicated in the pathogenesis of these structural malformations. Despite an increasing number of research studies, using a variety of methodological approaches, the role of genetic factors in the etiology of orofacial clefts and tooth agenesis is still not well elucidated. The most consistent findings across studies concerning the genetic factors influencing the risk to orofacial clefts include the association of polymorphic variants of the IRF6 gene and the chromosomal locus 8q24.21. The major candidate gene for tooth agenesis in the European populations is WNT10A; its pathogenic mutations are present in more than 50% of patients with this dental anomaly. It has been found that both orofacial clefts and tooth agenesis, which co-occurrence is often reported, may share common candidate genes.

Polymorphisms of T helper cell cytokine-associated genes and survival of hemodialysis patients - a prospective study

BACKGROUND

Circulating pro-inflammatory cytokines were associated with increased relative mortality risk, while immune parameters reflecting improved T-cell function were predictors of survival in hemodialysis (HD) patients. We evaluated in the prospective study whether variants in T helper cell cytokine-associated genes are determinants of mortality in HD patients.

METHODS

The study was carried out in 532 prevalent HD subjects who were followed-up for 7 years. HRM analysis was used for IFNL3, IL12A, IL13, and IL4R genotyping. CCL2, IL12B, and IL18 were genotyped using PCR-RFLP analysis. Survival analyses were conducted using the Kaplan-Meier method and the Cox proportional hazard model.

RESULTS

In univariate analyses, IFNL3 rs8099917 was associated with all-cause mortality in recessive model of inheritance (log-rank test P = 0.044), IL12A rs568408 - in dominant model (log-rank test P = 0.029). Minor homozygotes (the genotype GG) in IFNL3 rs8099917 showed shorter survival during the study (3.6, 1.0-7.0 years vs 4.7, 0.1-7.0 years, P = 0.009) than the major allele (T) bearers. The rs8099917 GG patients demonstrated higher risk of death than the remaining patients (GT + TT) (OR 1.94, 95%CI 1.11-3.40, P = 0.020). Major homozygosity (the genotype GG) in IL12A rs568408 was associated with higher mortality than that shown in bearers of the minor allele (AA + AG) (HR 1.31, 95%CI 1.02-1.69, P = 0.035). In multivariate analyses, however, the mentioned polymorphisms were not independent predictors of survival.

CONCLUSIONS

Polymorphisms of IFNL3 rs8099917 and IL12A rs568408 contribute to survival of HD patients, but not as independent factors.

Associations of the calcium-sensing receptor gene CASR rs7652589 SNP with nephrolithiasis and secondary hyperparathyroidism in haemodialysis patients

Nephrolithiasis, secondary hyperparathyroidism (sHPT), and cardiovascular complications are associated with disturbances in Ca handling and contribute to morbidity/mortality during haemodialysis (HD). Calcimimetics, activators of the calcium-sensing receptor (CaSR), provide an effective means of reducing parathyroid hormone (PTH) secretion in sHPT. Polymorphism in CaSR gene (CASR) influences Ca-related parameters, however it was not shown in HD patients for CASR rs7652589. The minor allele at this polymorphism modifies the binding sites of transcription factors and CaSR expression. We hypothesized that CASR rs7652589 variants may also influence CaSR in end stage renal disease (ESRD). We aimed to determine the associations of rs7652589 with nephrolithiasis-related ESRD, Ca, P, ALP, PTH, response to treatment with cinacalcet, prevalence of coronary artery disease, and all-cause/cardiovascular mortality in HD patients (n = 1162). Healthy individuals (n = 918) were controls. This study shows that the A allele of rs7652589 is a risk allele for nephrolithiasis-related ESRD. The AA genotype is associated with more severe sHPT (higher Ca and PTH concentrations). The A allele is associated with reduced CaSR transcript level in peripheral blood mononuclear cells. According to computational analysis, potential binding sites for GLI3, AHR and TP53 are removed by the A allele, whereas binding sites for SOX18 and TP63 are created.

Antibodies to HBV surface antigen in relation to interferon-λ3 in hemodialysis patients

AIM

To investigate circulating IFN-λ3 and IFNL3 polymorphisms in hemodialysis (HD) patients differing in HBV surface antigen antibody (anti-HBs) production.

METHODS

The study included 106 HBV-vaccinated HD patients (88 developed anti-HBs) and 36 HBV-infected HD subjects (27 developed anti-HBs). Plasma IFN-λ3 (enzyme-linked immunosorbent assay) and rs12979860 (C>T) and rs8099917 (T>G) in IFNL3 (high-resolution melting curve analysis) were analyzed with regard to the association with anti-HBs production in response to HBV vaccination or infection. The results were adjusted for gender, age, cause of renal disease, dialysis vintage, dialysis modality, IFN-λ3, and 25(OH)D as appropriate.

RESULTS

HBV vaccine responders had higher circulating IFN-λ3 (ng/L) than non-responders (120, 36-233 vs. 53, 33-109, P<0.000001). Patients who generated anti-HBs after HBV infection also had higher circulating IFN-λ3 levels than those who did not (133, 35-215 vs. 71, 9-229, P=0.043). The IFN-λ3 concentration correlated with the anti-HBs titer in vaccinated (r=0.614, P<0.000001) and infected patients (r=0.589, P=0.0002). Plasma IFN-λ3 was the only significant indicator of responsiveness to HBV vaccination (adjusted P=0.018) and remained the only significant associate for the development of post-infection anti-HBs (adjusted P=0.049). A plasmaIFN-λ3 level of 85.5ng/L was thecut-off value for theprognosis of an anti-HBs titer below vs. equal to or over 10IU/L in the entire group of HD patients (ROC sensitivity 68.7%, specificity 85.2%, and AUC 0.827). Significant associations were not found between IFN-λ3 and IFNL3 rs12979860. Subjects treated with low flux HD that harbored the TT genotype in rs8099917 showed higher IFN-λ3 levels than patients bearing the G allele in rs8099917 (139, 68-233 vs. 103, 9-208, P=0.049).

CONCLUSION

In HD patients, circulating IFN-λ3 strongly correlates with anti-HBs production after HBV vaccination and infection. IFNL3 rs8099917 polymorphisms seem to be associated with IFN-λ3 plasma levels in HD subjects.

Searching for new genes and loci involved in cleft lip and palate in the Polish population – genome-wide association study

The project “Searching for new genes and loci involved in cleft lip and palate in the Polish population – genome-wide association study” is a case-control study in a group of unrelated subjects with non-syndromic cleft lip with or without cleft palate (NSCL/P) and healthy individuals with no family history of clefting or other congenital disorders. The overall goal of this grant proposal is to identify novel genetic factors, which can play a significant role in the pathogenesis of orofacial clefts in the Polish population. To accomplish the proposed aim, a two stage genome-wide association study will be performed. In the first stage, Illumina's HumanOmni Express BeadChips arrays will be used to genotype over 700,000 polymorphisms in NSCL/P patients and controls. In the second stage, SNPs showing the most compelling association with the risk of orofacial clefts will be tested in an independent sample set using standard genotyping methods. This research project is expected to be completed in July 2015.

Polymorphisms of Vitamin D Signaling Pathway Genes and Calcium-Sensing Receptor Gene in respect to Survival of Hemodialysis Patients: A Prospective Observational Study

We evaluated in the 7-year prospective study whether variants in vitamin D pathway genes and calcium-sensing receptor gene (CASR) are determinants of mortality in hemodialysis (HD) patients (n = 532). HRM analysis was used for GC rs2298849, GC rs1155563, RXRA rs10776909, RXRA rs10881578, and CASR rs7652589 genotyping. GC rs7041, RXRA rs749759, VDR rs2228570, and VDR rs1544410 were genotyped using PCR-RFLP analysis. The minor allele in GC rs2298849 was associated with all-cause mortality in univariate analysis (HR 1.330, 95% CI 1.046-1.692, P = 0.020). Bearers of the minor allele in GC rs2298849 demonstrated higher infection/neoplasm mortality than major allele homozygotes also in multivariate analysis (HR 2.116, 95% CI 1.096-4.087, P = 0.026). Cardiovascular mortality was associated with major homozygosity (CC) in VDR rs2228570 (HR 1.896, 95% CI 1.163-3.091, P = 0.010). CC genotype patients were more often dyslipidemic than TT genotype subjects (46.1% versus 31.9%, P = 0.047). Dyslipidemics showed higher frequency of rs1544410_rs2228570 haplotype AC than nondyslipidemics (26 versus 18%, P corr = 0.005), whereas TT genotype patients were at lower risk of dyslipidemia compared with CC/CT genotype patients (HR 0.59, 95% CI 0.37-0.96, P = 0.04). In conclusion, GC rs2298849 and VDR rs2228570 SNPs are associated with survival on HD. VDR-related cardiovascular mortality may occur due to connections of rs2228570 with dyslipidemia.

Nucleotide Variants of the BH4 Biosynthesis Pathway Gene GCH1 and the Risk of Orofacial Clefts

A deficiency of GTP cyclohydrolase, encoded by the GCH1 gene, results in two neurological diseases: hyperphenylalaninaemia type HPABH4B and DOPA-responsive dystonia. Genes involved in neurotransmitter metabolism and motor systems may contribute to palatogenesis. The purpose of the study was to analyse polymorphic variants of the GCH1 gene as risk factors for non-syndromic cleft lip with or without cleft palate (NSCL/P). Genotyping of nine polymorphisms was conducted in a group of 281 NSCL/P patients and 574 controls. The GCH1 variant rs17128077 was associated with a 1.7-fold higher risk for NSCL/P (95 %CI = 1.224-2.325; p = 0.001). We also found a significant correlation between the rs8004018 and rs17128050 variants and an increased risk of oral clefts (p trend = 0.003 and 0.004, respectively). The best evidence of the global haplotype association was observed for rs17128050 and rs8004018 (p corr = 0.0152). This study demonstrates that the risk of NSCL/P is associated with variants of the GCH1 gene related to BH4 metabolism and provides some evidence of the relationships between morphological/functional shifts in the central nervous system and orofacial clefts.

Clinical aspects of vitamin D-binding protein gene polymorphisms in hemodialysis patients

INTRODUCTION

There are scarce data on the associations between vitamin D-binding protein gene (GC) polymorphisms and manifestations of chronic kidney disease.

OBJECTIVES

We evaluated the frequency distribution of GC polymorphic variants in hemodialysis (HD) patients and healthy subjects as well as the differences in the prevalence of coronary artery disease (CAD) and myocardial infarction (MI) and selected clinical and laboratory indices of secondary hyperparathyroidism in HD patients (women and men) with different GC polymorphic variants.

PATIENTS AND METHODS

HD patients (n = 1056; 625 men) and healthy controls (n = 313; 150 men) were enrolled into the study. The tested GC polymorphisms included rs2298849, rs7041, and rs1155563. We analyzed clinical data (prevalence of CAD and MI; treatment with parathyroidectomy or cinacalcet) and laboratory results (serum calcium, phosphorus, alkaline phosphatase, parathyroid hormone, and 25-hydroxy vitamin D [25(OH)D] in relation to the gene polymorphisms.

RESULTS

There were no differences between the study groups themselves and between the study groups and controls in terms of the frequency distribution of GC polymorphisms (Ptrend <0.05). Lower plasma 25(OH)D levels were shown in subjects with the rs7041 TT genotype compared with those with the GG genotype (12.7, 5.7-20.9 ng/ml vs. 15.9, 8.0-50.0 ng/ml, P = 0.02). Women with the rs7041 TT genotype compared with those with the GG genotype showed higher serum phosphorus levels (5.58, 3.40-8.97 mg/dl vs. 5.03, 1.75-9.33 mg/dl, P = 0.007).

CONCLUSIONS

HD patients do not differ in the distribution of GC polymorphisms rs2298849, rs7041, and rs1155563 from healthy subjects. In HD patients, the GC polymorphism is associated with plasma 25(OH)D levels. Sex-related factors may be important in the expression of associations between GC polymorphic variants and mineral disorders.