Association of NFKB1 -94ATTG ins/del polymorphism (rs28362491) with pemphigus vulgaris.

Pemphigus vulgaris is a rare chronic blistering skin disease resulting from IgG autoantibodies directed against transmembrane desmosomal glycoprotein desmoglein 3 and is the most common form of pemphigus. Since interleukin-1 receptor-associated kinase (IRAK-1)/nuclear factor-kappa B (NF-kappa B) pathway plays an essential role in the pathogenesis of autoimmune diseases, the aim of the present study was to explore the role of polymorphisms in three genes, named IRAK1 (rs3027898), NFKBIA (rs696) and NFKB1 (-94ATTG insertion/deletion variant, - rs28362491), in PV susceptibility. Forty-four unrelated patients with PV (23 males) were enrolled in the study. Additionally, 77 ethnic matching healthy volunteers (45 males) with no personal or family history of chronic autoimmune or infectious diseases were studied. Strong statistical significant difference was observed between PV patients and controls for polymorphism -94 insertion/deletion ATTG in the promoter region of NFKB1 gene (P = 0.00005). Additional dedicated studies in larger groups of patients of various ethnicities are needed to replicate and confirm the preliminary findings.

Ethnicity-Based Differences in the Association of LOXL1 Polymorphisms with Pseudoexfoliation/Pseudoexfoliative Glaucoma: A Meta-Analysis.

Pseudoexfoliation (PEX) is an age-related disorder of the extracellular matrix; it is strongly associated with glaucoma, the leading cause of irreversible blindness worldwide. We conducted an ethnic-based meta-analysis of the association of LOXL1 polymorphisms with PEX/pseudoexfoliative glaucoma (PEXG). Association studies were retrieved systematically from PubMed, EMBASE, and Web of Knowledge. Allelic and genotype frequencies of rs3825942, rs1048661, and rs2165241 were compared between PEX/PEXG and controls. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using a random effects model. Overall, 39 independent cohorts were included. Rs3825942 (G) was an at risk allele for PEX/PEXG in Caucasians, Japanese, Koreans, Chinese, South Asians, and Middle Easterners, but protective in Black South Africans (OR = 0.10, 95%CI:0.06-0.16). Rs1048661 (G) was an at risk allele for PEX/PEXG in Caucasians, South Asians, Middle Easterners and Black South Africans, but was protective in Japanese (OR = 0.03, 95%CI:0.02-0.06) and Koreans (OR = 0.10, 95%CI:0.05-0.22). These associations we-re confirmed for the genotypic recessive models. Rs2165241 (C) was a protective allele for PEX/PEXG in Caucasians, but was an at risk allele in Japanese (OR = 7.49, 95%CI:3.22-17.41) and Koreans (OR = 6.63, 95%CI:2.60-16.90). This was confirmed for the genotypic dominant model. Other genetic and/or environmental factors may modify the effect of LOXL1 polymorphisms in certain ethnic groups.

Absence of association of FCGR2A gene polymorphism rs1801274 with Kawasaki disease in Greek patients.

Kawasaki disease is an acute, febrile syndrome in infancy, characterised by vasculitis of medium-sized arteries, and affects predominantly young children. Family-based studies on Kawasaki disease supports the contribution of genetic factors in disorder manifestation. In a recent genome-wide association study, the polymorphism rs1801274 of FCGR2A [Fc fragment of immunoglobulin G, low-affinity IIa, receptor] gene has been implicated in disease pathogenesis. The aim of the present study was to explore the association of this variant, for the first time, in a group of Kawasaki-diseased patients of Greek origin. A total of 47 Kawasaki-diseased children and 50 control subjects were enrolled in the study. Polymerase chain reaction-restriction fragment length polymorphism assay was performed in rs1801274 genotyping. No association was observed between this polymorphism genotypes' or alleles' distribution between Kawasaki-diseased patients and controls. Furthermore, no association was revealed between this polymorphism and cardiovascular complications in Kawasaki-diseased patients. In the literature, the reported data over this polymorphism association with Kawasaki disease in Caucasian patients are contradictory. In addition, the disease shows low prevalence in the Caucasian populations. Therefore, the independent genetic association studies on rs1801274 with Kawasaki disease in various Caucasian groups increase the amount of genetic data, which could be used in a future meta-analysis, increasing the statistical power of the resultant conclusions.

Role of 9p21 and 2q36 variants and arterial stiffness in the prediction of coronary artery disease.

BACKGROUND: Genetic polymorphisms and arterial stiffness indices have been associated with cardiovascular prognosis and the presence and extent of angiographic coronary artery disease (CAD). We aimed to investigate whether arterial stiffness indices and 9p21 and 2q36 variants may improve prediction of CAD presence and extent when added to classical cardiovascular risk factors in patients at high risk for CAD. MATERIALS AND METHODS: In this cross-sectional study, we enrolled 183 consecutive patients with suspected stable CAD (age 61 ± 9 years, 134 males) referred for diagnostic coronary angiography. Framingham risk score (FRS) was calculated. Arterial stiffness was assessed by carotid-femoral pulse wave velocity (PWV) and central augmentation index (AIx) using applanation tonometry. Genetic polymorphisms of 9p21 (rs1333049) and 2q36 (rs2943634) loci were also analysed. RESULTS: Higher FRS and PWV and the presence of rs2943634 risk allele were independent predictors of CAD (Nagelkerke R(2) 0·252, P < 0·001), while higher FRS and the presence of rs1333049 risk allele were independent predictors of multivessel CAD (Nagelkerke R(2) 0·190, P < 0·001). Genetic polymorphisms and vascular indices did not improve the predictive accuracy of FRS-based models (P > 0·1 for all) for CAD presence or extent. CONCLUSIONS: In these high-risk patients, 9p21 and 2q36 variants and PWV were independently associated with CAD presence and extent, but the addition of both genetic data and arterial stiffness indices to FRS did not improve the prediction of CAD compared with FRS alone. Further studies are needed to clarify the prognostic role of genetic and vascular indices in the prediction of angiographic CAD.

Non-HLA genes in ankylosing spondylitis: what meta-analyses have shown?

HLA-B27 association with ankylosing spondylitis (AS) is one of the strongest ever reported in the literature. However, only a small proportion of 5-8% of HLA-B27 positive individuals of the general population develops the disease. In recent years, polymorphisms of many non-HLA genes were reported to be associated with AS. In this review, we summarise the current knowledge of non-HLA genetic factors contributing to AS susceptibility based on meta-analyses in order to overcome the limitations of individual genetic studies e.g. the small samples' sizes, the small samples' origin diversities, and the low statistical power of statistical analyses.

SNPs as Stochastic Oscillators in Inheritance of Human Diseases.

BACKGROUND/AIM: Genetic variants contribute to differences in disease susceptibility. The aim of the study was to elucidate if variants can affect human disease inheritance. MATERIALS AND METHODS: Recently, a list of germline hotspot genetic variants across human autosomal chromosomes was published. Recording the genetic variant hotspots across autosomal chromosomes, their frequency was calculated for each distinct type of genetic variant hotspot and for each autosomal chromosome. Then, OMIM autosomal dominant (AD) and recessive diseases (AR) were counted across each chromosome having maximum and minimum coverage of each type of genetic variant hotspot and the data were compared. Subsequently, the study focused on chromosome 16 with the maximum and chromosome 13 with the minimum number of SNP hotspots. AD and AR diseases were recorded, inside or near the reported SNP variant hotspots of chromosome 16 and 13, and the data were compared. The SPSS software was used for statistical analyses. RESULTS: Autosomal dominant diseases were mainly found in low SNP hotspot chromosomal regions compared to recessive ones, underlying SNPs' possible regulatory role in allelic imbalance. The haplotypic background may be the key factor for variant classification, which could explain the current inconsistencies among scientists with the same genetic variant to be classified as pathogenic, likely pathogenic, or of unknown significance. CONCLUSION: Which came first: the SNPs or the type of inheritance? Third next-generation sequencing with long reads could answer by phasing SNP alleles' haplotypes and tracing their in-cis and in-trans modulator function in human Mendelian and Complex inheritance.

The Association of Vitamin D Receptor Polymorphisms with COVID-19 Severity.

BACKGROUND: Association studies of vitamin D receptor (VDR) polymorphisms with COVID-19 severity have produced inconsistent results in different populations. Herein we examined VDR gene polymorphisms in a Caucasian Greek cohort of COVID-19 patients. METHODS: This was a case-control study in a tertiary university hospital in Greece including 137 COVID-19 patients with varying disease severities and 72 healthy individuals. In total 209 individuals were genotyped for the FokI (rs10735810), ApaI (rs7975232), TaqI (rs731236) and BsmI (rs1544410) single-nucleotide polymorphisms (SNP) of the VDR gene by polymerase chain reaction and restriction fragment length polymorphism analysis (PCR-RFLPs). Statistical analyses were performed to determine the association between genotype and disease severity, adjusting for various confounding factors. RESULTS: Genotype distribution of the studied VDR SNPs in the control group was in Hardy-Weinberg equilibrium. The TaqI variant was differentially distributed between controls and COVID-19 patients according to the additive model (p = 0.009), and the CC genotype was significantly associated with an increased risk for severe COVID-19 according to the recessive model [OR: 2.52, 95%CI:1.2-5.29, p = 0.01]. Multivariate analysis demonstrated a robust association of COVID-19 severity and TaqI polymorphism in the recessive model even after adjusting for multiple confounders, including age, sex and CRP levels [Adj.OR:3.23, 95%CI:1.17-8.86, p = 0.023]. The distribution of FokI, ApaI and BsmI genotypes was similar between COVID-19 patients and controls. CONCLUSIONS: The CC genotype of TaqI polymorphism is significantly associated with an increased risk for severe COVID-19 independently of age, sex or degree of inflammation.

A Pilot Study of the Association VDR Polymorphisms With Primary Hyperparathyroidism.

BACKGROUND/AIM: Primary hyperparathyroidism (PHPT) is the third most common endocrine disorder characterized by autonomous parathyroid hormone (PTH) production from one or more parathyroid glands and hypocalcemia. Vitamin D through its receptor is a principal regulator of parathyroid glands function. VDR gene polymorphisms, which affect the expression or structure of VDR protein, may be involved in the genetic pathogenesis of PHPT. The aim of this study was to investigate the role of FokI, ApaI, TaqI, and BsmI VDR gene polymorphisms as genetic predisposing factors for PHPT. PATIENTS AND METHODS: Fifty unrelated patients with sporadic PHPT and an equal number of corresponding ethnicity, sex and age range healthy volunteers were enrolled in the study. Genotyping was performed with polymerase chain reaction and restriction fragment length polymorphism assay. RESULTS: Statistically significant difference was observed in TaqI genotype distribution between PHPT patients and controls, while no association was detected for the other studied polymorphisms. CONCLUSION: TaqI TT and TC genotypes may be associated with PHPT risk in Greek population. Further independent studies are needed to replicate and validate the role of VDR TaqI polymorphism in PHPT predisposition.

Sporadic parathyroid adenoma: an updated review of molecular genetics.

Introduction: Primary HPT (PHPT) is a common disorder, affecting approximately 1% of the general population. Parathyroid adenomas emerge as non-familial sporadic in 90% of cases. The aim of this review is to give a detailed update of molecular genetics of sporadic parathyroid adenoma reported in international literature. Methods: A bibliographic research was conducted in PubMed, Google Scholar, and Scopus. Results: Seventy-eight articles were included in our review. CaSR, MEN1, CCND1/PRAD, CDKI, angiogenic factors like VEGF, FGF, TGFß, and IGF1, and apoptotic factors are important genes in parathyroid adenomas pathogenesis that have been established by several studies. A huge list of proteins is differently expressed in parathyroid adenomas measured by Western Blotting, MALDI/TOF, MS spectrometry, and immunohistochemistry. These proteins take part in several cell processes such as cell metabolism, cytoskeleton structural stability, cell oxidative stress regulation, cell death, transcription, translation, cell connection, and cell signaling transmission, while they can be found over- or underexpressed in abnormal tissues. Conclusion: This review gives a detailed analysis of all reported data on genomics and proteomics of parathyroid adenoma. Further studies should be applied on understanding parathyroid adenoma pathogenesis and introducing new biomarkers for early detection of primary hyperparathyroidism.

The Implication of X-Linked Genetic Polymorphisms in Susceptibility and Sexual Dimorphism of Cancer.

The X-chromosome is implicated in cancer development through various mechanisms, including X-inactivation defects, loss of heterozygosity, and germline and somatic alterations of X-linked genes. Sex is a key factor which influences cancer susceptibility as many cancer types show sexual dimorphism in their incidence. The aim of this review was to summarize the germline genetic polymorphisms lying on the X-chromosome that have been associated with cancer susceptibility and to evaluate their possible implication in cancer-related sexual dimorphism. PubMed and Web of Science were searched using the terms "X-chromosome", "polymorphism" and "cancer". The literature review revealed 39 articles reporting 33 genetic variants in 22 X-linked genes as being associated with cancer risk. Most of these genes interact with each other in a direct or indirect way, as GeneMANIA software revealed, demonstrating the complication of the mechanisms through which they are involved in tumorigenesis. Polymorphisms in eight genes [androgen receptor (AR), fibroblast growth factor 13 (FGF13), forkhead box P3 (FOXP3), L1 cell adhesion molecule (L1CAM), nudix hydrolase 11 (NUDT11), Shroom family member 2 (SHROOM2), transcription elongation factor A-like 7 (TCEAL7) and TIMP metallopeptidase inhibitor 1 (TIMP1)] are reported to have a sex-specific association with cancer susceptibility, which might explain the sexual dimorphism of certain cancer types. All of the above eight mentioned genes, with the exception of L1CAM, exhibit differences in their expression pattern between breast tumor (sex-specific)/thyroid tumor (sex-influenced) vs. normal tissues according to our analysis using GENT2 software. Additionally, differences in breast or thyroid tumor compared with normal tissues were also observed in five genes analyzed with GENT2 software that were previously related to sex-influenced cancer according to literature. Finally, the present review points out the need for the development of appropriate free and user-friendly statistical software in order to reduce bias/errors in statistical analyses and overcome researchers' reluctance to include X-chromosome variants in their genetic-association studies.

MicroRNAs in Papillary Thyroid Cancer: What Is New in Diagnosis and Treatment.

INTRODUCTION: Papillary thyroid cancer (PTC) accounts for up to 80% of thyroid malignancies. New diagnostic and therapeutic options are suggested including innovative molecular methods. MicroRNAs (miRNAs) are nonprotein coding single-stranded RNAs that regulate many cell processes. The aim of the present study is to review the deregulated miRNAs associated with PTCs. METHODS: A bibliographic research was conducted, resulting in 272 articles referred to miRNAs and PTC. Regarding our exclusion criteria, 183 articles were finally included in our review. RESULTS: A remarkably large number of miRNAs have been found to be deregulated during PTC manifestation in the literature. The deregulated miRNAs are detected in tissue samples, serum/plasma, and FNA samples of patients with PTC. These miRNAs are related to several molecular pathways, involving genes and proteins responsible for important biological processes. MiRNA deregulation is associated with tumor aggressiveness, including larger tumor size, multifocality, extrathyroidal extension, lymphovascular invasion, lymph node and distant metastasis, and advanced tumor node metastasis stage. CONCLUSION: MiRNAs are proposed as new diagnostic and therapeutic tools regarding PTC. They could be essential biomarkers for PTC diagnosis applied in serum and FNA samples, while their contribution to prognosis is of great importance.

DNA methylation patterns of RAR-ß2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions.

BACKGROUND: Promoter hypermethylation is common in Breast Cancer (BC) with studies mainly in histological specimens showing frequent methylation of tumor suppressor genes (TSGs) compared with normal tissues. The aim of this study was to estimate the frequency of promoter methylation of RAR-ß2 and RASSF1A genes in breast FNAB material aiming to evaluate the methylation status of these two genes as biomarker for detecting BC in Greek population. METHODS: FNAB material from 104 patients was collected for cytological evaluation and epigenetic analysis. DNA was extracted and subjected to bisulfite conversion. A methylation-specific PCR was carried out and the final products were separated with electrophoresis in 2% agarose gels. RESULTS: From 104 samples, RASSF1A hypermethylation was observed in 78 (75%) and RAR-ß2 hypermethylation in 64 (61.6%). 84% and 78% of the cases diagnosed with breast malignancy (n = 50) were methylated for RASSF1A and RAR-ß2, respectively. Methylated RASSF1A and RAR-ß2 were also detected in 88.3% and 76.5% in samples diagnosed as suspicious for malignancy (n = 17) and in 57.2% of samples diagnosed with atypia (n = 14). The Odds Ratio for breast malignancy was 4.545 in patients with RASSF1A hypermethylation and 9.167 in patients with RAR-ß2 hypermethylation underlying their promoter's methylation positive correlation with breast malignancy. CONCLUSION: To optimize the sensitivity and specificity of this epigenetic setting, more TSGs related to BC should be gradually imported in our evaluated methylation panel and be validated in a larger study sample with the aim that the obtained epigenetic profiles will provide clinicians with valuable tools for management of BC patients in Greece.

Association of IRAK1 Gene Polymorphism rs3027898 With Papillary Cancer Restricted to the Thyroid Gland: A Pilot Study.

BACKGROUND/AIM: The incidence of thyroid cancer has increased predominantly due to an increase in papillary thyroid cancer (PTC). Alteration of toll-like receptor function has been reported to play a crucial role in carcinogenesis. The aim of the present study was to investigate predisposition to PTC associated with genetic markers of toll-like receptor and interleukin-1 receptor pathways involving nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-ĸB) stimulation. Specifically, the study focused on the following genes: interleukin-1 receptor-associated kinase 1 (IRAK1, rs3027898), NF-ĸB inhibitor alpha (NFKBIA, rs696), NF-ĸB subunit 1 (NFKB1, rs28362491), and microRNA-146a (miR-146a, rs2910164). PATIENTS AND METHODS: Forty-eight unrelated patients with papillary cancer restricted to the thyroid gland and 93 healthy volunteers were enrolled in the study. RESULTS: A strong statistically significant difference was observed between patients with PTC and controls for IRAK1 rs3027898 variant. When the statistical analysis was replicated taking into account patient's sex, the rs3027898 A allele was revealed to be the risky variant in males. CONCLUSION: Additional studies in larger groups of patients of various origins are needed to validate these preliminary findings.

Distinct association of SLC19A1 polymorphism -43T>C with red cell folate levels and of MTHFR polymorphism 677C>T with plasma folate levels.

OBJECTIVES: The role of SLC19A1 -43T>C, MTHFR 677C>T and MS 2756A>G polymorphisms on red cell and plasma folate levels. DESIGN AND METHODS: Genotype analysis of the three polymorphisms. Red cell and plasma folate measurements in 64 patients with coronary artery disease. RESULTS: The non-wild type allele of SLC19A1 polymorphism -43T>C was associated with low red cell folate levels and the non-wild type allele of MTHFR polymorphism 677C>T with low plasma folate levels. CONCLUSION: SLC19A1 and MTHFR genes are differently associated with red cell and plasma folate levels.

An Extensive Study of the Functional Polymorphisms of Kinin-Kallikrein System in Rheumatoid Arthritis Susceptibility.

OBJECTIVES: This study aims to examine the following functional polymorphisms in rheumatoid arthritis (RA) susceptibility: (i) the 587C>T of kininogen gene, (ii) the 287 bp Alu repeat insertion of angiotensin converting enzyme gene, (iii) the 9 bp insertion of bradykinin receptor 2 gene, (iv) the -58T>C of bradykinin receptor 2 gene, and (v) the -699G>C of bradykinin receptor 1 gene. PATIENTS AND METHODS: The study included 136 RA patients (27 males; 109 females; mean age 60.8 years; range 39 to 75 years) and 149 ethnic matching controls (30 males, 119 females; mean age 56.2 years; range 35 to 78 years). Polymerase chain reaction coupled with restriction assay was performed for 587C>T, -58T>C, and -699G>C. RESULTS: Rheumatoid arthritis patients and controls carried the wild type allele of 587C>T; therefore, produced the high molecular weight kininogen. No significant difference was observed in genotype or allele distribution of the studied functional polymorphisms between RA patients and controls. CONCLUSION: Kinin-kallikrein system related genes might not be major RA susceptibility loci.

MicroRNA-related polymorphisms in pseudoexfoliation syndrome, pseudoexfoliative glaucoma, and primary open-angle glaucoma.

BACKGROUND: Pseudoexfoliation syndrome (PEX) and glaucoma (pseudoexfoliative glaucoma; PEXG, primary open-angle glaucoma; POAG) have mainly been studied for their associations with genes' polymorphisms. The purpose of this exploratory study was to investigate the role of polymorphisms in genes encoding for micro RNAs (miRNAs) and in genes related to miRNA biogenesis. MATERIAL AND METHODS: In the present genetic association study, ninety-two polymorphisms were investigated for their contribution to PEX (n = 203), PEXG (n = 38), and POAG (n = 40) pathogenesis compared to a control group (n = 188). The next generation sequencing (NGS) genotypic analysis revealed data for additional 28 variants. RESULTS: A protective association was found between PEX and polymorphism 11382316 (mir-3161) [odds ratio (OR) = 0.64, 95% confidence interval (CI): 0.47-0.86, p = 0.003], rs2155248 (mir-1304) [OR = 0.66, 95%CI: 0.47-0.94, p = 0.019], and rs28635903 (mir-1268a) [OR = 0.30, 95%CI: 0.10-0.94, p = 0.029]. Polymorphism rs113297757 (mir-3196) was associated with an increased risk of POAG [OR = 7.75, 95%CI: 2.13-28.76, p = 3 × 10-4]. Polymorphism rs1057035 (DICER) and rs55671916 (XPO5) in the 3'-UTR of genes related to miRNA biogenesis was associated with decreased risk of PEX [OR = 0.65, 95%CI: 0.46-0.92, p = 0.014] and increased risk of PEXG [OR = 2.84, 95%CI: 1.02-7.94, p = 0.038], respectively. The aforementioned associations according to the allelic model were further supported by the genotypic models of statistical analyses. CONCLUSIONS: This is the first study to report distinct associations of PEX, PEXG, and POAG in the same population with variants of genes involved in miRNA biogenesis and with miRNA genes' polymorphisms. Further studies in larger groups of patients of various origins are needed to confirm the reported preliminary results.

Evidence of ERBB3 gene association with rheumatoid arthritis predisposition.

AIM: ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 3) gene was reported to be related with susceptibility to several autoimmune diseases. Taking this into account, we searched, for the first time, the ERBB3 gene association with rheumatoid arthritis liability. METHODS: One hundred and eighty-six RA patients and 147 controls were enrolled in the study. Polymerase chain reaction - restriction fragment length polymorphism assay was conducted in rs2271189 and rs2292239 genotyping. RESULTS: A statistically significant difference was observed in rs2271189 allele distribution between RA patients and controls (P = 0.029, odds ratio: 1.460, 95% confidence interval: 1.040-2.050). CONCLUSION: As far as we know, this is the first study which correlates ERBB3 gene with RA susceptibility, adding to a previous report of chromosome 12q13 association with RA liability. Furthermore, we confirmed that polymorphism rs2271189 can predict better ERBB3 gene association with disorders than the previously reported ERBB3 variants. More studies in other ethnic groups of patients are needed so as to reveal the extent of the herein observed genetic association.