Verification of the Chromosome Region 9q21 Association with Pelvic Organ Prolapse Using RegulomeDB Annotations

Interactions between genetic variants and environmental risk factors are associated with the severity of pelvic organ prolapse

OBJECTIVE

Both environmental and genetic risk factors contribute to pelvic organ prolapse (POP). No genome-wide study has investigated the gene-environment (G × E) interactions. In this study, we aim to identify single nucleotide polymorphisms (SNPs) that may interact with the potential environmental factors, maximum birth weight, and age in Chinese women.

METHODS

We recruited 576 women for phase 1 and 264 women for phase 2 with stages III and IV prolapse from six geographic regions of China. Genomic DNAs from blood samples were genotyped using Affymetrix Axiom Genome-Wide CHB1 Array of 640,674 SNPs for phase 1 and Illumina Infinium Asian Screening Array of 743,722 SNPs for phase 2. Meta-analysis was used to combine the two results. Interactions of genetic variants with maximum birth weight and age on POP severity were identified.

RESULTS

In phase 1, 502,283 SNPs in 523 women passed quality control and 450 women had complete POP-quantification measurements. In phase 2, 463,351 SNPs in 257 women passed quality control with complete POP-quantification measurements. Three SNPs rs76662748 ( WDR59 , Pmeta = 2.146 × 10 -8 ), rs149541061 ( 3p26.1 , Pmeta = 9.273 × 10 -9 ), and rs34503674 ( DOCK9 , Pmeta = 1.778 × 10 -9 ) respectively interacted with maximum birth weight, and two SNPs rs74065743 ( LINC01343 , Pmeta = 4.386 × 10 -8 ) and rs322376 ( NEURL1B - DUSP1 , Pmeta = 2.263 × 10 -8 ), respectively, interacted with age. The magnitude of disease severity associated with maximum birth weight and age differed according to genetic variants.

CONCLUSIONS

This study provided preliminary evidence that interactions between genetic variants and environmental risk factors are associated with POP severity, suggesting the potential use of combining epidemiologic exposure data with selected genotyping for risk assessment and patient stratification.

Advances in molecular mechanisms of pelvic organ prolapse (Review)

Pelvic organ prolapse (POP) is a common gynecological benign disease occurring in middle-aged and elderly females. Its incidence increases every year. To date, the majority of studies investigating its etiology have not evaluated the underlying molecular mechanisms, which has caused substantial difficulties in the prevention, treatment and prognosis of POP. In the present narrative review, recent research studies concerning the molecular mechanisms of POP were systematically reviewed and the advances were summarized. The association between the incidence of POP and the reduction of the extracellular matrix, activation of oxidative stress, genetic susceptibility, denervation of the pelvic floor and reduction of estrogen infiltration were explored. POP is mainly associated with damage of pelvic floor muscles and connective tissue, which are directly caused by pregnancy and vaginal delivery. The majority of the molecular and genetic mutations associated with POP involve specific components of connective tissue synthesis and degradation. It is likely that macroscopic parameters, such as anatomy, lifestyle and reproductive factors, interact with microscopic parameters, such as physiology and genetics in the female pelvic floor, leading to POP. Additional research studies investigating the molecular mechanisms of POP should be performed, since they may aid public health strategies. In the present narrative review, a summary of these molecular mechanisms underlying the development of POP is provided. This included the relevant proteins and genes involved. On this basis, countermeasures were proposed.

Systematic review and meta-analysis of genetic association studies of pelvic organ prolapse

INTRODUCTION AND HYPOTHESIS

Family and twin studies demonstrate that pelvic organ prolapse (POP) is heritable, but the genetic etiology is poorly understood. This review aimed to identify genetic loci and specific polymorphisms associated with POP, while assessing the strength, consistency, and risk of bias among reported associations.

METHODS

Updating an earlier systematic review, PubMed and HuGE Navigator as well as relevant conference abstracts were searched using genetic and phenotype keywords from 2015 to 2020. Screening and data extraction were performed in duplicate. Fixed and random effects meta-analyses were conducted using co-dominant models of inheritance. We assessed credibility of pooled associations using interim Venice criteria.

RESULTS

We screened 504 new abstracts and included 46 published and 7 unpublished studies. In pooled analyses we found significant associations for four polymorphisms: rs2228480 at the ESR1 gene (OR 0.67 95% CI 0.46-0.98, I² = 0.0%, Venice rating BAB), rs12589592 at the FBLN5 gene (OR 1.46 95% CI 1.11-1.82, I² = 36.3%, Venice rating BBB), rs484389 in the PGR gene (OR 0.61 95% CI 0.39-0.96, I² = 32.4%, Venice rating CBB), and rs1800012 at the COL1A1 gene (OR 0.80 95% CI 0.66-0.96, I² = 0.0%, Venice rating BAB). Further credible novel variants have also been recently identified in genome-wide association studies.

CONCLUSION

The genetic contributions to POP remain poorly understood. Several biologically plausible variants have been identified, but much work is required to establish the role of these genes in the pathogenesis of POP or to establish a role for genetic testing in clinical practice.

Polymorphism on chromosome 20p13 near the IDH3B gene is associated with uterine prolapse

OBJECTIVES

Previous studies have found evidence for a genetic basis for pelvic organ prolapse (POP), but no genetic studies have differentiated between types of POP. This study investigated whether genetic variants in six previously suggested candidate loci for POP modify the risk of uterine prolapse (UP).

STUDY DESIGN

One hundred patients, aged 30-55 years, who had undergone surgery due to total UP and 105 healthy controls were included in this study. After extracting the genomic DNA from peripheral blood, six single nucleotide polymorphisms (SNPs) previously identified for POP were genotyped, and association analysis was performed for contributing risk factors. RNA expression was determined from sacrouterine ligaments of patients and controls using quantitative reverse transcription polymerase chain reaction.

RESULTS

The dominant genotype model for the T allele for SNP rs6051098 at the chromosome 20p13 locus was significant, and this remained significant with the risk factor regression model (p=0.046; odds ratio 1.93, 95 % confidence interval 1.01-3.66). The isocitrate dehydrogenase 3 beta (IDH3B) gene was the only potential candidate gene in the 20p13 locus that was significantly upregulated in sacrouterine biopsies in women with UP compared with controls (p = 0.034).

CONCLUSION

To the best of the authors' knowledge, this is the first study to show that genetic risk factors contribute to UP, and suggested rs6051098 as the best candidate risk factor associated with UP. According to expression data in sacrouterine tissue, this study suggests that the IDH3B gene plays a role in the pathogenesis of UP.

Putative functional variants of lncRNA identified by RegulomeDB were associated with knee osteoarthritis susceptibility

BACKGROUND

Knee osteoarthritis (KOA) is the most common form of chronic degenerative joint disease worldwide. Its incidence has increased in recent years. Aberrant expression profile of lncRNAs in damaged bone and cartilage of KOA patients has been reported recently, indicating its potential contributions in KOA development and a promising target for disease diagnosis and treatment. The aim of this study was to identify the association between genetic variation in lncRNA and KOA.

METHODS

We retrieved relevant articles from the PubMed, Medline and Embase databases up to Jul 2017 investigating the association between lncRNA and the risk of osteoarthritis. There are 15 lncRNAs which show connection with osteoarthritis. We selected potential functional polymorphisms identified by RegulomeDB database in these lncRNAs. A case-control study was conducted which contained 278 KOA patients and 289 OA-free controls.

RESULTS

Logistic regression analyses revealed that H19 rs2067051 T allele was significantly associated with decreased risk of KOA after adjusted for age, gender and BMI in recessive genetic model (OR = 0.63, P = 0.03) and additive genetic model (OR = 0.79, P = 0.03). MEG3 rs4378559 T allele was significantly associated with increased risk of KOA in additive genetic model (OR = 1.32, P = 0.04). Heterogeneity tests proved that H19 rs2067051, MEG3 rs4378559 and HOTTIP rs202384's risk effects on KOA were more remarkable for female, BMI ≥ 25 and younger age (age < 60), respectively.

CONCLUSION

The results indicate that potential functional genetic variation in lncRNA plays an important role in the pathogenesis of KOA.

Identification of key genes and pathways in pelvic organ prolapse based on gene expression profiling by bioinformatics analysis

PURPOSE

The aim of this study was to elucidate the molecular mechanisms and to identify the key genes and pathways for pelvic organ prolapse (POP) using bioinformatics analysis.

METHODS

The microarray data for GSE53868 included 12 POP and 12 non-POP anterior vaginal wall samples. Differentially expressed genes (DEGs) were identified by GEO2R online tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database, and a DEG-associated protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape. MCODE was used for module analysis of the PPI network.

RESULTS

A total of 257 upregulated and 333 downregulated genes were identified. GO and KEGG pathway enrichment analyses showed that the upregulated DEGs were strongly associated with immune response, complement activation, classical pathway, phagocytosis, and recognition; the downregulated genes were mainly associated with cellular response to zinc ion, negative regulation of growth, and apoptotic process. Based on the PPI network, IL6, MYC, CCL2, ICAM1, PTGS2, SERPINE1, ATF3, CDKN1A, and CDKN2A were screened as hub genes. The four most significant sub-modules of DEGs were extracted after network module analysis. These genes were mainly associated with the negative regulation of growth and inflammatory response. The KEGG pathway enrichment analysis revealed that these genes were associated with Mineral absorption, Jak-STAT signaling pathway, cytokine-cytokine receptor interaction, and chemokine signaling pathway.

CONCLUSIONS

These microarray data and bioinformatics analyses provide a useful method for the identification of key genes and pathways associated with POP. Moreover, some crucial DEGs, such as IL6, MYC, CCL2, ICAM1, PTGS2, SERPINE1, ATF3, CDKN1A, and CDKN2A, potentially play an important role in the development and progression of POP.

Collagen XVIII and LOXL-4 polymorphisms in women with and without advanced pelvic organ prolapse

INTRODUCTION AND HYPOTHESIS

We verified the presence of single nucleotide polymorphisms (SNP) rs2236479 of the collagen 18 (COL18A1) and rs2862296 of the lysyl oxidase-like 4 (LOXL-4) genes and the association with pelvic organ prolapse (POP) in Brazilian women and determined risk factors for POP development.

METHODS

We assessed 532 postmenopausal women divided into POP (stages III and IV) and control (stages 0 and I) groups by examination and peripheral blood sample collection. DNA sequences of interest were analyzed by real-time reverse-transcriptase polymerase chain reaction (RT-PCR). We used logistic regression models for the analyses, with p < 0.005 for significance.

RESULTS

The frequency of homozygous polymorphic alleles (AA) in COL18A1 and (GG) in LOXL-4 were similar in both groups (17.5% and 15.4% for COL18A1 and 18.9% and 20.6% for LOXL-4, respectively). There were no associations between those polymorphisms or other genotypes and POP. Multiple logistic regression analysis identified age [odds ratio (OR) = 1.10, confidence interval (CI) 95% = 1.07; 1.14), number of vaginal births (OR = 1.66, CI 95% = 1.36; 2.03), and family history (OR = 2.55 CI 95% = 1.43; 4.55) as independent risk factors for POP.

CONCLUSION

Our study suggests lack of association between DNA polymorphisms rs2236479 of COL18A1 and rs2862296 of LOXL-4 with advanced POP in this population.