Putative functional variants of PI3K/AKT/mTOR pathway are associated with knee osteoarthritis susceptibility.

BACKGROUND: Osteoarthritis (OA) is a degenerative musculoskeletal disease which causes joint deformity and pain and finally leads to limb dysfunction. Knee osteoarthritis (KOA) has the highest incidence among all kinds of OA. Strong evidence leads to the understanding that P13K/AKT/mTOR signaling is very important in cartilage degeneration. METHODS: This research sought to understand the association between genetic variation of PI3K/AKT/mTOR genes and KOA susceptibility among Chinese population. All the genetic variants of PI3K/AKT/mTOR pathway were graded and selected using RegulomeDB database, and then, an association study including 278 osteoarthritis patients and 289 controls was conducted. RESULTS: Finally, eight SNPs' genotypes' distributions and susceptibility to KOA were presented. AKT1 rs2498789 was associated with KOA susceptibility in dominate genetic model (AA + GA vs GG) after adjusted for BMI, age, and gender: OR = 1.46, 95% CI: 1.03-2.05, P = .03. PIK3CA rs7646409 was also associated with KOA susceptibility (TC vs TT) after adjusted for BMI, age, and gender: OR = 0.58, 95% CI: 0.36-0.93, P = .02. PIK3CA rs7646409 (TC vs TT) with KOA risk was more significant in age < 60 group (P for heterogeneity was .03). Risk score showed significant association with KOA susceptibility after cumulative analysis (OR = 2.45, 95% CI: 1.35-4.45, P = .003). CONCLUSIONS: This study shows that genetic variation of PI3K/AKT/mTOR is associated with KOA susceptibility in Chinese Han population, indicating that PI3K/AKT/mTOR is very important in KOA pathogenesis.

Functional intronic variant of SLC5A10 affects DRG2 expression and survival outcomes of early-stage non-small-cell lung cancer.

RegulomeDB is a new tool that can predict the regulatory function of genetic variants. We applied RegulomeDB in selecting putative functional variants and evaluated the relationship between these variants and survival outcomes of surgically resected non-small-cell lung cancer. Among the 244 variants studied, 14 were associated with overall survival (P < 0.05) in the discovery cohort and one variant (rs2257609 C>T) was replicated in the validation cohort. In the combined analysis, rs2257609 C>T was significantly associated with worse overall and disease-free survival under a dominant model (P = 2 × 10-5 and P = 0.001, respectively). rs2257609 is located in the SLC5A10 intron, but RegulomeDB predicted that this variant affected DRG2, not SLC5A10 expression. The expression level of SLC5A10 was not different with the rs2257609 genotype. However, DRG2 expression was different according to the rs2257609 genotype (Ptrend   = 0.03) and was significantly higher in tumor than in non-malignant lung tissues (P = 1 × 10-5 ). Luciferase assay also showed higher promoter activity of DRG2 in samples with the rs2257609 T allele (P < 0.0001). rs2257609 C>T affected DRG2 expression and, thus, influenced the prognosis of early-stage non-small-cell lung cancer. This study was approved by the Institutional Review Broad of Kyungpook National University of Hospital (Approval No. KNUMC 2014-04-210-003).

Association of CIITA (rs8048002) and CLEC2D (rs2114870) gene variants and type 1 diabetes mellitus.

Background: Type I diabetes mellitus (T1DM) is a significant health challenge, especially for children, owing to its chronic autoimmune nature. Although the exact etiology of T1DM remains elusive, the interplay of genetic predisposition, immune responses, and environmental factors are postulated. Genetic factors control immune reactivity against ß-cells. Given the pivotal roles of CIITA and CLEC2D genes in modulating a variety of immune pathologies, we hypothesized that genetic variations in CIITA and CLEC2D genes may impact T1DM disease predisposition. This study was designed to explore the association between gene polymorphisms in CIITA (rs8048002) and CLEC2D (rs2114870) and type 1 diabetes (T1DM), with a focus on analyzing the functional consequence of those gene variants. Methods: The study enlisted 178 healthy controls and 148 individuals with type 1 diabetes (T1DM) from Suez Canal University Hospital. Genotyping for CIITA and CLEC2D was done using allelic-discrimination polymerase chain reaction (PCR). Levels of glycated hemoglobin (HbA1c) and lipid profiles were determined through automated analyzer, while fasting blood glucose and insulin serum levels were measured using the enzyme-linked immunosorbent assay (ELISA) technique. RegulomeDB was used to examine the regulatory functions of CIITA (rs8048002) and CLEC2D (rs2114870) gene variants. Results: Analysis of the genotype distribution of the CIITA rs8048002 polymorphism revealed a significantly higher prevalence of the rare C allele in T1DM patients compared to the control group (OR = 1.77; P = 0.001). Both the CIITA rs8048002 heterozygote TC genotype (OR = 1.93; P = 0.005) and the rare homozygote CC genotype (OR = 3.62; P = 0.006) were significantly more frequent in children with T1DM when compared to the control group. Conversely, the rare A allele of CLEC2D rs2114870 was found to be significantly less frequent in T1DM children relative to the control group (OR = 0.58; P = 0.002). The heterozygote GA genotype (OR = 0.61; P = 0.033) and the rare homozygote AA genotype (OR = 0.25; P = 0.004) were also significantly less frequent in T1DM patients compared to the control group. Both CIITA (rs8048002) and CLEC2D (rs2114870) gene variants were predicted to have regulatory functions, indicated by a RegulomeDB score of (1f) for each. Conclusion: The rare C allele of CIITA rs8048002 genetic variant was associated with an increased risk of developing T1DM, while the less common A allele of CLEC2D rs2114870 was associated with a reduced risk of T1DM. Supplementary Information: The online version contains supplementary material available at 10.1007/s40200-024-01402-w.

The prolactin receptor gene (PRLR) is linked and associated with the risk of polycystic ovarian syndrome.

The prolactin receptor gene (PRLR) may contribute to polycystic ovarian syndrome (PCOS) since it plays important roles in physiological ovarian functions. PRLR-knockout mice have irregular cycles and subfertility and variants in or around the PRLR gene were associated in humans with female testosterone levels and recurrent miscarriage. We tested 40 variants in the PRLR gene in 212 Italian families phenotyped by type 2 diabetes (T2D) and PCOS and found two intronic PRLR-variants (rs13436213 and rs1604428) significantly linked to and/or associated with the risk of PCOS. This is the first study to report PRLR as a novel risk gene in PCOS. Functional studies are needed to confirm these results.

Associations of ARHGAP26 Polymorphisms with Alzheimer's Disease and Cardiovascular Disease.

The Rho GTPase activating protein 26 (ARHGAP26) gene has been reported to be associated with neuropsychiatric diseases and neurodegenerative diseases including Parkinson's disease. We examined whether the ARHGAP26 gene is associated with Alzheimer's disease (AD) and/or cardiovascular disease (CVD). Multivariable logistic regression model was used to examine the associations of 154 single nucleotide polymorphisms (SNPs) within the ARHGAP26 gene with AD and CVD using the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort. Fourteen SNPs were associated with AD (top SNP rs3776362 with p = 3.43 × 10-3), while 37 SNPs revealed associations with CVD (top SNP rs415235 with p = 2.06 × 10-4). Interestingly, 13 SNPs were associated with both AD and CVD. SNP rs3776362 was associated with CVD, Functional Activities Questionnaire (FAQ), and Clinical Dementia Rating Sum of Boxes (CDR-SB). A replication study using a Caribbean Hispanics sample showed that 17 SNPs revealed associations with AD, and 12 SNPs were associated with CVD. The third sample using a family-based study design showed that 9 SNPs were associated with AD, and 3 SNPs were associated with CVD. SNP rs6836509 within the ARHGAP10 gene (an important paralogon of ARHGAP26) was associated with AD and cerebrospinal fluid total tau (t-tau) level in the ADNI sample. Several SNPs were functionally important using the RegulomeDB, while a number of SNPs were associated with significant expression quantitative trait loci (eQTLs) using Genotype-Tissue Expression (GTEx) databases. In conclusion, genetic variants within ARHGAP26 were associated with AD and CVD. These findings add important new insights into the potentially shared pathogenesis of AD and CVD.

Regulatory variants in cancer-related pathway genes predict survival of patients with surgically resected non-small cell lung cancer.

BACKGROUND: We conducted this study to identify genetic variants in cancer-related pathway genes which can predict prognosis of NSCLC patients after surgery, using a comprehensive list of regulatory single nucleotide polymorphisms (SNPs) prioritized by RegulomeDB. METHOD: A total of 509 potentially functional SNPs in cancer-related pathway genes selected from RegulomeDB were evaluated. These SNPs were analyzed in a discovery set (n=354), and a replication study was performed in an independent set (n=772). The association of the SNPs with overall survival (OS) and disease-free survival (DFS) were analyzed. RESULTS: In the discovery set, 76 SNPs were significantly associated with OS or DFS. Among the 76 SNPs, the association was consistently observed for 5 SNPs (ERCC1 rs2298881C>A, BRCA2 rs3092989G>A, NELFE rs440454C>T, PPP2R4 rs2541164G>A, and LTBP4 rs3786527G>A) in the validation set. In combined analysis, ERCC1 rs2298881C>A, BRCA2 rs3092989, NELFE rs440454C>T, and PPP2R4 rs2541164G>A were significantly associated with OS and DFS (adjusted HR ·aHR· for OS=1.46, 0.62, 078, and 0.76, respectively; P=0.003, 0.002, 0.007, and 0.003 respectively; and aHR for DFS=1.27, 0.69, 0.86, and 0.82, respectively; P=0.02, 0.002, 0.03, and 0.008, respectively). The LTBP4 rs3786527G>A was significantly associated with better OS (aHR=0.75; P=0.003). CONCLUSION: Our results suggest that five SNPs in the cancer-related pathway genes may be useful for the prediction of the prognosis in patients with surgically resected NSCLC.

Intronic variant of EGFR is associated with GBAS expression and survival outcome of early-stage non-small cell lung cancer.

BACKGROUND: Genome-wide association studies have indicated that most of the currently identified disease and trait-associated single nucleotide polymorphisms (SNPs) are intronic or intergenic. RegulomeDB is a recently developed database that provides functional annotations for regulatory features of SNPs located in non-coding regions. We evaluated the potential regulatory SNPs in the EGFR gene region using RegulomeDB and their associations with prognosis after surgery in non-small cell lung cancer (NSCLC) patients. METHODS: A total of 698 patients with surgically resected NSCLC were enrolled and seven SNPs were selected based on the RegulomeDB database. All SNPs were genotyped using SEQUENOM MassARRAY iPLEX assay. RESULTS: Among the seven SNPs evaluated, rs9642391 (EGFR ivs19+2851C>G) was significantly associated with survival outcome (adjusted hazard ratio [HR] for overall survival = 0.70, 95% confidence interval [CI] 0.56-0.87, P = 0.001; adjusted HR for disease-free survival = 0.82, 95% CI 0.70-0.97, P = 0.02; under a codominant model). According to RegulomeDB, rs9642391C>G, which is located in intron 19 of EGFR, was predicted to influence the expression of GBAS but not EGFR. As predicted, rs9642391C>G was associated with GBAS (P = 0.024) but not EGFR messenger RNA expression in tumor tissues. CONCLUSION: In conclusion, our study provides evidence that rs9642391C>G in the intron of EGFR is associated with GBAS expression and survival outcomes of patients with surgically resected early-stage NSCLC.

An expression quantitative trait locus variant for LKB1 gene predicts the clinical outcomes of chemotherapy in patients with non-small cell lung cancer.

BACKGROUND: We conducted this study to identify regulatory variants in cancer-related pathway genes which can predict clinical outcomes of chemotherapy in advanced NSCLC, using a comprehensive list of regulatory SNPs prioritized by RegulomeDB. METHODS: A total of 509 potentially functional SNPs in cancer-related pathway genes were evaluated. The SNPs were analyzed in a discovery set (n = 198), and an independent validation set (n = 181). The associations of the SNPs with chemotherapy response and overall survival (OS) were analyzed. RESULTS: In the discovery set, 95 SNPs were significantly associated with clinical outcomes. Among the 95 SNPs, only rs10414193A > G in the intronic region of ARID3A, an eQTL for LKB1, was consistently associated with chemotherapy response and OS in the validation set. In combined analysis, the rs10414193A > G was significantly associated with worse response to chemotherapy (adjusted odds ratio = 0.63, 95% CI = 0.47-0.85, P = 0.002), and with worse OS (adjusted hazard ratio = 1.25, 95% CI = 1.08-1.45, P = 0.004). Luciferase assay showed a significantly higher LKB1 promoter activity associated with rs10414193G allele compared with rs10414193A allele (P = 0.0009). CONCLUSIONS: Our results suggest that rs10414193A > G may be useful for the prediction of clinical outcomes of chemotherapy in advanced NSCLC.

Bridging the gap by discerning SNPs in linkage disequilibrium and their role in breast cancer.

Breast Cancer is the most common cancer among women with several genes involved in disease susceptibility. As majority of genome-wide significant variants fall outside the coding region, it is likely that some of them alter specific gene functions. GWAS database was used to interpret the regulatory functions of these genetic variants. A total of 320 SNPs for breast cancer were selected via GWAS, which were entered into the SNAP web portal tool, to determine the one's found to be in Linkage Disequilibrium (r2 < 0.80). The resulting 2024 proxy SNP's were processed in RegulomeDB to predict their regulatory role. Of these, 1440 produced a score ranging from 1-6, whereas the remaining produced no data. Only the variants under score 4 (cut-off value) in RegulomeDB has been studied further. From these variants, 221 had scores of less than 4, indicating a high degree of potential regulatory role associated with them. Further study revealed that 61 of the 221 SNPs were reported to be genome-wide significant for breast cancer, 52 to be associated with other diseases, 99 as unconfirmed for association with breast cancer, leaving only 9 to be novel proxy SNPs linked to breast cancer. Therefore, the study further confirmed postulation of non-coding variants being linked to disease risk thereby, requiring additional validation through genome-wide association studies to substantiate their underlying mechanism.

Data integration for functional annotation of regulatory single nucleotide polymorphisms associated with Alzheimer's disease susceptibility.

BACKGROUND: Alzheimer's disease (AD), the most common form of dementia affects 24.3 million people worldwide. More than twenty genetic loci have been associated with AD and a significant number of genetic variants were mapped within these loci. A large proportion of genome wide significant variants lie outside the coding region. However, the plausible function of these variants is still unexplored. OBJECTIVE: The present study aimed to unravel the regulatory role of proxy single nucleotide polymorphisms (SNPs), to determine their risk of developing AD. METHODS: The RegulomeDB was employed to predict the regulatory role of proxy SNPs. Protein association network and functional enrichment analysis was performed using String10.5 and gene ontology, respectively. RESULTS: A total of 451 SNPs were examined through SNAP web portal (r2 ≤ 0.80) which returned 2186 proxy SNPs in linkage disequilibrium (LD) with genome wide significant SNPs for AD. Out of 2186 SNPs analyzed in RegulomeDB, 151 had the scores < 3 that indicates the high degree of their potential regulatory function. Further analysis revealed that out of these 151 SNPs, 37 were genome wide significant for AD, 17 were significantly associated with diseases other than AD, 89 were proxy SNPs (not genome wide significant) for various diseases including AD while 8 SNPs were novel proxy SNPs for AD. CONCLUSION: These findings support the notion that the non-coding variants can be strongly associated with disease risk. Further validation through genome wide association studies will be helpful for the elucidation of their regulatory potential.

MAPK and ERK polymorphisms are associated with PCOS risk in Chinese women.

In this case-control study, we analyzed the association between eight RegulomeDB-annotated single nucleotide polymorphisms (SNPs) in the MEK1, MEK2, ERK1 and ERK2 genes and polycystic ovarian syndrome (PCOS). Logistic regression analysis demonstrated that MEK1 rs12050732 (OR = 1.29 [95%CI: 1.06-1.58], P = 0.012), ERK2 rs2266966 (OR = 0.81 [95%CI: 0.67-0.99], P = 0.040) and ERK2 rs5999521 (OR = 0.66 [95%CI: 0.51-0.86], P = 0.002) were associated with PCOS risk without adjusting for age and body mass index. Moreover, PCOS risk increased with allele dosage when these three polymorphisms were combined (Ptrend = 0.001). These findings suggest that genetic variants in key MAPK and ERK genes contribute to PCOS risk in Chinese women.

Functional intronic ERCC1 polymorphism from regulomeDB can predict survival in lung cancer after surgery.

We searched for potential regulatory single nucleotide polymorphisms (SNPs) in excision repair cross-complementing group 1 (ERCC1) using RegulomeDB, a database integrating information from the Encyclopedia of DNA Elements (ENCODE) project, and investigated their association with survival after surgery in non-small cell lung cancer (NSCLC). Among 364 SNPs found within ERCC1 region using RegulomeDB, four top priority SNPs (rs2298881C>A, rs1049739A>G, rs10415949A>G and rs6509214G>T) were selected for this study. The four SNPs were investigated in 316 patients. A replication study was performed (n = 579). Of the four SNPs analyzed in the discovery set, rs2298881C>A and rs6509214G>T were significantly associated with survival outcomes. The association was consistently observed only for rs2298881C>A in the validation cohort. In combined analysis, rs2298881C>A was significantly associated with worse overall survival and disease-free survival (P = 0.0002 and 0.02, respectively). A decreased reporter gene expression for rs2298881 A allele was observed compared with C allele by luciferase assay (P = 0.02). ERCC1 rs2298881C>A, an intronic SNP, is the first genetic polymorphism with functional evidence of regulating its expression, and the SNP is associated with prognosis of NSCLC. Our result supports the role of RegulomeDB as a comprehensive source of prioritized candidate SNPs for genetic association studies.

Putative functional variants of XRCC1 identified by RegulomeDB were not associated with lung cancer risk in a Korean population.

The Encyclopedia of DNA elements (ENCODE) project revealed that nearby or distantly located non-coding DNA regulates the expression of coding genes. RegulomeDB (http://regulome.stanford.edu) is a new database that can be used to predict whether a variant affects transcription factor binding and gene expression. We investigated the association between lung cancer risk and potentially functional polymorphisms of XRCC1 that were selected using RegulomeDB in a Korean population. A total of 185 polymorphisms of XRCC1 were evaluated using RegulomeDB. Strong evidence suggested that 10 polymorphisms, from among the 185, affected XRCC1 expression with scores of 1a-1f that were based on the RegulomeDB scoring system. The rs2854510 polymorphism was rare in Asians (minor allele frequency < 0.05). Eight polymorphisms were in strong linkage disequilibrium (LD). The rs2854509 polymorphism, which was one of the 8 polymorphisms in LD, and rs7248167, which was not in the LD block, were genotyped in 610 lung cancer patients and 607 age- and sex-matched controls. Additionally, four polymorphisms of XRCC1 (rs25487, rs25489, rs1799782, and rs3213245), which were investigated with regard to their association with lung cancer risk in previous studies, were also genotyped. Two polymorphisms (rs2854509 and rs7248167) that were predicted to affect XRCC1 expression based on their RegulomeDB scores were not associated with lung cancer risk (P = 0.31 and 0.93, respectively). When stratified according to age, gender, smoking status, and tumor histology, the two polymorphisms of XRCC1 were not associated with lung cancer risk. Among the four polymorphisms that were previously studied, only rs25489 of XRCC1 was significantly associated with lung cancer risk (dominant model, adjusted odds ratio = 0.61, 95% confidence interval = 0.46-0.83, P = 0.002). Although RegulomeDB is an attractive tool for predicting the regulatory potential of variants, the two polymorphisms that were selected using RegulomeDB were not associated with lung cancer risk.