Genome-wide association study combined with biological context can reveal more disease-related SNPs altering microRNA target seed sites

A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis

We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. With unsupervised clustering algorithms we group these patient-specific networks into four distinct clusters driven by PRKCB, HLA, SNAI1/CEBPB/PTPN1 and VEGFA/XPO5/POLH hubs. The pathway analysis identifies calcium homeostasis, wound healing and cell motility as key processes in UC pathogenesis. Using transcriptomic data from an independent patient cohort, with three complementary validation approaches focusing on the SNP-affected genes, the patient specific modules and affected functions, we confirm the regulatory impact of non-coding SNPs. iSNP identified regulatory effects for disease-associated non-coding SNPs, and by predicting the patient-specific pathogenic processes, we propose a systems-level way to stratify patients.

Single Nucleotide Polymorphisms (SNPs) affect cellular regulatory networks, and SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Here the authors introduce iSNP, a precision medicine pipeline that combines genomics and network biology approaches to uncover patient specific pathways affected in complex diseases.

Impact of miRNA-binding site polymorphisms in STAT3 gene on occurrence and clinical characteristics of systemic lupus erythematosus

BACKGROUND

Signal transducer and activator of transcription 3 (STAT3) is a major regulator of immune response and chronic inflammatory conditions acting through regulation of B cells, T-helper 17 (Th17) cells, and IL-17 production. Previous studies have demonstrated that dysregulation of STAT3 is crucial for SLE pathogenesis and disease severity. It is believed that single nucleotide polymorphisms (SNPs) located at the 3'-UTR sequence of the target genes could dysregulate their expression by disrupting the binding site of miRNAs. In the present study, we assessed the possible association between rs1053005 and rs1053023 SNPs at miRNA binding sites in the STAT3 gene and the risk of SLE in the Iranian population for the first time.

METHODS

112 SLE cases and 120 healthy controls were genotyped for rs1053005 (A>G) and rs1053023 (A>G) polymorphisms in STAT3 using real-time PCR high resolution melting method (HRM).

RESULTS

Our results revealed substantial associations between GG genotype and G allele of rs1053023 with enhanced risk of SLE (OR for GG genotype= 3.13; 95%CI [1.61-6.1], OR for G allele = 2.22; 95%CI [1.51-3.25]). However, no important correlations have been found between rs1053005 polymorphism and SLE susceptibility in this population (p>0.05). Moreover, stratification analysis showed that these polymorphisms are correlated with parameters indicating disease activity and more severe course of the disease. These factors include some laboratory test results and clinical manifestations such as renal involvements.

CONCLUSION

The current study suggests a significant association between STAT3 polymorphisms and augmented risk of SLE, clinical symptoms, disease activity, and severity.

MiR-139-5p has an antidepressant-like effect by targeting phosphodiesterase 4D to activate the cAMP/PKA/CREB signaling pathway

Background

Phosphodiesterase 4D (PDE4D) inhibitor is commonly used to treat depression, but side effects seriously decrease its efficacy. PDE4D was a downstream target mRNA of miR-139-5p. Therefore, we examined the effects of hippocampal miR-139-5p gain- and loss-of-function on depression-like behaviors, the expression level of PDE4D, and hippocampus neurogenesis.

Methods

Bioinformatic analyses were carried out to to screen differential genes. Quantitative real-time polymerase chain reaction (qRT-PCR) and luciferase reporter assay were used to confirm the relationship between miR-139-5p and PDE4D. MiR-139-5p mimics, miR-139-5p inhibitor, or miR-NC were used to explore the function of miR-139-5p in HT-22 cells. We further explored the role of miR-139-5p in vivo using AAV-injection. Elisa, western blotting, and fluorescence in situ hybridization (FISH) were used to detect the expression of miR-139-5p and PDE4D in CRC tissues.

Results

Here, we showed that PDE4D messenger RNA (mRNA) was a direct target of microRNA (miR)-139-5p, which was downregulated in a chronic ultra-mild stress (CUMS)-induced depression mouse model. Moreover, in experiments in vitro, miR-139-5p mimic repressed PDE4D expression in HT-22 cells, but promoted phosphorylated cyclic-AMP response element-binding protein (p-CREB) and brain-derived neurotrophic factor (BDNF) expression. Interestingly, adeno-associated virus (AAV)-miR-139-5p downregulated susceptibility to stress-induced depression-like behaviors in mice. AAV-miR-139-5p suppressed PDE4D in mouse hippocampal cells, increasing expression level of cyclic adenosine monophosphate (cAMP), p-CREB, and BDNF, and stimulating mouse hippocampal neurogenesis.

Conclusions

Our findings suggested that miR-139-5p acted like an antidepressant by targeting PDE4D, thereby regulating the cAMP/protein kinase A (PKA)/CREB/BDNF pathway to improve depression.

Genetic Association Analysis Implicates Six MicroRNA-Related SNPs With Increased Risk of Breast Cancer in Australian Caucasian Women

INTRODUCTION

Breast cancer (BC), a heterogeneous disease, features microRNA-related single nucleotide polymorphisms (miRSNPs) as underlying factors of BC development, thus providing targets for novel diagnostic and therapeutic strategies. This study investigated miRSNPs in BC susceptibility in Australian Caucasian women.

PATIENTS AND METHODS

The study population included patients 33 to 80 years of age stratified by molecular subtypes of breast tumors (luminal A, 47.59%), stage (stage I, 36.96%), tumor-type (ductal, 44.95%), grading (intermediate, 35.52%), size (10.1-25 mm, 31.14%), and lymph node (sentinel negative, 38.93%). Sixty-five miRSNPs underwent allelic analysis in two independent case-control cohorts (GU-CCQ-BB, 377 cases and 521 controls; GRC-BC, 267 cases and 201 controls) using a MassARRAY platform. GU-CCQ-BB, GRC-BC, and the combined populations (BC-CA) (644 cases and 722 controls) underwent independent statistical analysis.

RESULTS

In the GU-CCQ-BB population, miRSNPs TET2-rs7670522, ESR1-rs2046210, FGFR2-rs1219648, MIR210-rs1062099, HIF1A-rs2057482, and CASC16-rs4784227 were found to be associated with increased BC risk (P ≤ .05). Only ESR1-rs2046210 was also significantly associated (P ≤ .05) when replicated in the GRC-BC and BC-CA populations. No significant association was correlated with BC-clinical features (pathological types and ER/PR/HER2 status); however, MIR210-rs1062099 was found to be significantly associated (P ≤ .05) with age (>50 years) in the GU-CCQ-BB cohort.

CONCLUSION

This is the first study to demonstrate the association of MIR210-rs1062099 and TET2-rs7670522 with increased BC risk. Additionally, four previously reported SNPs (ESR1-rs2046210, FGFR2-rs1219648, HIF1A-rs2057482, and CASC16-rs4784227) were confirmed as BC risk variants. Replication and functional studies in larger Caucasian cohorts are necessary to elucidate the role of these miRSNPS in the development of BC.

Influence of single nucleotide polymorphisms in pri-miR-124-1 and STAT3 genes on gastric cancer susceptibility

INTRODUCTION

MicroRNAs (miRNAs) are small ribonucleic acids that modulate the expression of downstream target genes. There is considerable evidence of their involvement in many malignancies, such as oesophageal and gastric. We hypothesised altered expressions of pri-miR-124-1 rs531564 and STAT3 rs1053023 polymorphisms in gastric cancer.

MATERIALS AND METHODS

Genomic DNA was extracted from peripheral blood of 250 patients with gastric cancer and 310 healthy individuals. The RFLP method was applied for determination of pri-miR-124 polymorphism and the AS-PCR method for STAT3 polymorphism.

RESULTS

The distribution of rs531564 genotypes in cases and controls was different: the G allele carriers had a reduced gastric cancer risk (OR = 0.62; 95%CI = 0.49-0.80, P = 0.0002). Presence of the minor allele of STAT3 (rs1053023) was linked with higher risk of gastric cancer (OR = 2.29; 95% CI = 1.79-2.93, P < 0.0001). Compared with the most frequent haplotype C-G [the SNP order was pri-miR-124-1 (rs531564) and STAT3 (rs1053023)] in controls, C-A haplotype was associated with a significantly increased risk of gastric cancer (OR = 2.28; 95%CI = 1.64-3.09, P < 0.0001).

CONCLUSION

There is a strong link between pri-miR-124-1 rs531564 and STAT3 rs1053023 and gastric cancer that may be pathogenic, and so worthy of further investigation.

Distinguishing the disease-associated SNPs based on composition frequency analysis

Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and thus arouse posttranscriptional level abnormality. Therefore, SNP has a strong correlation with diseases. Although enormous SNPs have been experimentally identified, only a tiny proportion of them are truly disease-associated SNPs (dSNPs) that relate to microRNA modification and then are involved in disease causing process. Therefore, it is important to distinguish dSNPs from the usual SNPs. Analysis here shows that composition is different between sequence segments centered by dSNP and SNP. Inspired by the composition, transition and distribution features which are meaningful and effective in characterizing proteins' sequence information, we improved and applied it to represent the frequency and physicochemical properties of a gene sequence. Binary encoding scheme was also used for further labelling four nucleic acids (A, T, C, and G). First, clustering analysis was performed to gain reasonable negative samples. Then, optimization tests were implemented on different ratios of positive vs negative samples and different feature subsets retrieved by evaluation method of F score. The optimal model constructed by random forest achieves an accuracy of more than 90% on the testing data set. Moreover, the promising results of the external validation also demonstrate the practical applicability of our method. Finally, principal component analysis on the features indicates that all features in our method gain the gross contribution to the prediction model.

MicroRNA gene polymorphisms and the risk of colorectal cancer

The present study was carried out to demonstrate the epidemiological value of microRNA (miRNA) in colorectal cancer (CRC) by investigating the association between miRNA gene polymorphisms and the susceptibility to CRC. Multiple meta-analyses of reported data were conducted, and odds ratio values and 95% confidence intervals were used to assess these associations. Stata 11.0 software was used to analyze the data and the modified Jadad quality score was employed to evaluate the quality of the retrieved studies. We retrieved 38 studies on the association between miRNA polymorphisms and risk of CRC, however only 15 met the requirements of the inclusion criteria. In conclusion, we identified a variety of miRNAs (miRNA-let-7, miR-34b/c, miR-146a, miR-603 and miR-149) gene polymorphisms that are associated with susceptibility to CRC. However, some miRNAs (miR-192a, miR-608 and miR-27a) are associated with CRC, but not susceptibility to CRC. The results have limitations given the relatively low number of studies available. Therefore, it is necessary to collect data from large sample-size studies to further validate the results.