A functional SNP in the 3'-UTR of TAP2 gene interacts with microRNA hsa-miR-1270 to suppress the gene expression

Research hotspots and trends regarding microRNAs in hypertension: a bibliometric analysis

To investigate the research levels, hotspots, and development trends regarding microRNAs in hypertension, this study conducted a visual analysis of studies on miRNA in hypertension based on the Web of Science core collection database using CiteSpace and VOSviewer analysis software along with literature from 2005-2023 as information data. Using citation frequency, centrality, and starting year as metrics, this study analyzed the research objects. It revealed the main research bodies and hotspots and evaluated the sources of literature and the distribution of knowledge from journals and authors. Finally, the potential research directions for miRNAs in hypertension are discussed. The results showed that the research field is in a period of vigorous development, and scholars worldwide have shown strong interest in this research field. A comprehensive summary and analysis of the current research status and application trends will prove beneficial for the advancement of this field.

miRNA-767 and its binding site polymorphism in the mTOR gene act as potential biomarkers for female reproductive cancers

Aims: The present study aimed to understand the relationship between the mTOR gene SNP (rs2536) and reproductive cancer risk. The expression level of miRNA-767 was also assessed. Methods: 700 tumor samples (300 breast, 200 ovarian and 200 cervical cancers), along with adjacent uninvolved control tissue, were used. rs2536 was screened using Tetra-ARMS PCR and expression level of miRNA-767 was assessed using quantitative PCR. Results: The frequency of the homozygous mutant genotype of rs2536 was observed significantly higher in breast (p < 0.04), ovarian (p < 0.005) and cervical (p < 0.003) cancers. Significant downregulation of miRNA-767 was observed in tumors compared with controls. Conclusion: The present study demonstrates that increased mutant frequency of rs2536 and deregulation of miRNA-767 are associated with increased reproductive cancer risk.

SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility

The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.

Asian-specific 3'UTR variant in CDKN2B associated with risk of pituitary adenoma

BACKGROUND

Previous genomewide association studies (GWASs), single nucleotide polymorphisms (SNPs) on cyclin-dependent kinase inhibitor 2 A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and cyclin-dependent kinase inhibitor 2B antisense RNA1 (CDKN2B-AS1) were reported as risk loci for glioma, a subgroup of the brain tumor. To further characterize this association with the risk of brain tumors in a Korean population, we performed a fine-mapping association study of CDKN2A, CDKN2B, and CDKN2B-AS1.

METHODS AND RESULTS

A total of 17 SNPs were selected and genotyped in 1,439 subjects which were comprised of 959 patients (pituitary adenoma 335; glioma 324; meningioma 300) and 480 population controls (PCs). We discovered that a 3'untranslated region (3'UTR) variant, rs181031884 of CDKN2B (Asian-specific variant), had significant association with the risk of pituitary adenoma (PA) (Odds ratio = 0.58, P = 0.00003). Also, rs181031884 appeared as an independent causal variant among the significant variants in CDKN2A and CDKN2B, and showed dose-dependent effects on PA.

CONCLUSIONS

Although further studies are needed to verify the impact of this variant on PA susceptibility, our results may help to understand CDKN2B polymorphism and the risk of PA.

Association of miRNA targetome variants in LAMC1 and GNB3 genes with colorectal cancer and obesity

Background

Colorectal cancer (CRC) is one of the most common obesity‐associated cancers. Inflammation is also considered the most important factor between obesity and CRC. This study aimed to examine miRNAs binding sites variants on inflammatory genes identified using bioinformatics and systematic approach on clinical samples that were collected from CRC patients and controls.

Methods

The candidate variants related to CRC inflammatory genes were obtained from genome‐wide association studies and their population‐specific haplotypes. The variants were analyzed according to their genomic position on the miRNA targetome. Targetome variants in inflammation‐related genes were selected for genetic association study by TaqMan genotyping assay.

Results

The GG genotype of rs7473 decreased the risk of obesity (p < 0.05). Heterozygous genotype (GA) of rs1547715 decreased the risk of CRC (p < 0.05). In the rs7473/rs1547715 genotype and haplotype, the frequencies of AA/GA and GG/AA lessened in CRC and obesity, respectively (p < 0.05).

Conclusions

The variants of rs7473 and rs1547715 were associated with obesity and CRC, respectively. The above‐mentioned associations could be made based on the interactions of these variants with miRNAs.

LncRNA ASMTL-AS1/microRNA-1270 differentiate prognostic groups in gastric cancer and influence cell proliferation, migration and invasion

The objective of this study was to determine the expression levels of ASMTL-AS1 and miR-1270 in gastric cancer, and to explore whether ASMTL-AS1 and miR-1270 is associated with cancer prognosis and progression or not. ASMTL-AS1 and miR-1270 expression were quantified in gastric cancer tissues and adjacent normal tissues (n = 167) and cell lines. The potential of ASMTL-AS1 and miR-1270 as prognostic biomarkers was evaluated by the receiver operating characteristic (ROC) curve, Kaplan-Meier, and multivariate Cox regression analyses. The binding between ASMTL-AS1 and miR-1270 was verified by the Luciferase reporter assay and RNA pull-down assay. Functional roles of ASMTL-AS1/miR-1270 on cells were investigated in HGC-27 and NCI-N87 cells by MTS viability, Transwell migration, and Matrigel invasion assay. ASMTL-AS1 was significantly downregulated while miR-1270 was upregulated in gastric cancer tissues as compared with normal tissue and cell lines. According to the studies, ASMTL-AS1 and miR-1270 were related to unfavorable clinical parameters, such as the advanced TNM stage. Downregulated ASMTL-AS1 and upregulated miR-1270 were associated with reduced 5-year overall survival. Functional studies suggested that ASMTL-AS1 inhibits proliferation, migration, and invasion of HGC-27 and NCI-N87 cells by regulation of miR-1270. In summary, ASMTL-AS1 and miR-1270 are associated with poor prognosis of patients with gastric cancer. ASMTL-AS1 inhibited gastric cancer progression by regulating miR-1270. Therefore, ASMTL-AS1/miR-1270 may be a potential prognostic biomarker and novel strategy for gastric cancer targeted therapy.

An SNP at the target site of cid-miR-nov-1043 in the TOLLIP 3' UTR decreases mortality rate in grass carp subjected to ENU-induced mutagenesis following grass carp reovirus infection

N-ethyl-N-nitrosourea (ENU) selection is a useful technique to generate new mutations that may cause some functional changes in the gene. Through our previous genomic bulked segregant analysis (BSA), one single nucleotide polymorphism (SNP) at the 3' UTR of Toll interacting protein gene (TOLLIP^982T>C) was identified in grass carp (Ctenopharyngodon idella) subjected to ENU-induced mutagenesis. We found that the overexpression of cid-miR-nov-1043 mimics significantly suppressed the luciferase activity of the TOLLIP 3' UTR, but TOLLIP^982T>C mutation at the target site can decrease the binding affinity between the miRNA cid-miR-nov-1043 and TOLLIP 3' UTR, reducing the inhibition of TOLLIP mRNA transcription in grass carp subjected to ENU-induced mutagenesis. More importantly, we demonstrated that TOLLIP mRNA transcription levels in the gills, liver, kidney and the isolate white cells of the mutant grass carp were significantly (p < 0.01) higher than those in the corresponding tissues from the wild-type grass carp following infection with Grass Carp Reovirus (GCRV) for seven days, while the downstream gene of TOLLIP transforming growth factor β-activated kinase 1 (TAK1) and TAK1-binding protein 1 (TAB1), were higher expressed in wild-type grass carp. As a negative regulator in the pro-inflammatory pathway of NF-κB, TOLLIP inhibits the excessive inflammation in ENU grass carp after GCRV infection. Consistent with the TOLLIP expression, histopathological results demonstrated more severe inflammation in wild-type grass carp, compared to the TOLLIP^982T>C mutant grass carp on the seventh day. Severe inflammation will lead to thoroughly infiltration of chloride and inflammatory cells in the gill filaments. This seriously hindered the exchange of oxygen, which ultimately disrupted blood circulation. Meanwhile, the survival rate of the mutant grass carp was significantly (p < 0.01) higher than that of the wild-type grass carp, indicating that the TOLLIP^982T>C mutants showed strong anti-viral abilities. Our results revealed that an SNP in the TOLLIP 3' UTR may contribute to the suppression of serve inflammation subjected to ENU-induced mutagenesis following GCRV infection, which may be helpful for future resistant breeding development of grass carp.

miR-15a-3p Protects Against Isoniazid-Induced Liver Injury via Suppressing N-Acetyltransferase 2 Expression

Isoniazid (INH), an effective first-line drug for tuberculosis treatment, has been reported to be associated with hepatotoxicity for decades, but the underlying mechanisms are poorly understood. N-acetyltransferase 2 (NAT2) is a Phase II enzyme that specifically catalyzes the acetylation of INH, and NAT2 expression/activity play pivotal roles in INH metabolism, drug efficacy, and toxicity. In this study, we systematically investigated the regulatory roles of microRNA (miRNA) in NAT2 expression and INH-induced liver injury via a series of in silico, in vitro, and in vivo analyses. Four mature miRNAs, including hsa-miR-15a-3p, hsa-miR-628-5p, hsa-miR-1262, and hsa-miR-3132, were predicted to target the NAT2 transcript, and a negative correlation was observed between hsa-miR-15a-3p and NAT2 transcripts in liver samples. Further experiments serially revealed that hsa-miR-15a-3p was able to interact with the 3′-untranslated region (UTR) of NAT2 directly, suppressed the endogenous NAT2 expression, and then inhibited INH-induced NAT2 overexpression as well as INH-induced liver injury, both in liver cells and mouse model. In summary, our results identified hsa-miR-15a-3p as a novel epigenetic factor modulating NAT2 expression and as a protective module against INH-induced liver injury, and provided new clues to elucidate the epigenetic regulatory mechanisms concerning drug-induced liver injury (DILI).

Influence of the rs6736 Polymorphism on Ischemic Stroke Susceptibility in Han Chinese Individuals via the Disruption of miR-7-1 Binding to the C14orf119 Gene

This study investigates the association between the C14orf119 gene rs6736 polymorphism and ischemic stroke (IS) susceptibility, and explores the influence of the rs6736 polymorphism on the binding between miR-7-1 and the C14orf119 gene. mRNA expression levels were determined in 45 IS patients and 45 matched controls via real-time quantitative PCR. A total of 774 IS patients and 793 matched controls were recruited from a Han Chinese population for genotyping, performed with the Sequenom MassARRAY iPLEX platform. A dual-luciferase reporter assay was used for the analysis of miRNA-mRNA binding. The results showed that the mRNA expression of C14orf119 differed significantly between IS patients and controls (t =  -2.235, P = 0.030). Significant associations were noted between the C14orf119 gene rs6736 polymorphism and IS susceptibility in Han Chinese individuals under the additive model [OR_adj (95% CI) = 0.87 (0.76-1.00) P_adj = 0.048] and dominant model [OR_adj (95% CI) = 0.76 (0.61-0.94), P_adj = 0.014], with adjustment for age and sex. Mutations in the rs6736 polymorphism disrupted the binding of miR-7-1 and the C14orf119 gene. The results of this study show that the rs6736 polymorphism in the 3'-untranslated region of the C14orf119 gene not only is associated with IS but also modifies the binding between miR-7-1 and the C14orf119 gene. The C14orf119 gene may participate in the relationship between IS and miR-7-1.

Variations in the insulin receptor substrate 1 (IRS1) and its association with growth traits in Chinese black Tibetan sheep (Ovis aries)

This paper presented the results on the study of insulin receptor substrate 1 (IRS1) polymorphisms in Chinese black Tibetan sheep. Via DNA direct sequencing, four variations within 3' untranslated region (UTR) of IRS1, including g.9382T > G, g.9569T > G, g.9572C > T and g.9695A > C were detected in the black Tibetan sheep population. Based on the χ² test, those four loci deviated from Hardy-Weinberg equilibrium (p < 0.05). In g.9569T > G locus, genotype of GG possessed advantage on body weight (p < 0.05). In g.9572C > T locus, individuals with genotype of TT homozygous mutation decreased significantly on body weight, withers height, body length and chest circumference (p < 0.05 or p < 0.01). In g.9695A > C locus, the body weight and chest circumference were also higher in AA carriers than in CC carriers (p < 0.05). Our results provided evidence that polymorphisms in IRS1 were associated with growth efficiency traits by quantitative genetic analysis, and may be used for marker-assisted selection in Chinese indigenous sheep.

A functional SNP in miR-625-5p binding site of AKT2 3'UTR is associated with noise-induced hearing loss susceptibility in the Chinese population

The purposes of the current study were to investigate the association of a few of single nucleotide polymorphisms (SNPs) within the AKT2 gene and noise-induced hearing loss (NIHL) susceptibility and explore the potential mechanism underlying NIHL. Three SNPs (rs2304186, rs41275750, and rs76524493) were genotyped in a Chinese population which consists of 690 NIHL patients and 650 normal hearing controls. Bioinformatic analysis was conducted to predict the potential miRNA-binding site of SNPs. Plasmid construction, cell transfection, and dual-luciferase reporter assay were performed to investigate the potential molecular mechanism of SNPs involving in NIHL. The results revealed that rs2304186 GT genotype (OR = 1.41; 95% CI = 1.09-1.83) and TT genotype (OR = 1.51; 95% CI = 1.08-2.10) imparted increased risk of NIHL, and the increased risk could also be found in a dominant model (OR = 1.44; 95% CI = 1.12-1.84). The stratification analysis showed that rs2304186 GT/TT conferred a higher risk for NIHL, especially in subgroups of male, age (35-45 and > 45 years), noise exposure time (> 16 years), and noise exposure level (≤ 85 and ≥ 92 dB), when GG genotype as a reference. Furthermore, the haplotype TCCTACT (rs2304186-rs41275750-rs76524493) was found to be significantly associated with a high risk of NIHL (OR = 1.19; 95% CI = 1.02-1.40). Functional experiments showed that rs2304186 G allele combined with hsa-miR-625-5p mimics could significantly decrease the luciferase activity compared with T allele, indicating that rs2304186 altered the binding affinity of hsa-miR-625-5p to SNP rs2304186 mutation region, thus directly targeting AKT2 gene. In conclusion, our study provides evidence for the first time that SNP rs2304186 of AKT2 3'UTR might affect NIHL susceptibility by altering the binding affinity of has-miR-625-5p to mutation region in an allele-specific manner and it may act as a potential biomarker of NIHL susceptibility.

Evaluating the Effect of 3'-UTR Variants in DICER1 and DROSHA on Their Tissue-Specific Expression by miRNA Target Prediction

Untranslated gene regions (UTRs) play an important role in controlling gene expression. 3'-UTRs are primarily targeted by microRNA (miRNA) molecules that form complex gene regulatory networks. Cancer genomes are replete with non-coding mutations, many of which are connected to changes in tumor gene expression that accompany the development of cancer and are associated with resistance to therapy. Therefore, variants that occurred in 3'-UTR under cancer progression should be analysed to predict their phenotypic effect on gene expression, e.g., by evaluating their impact on miRNA target sites. Here, we analyze 3'-UTR variants in DICER1 and DROSHA genes in the context of myelodysplastic syndrome (MDS) development. The key features of this analysis include an assessment of both "canonical" and "non-canonical" types of mRNA-miRNA binding and tissue-specific profiling of miRNA interactions with wild-type and mutated genes. As a result, we obtained a list of DICER1 and DROSHA variants likely altering the miRNA sites and, therefore, potentially leading to the observed tissue-specific gene downregulation. All identified variants have low population frequency consistent with their potential association with pathology progression.

Determination of the effect of functional single-nucleotide polymorphisms associated with glycerolipid synthesis on intramuscular fat deposition in Korean cattle steer

Intramuscular fat deposition in the longissimus dorsi muscle (LM) of Korean cattle steer is regulated by several genes related to lipid metabolism. One of these genes encodes the enzyme bovine glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), which is located on the mitochondrial outer membrane and catalyzes the initial and committed step of glycerolipid synthesis in lipid metabolism of cattle. Previous studies have shown that the 3' -untranslated region (UTR) of the GPAM is quite extended and contains a polyadenylation signal site, erythroid 15-lipoxygenase differentiation control elements (15-LOX-DICEs), and cytoplasmic polyadenylation elements (CPEs) that affect the regulation of triacylglycerol synthesis. Therefore, the aim of this study was to identify single-nucleotide polymorphisms (SNPs) related to the regulation of glycerolipid synthesis in the 3' -UTR of GPAM and to verify the function of SNPs affecting the deposition of intramuscular fat in Korean cattle steer. In the present study, 11 SNPs were discovered in the 3' -UTR of GPAM. Among these SNPs, g.54853A > G, g.55441A > G, and g.55930C > T were significantly associated with marbling score in a Korean cattle steer population and were strongly correlated with each other within the GPAM gene. Furthermore, based on the results predicted by the RNAhybrid program, four putative microRNAs (miRNAs) were identified, and the above SNPs were found to present in the seed region of these miRNAs. These miRNAs have a differential binding affinity for each allele of SNPs g.54853A > G, g.55441A > G, and g.55930C > T. The in vivo evidence of intramuscular fat deposition in the LM tissue showed that these SNPs affected the regulation of intramuscular fat deposition in Korean cattle steer. Thus, the g.54853A > G, g.55441A > G, and g.55930C > T could be considered as causal mutations regulating intramuscular fat deposition in Korean cattle steer.

Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting resistance in wheat

Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality worldwide. Previously, we cloned a PHS resistance gene, TaPHS1, and identified two causal mutations for reduced seed dormancy (SD) and increased PHS susceptibility. Here we identified a novel allelic variation of C to T transition in 3'-UTR of TaPHS1, which associated with reduced SD and PHS resistance. The T allele occurred in wild wheat progenitors and was likely the earliest functional mutation in TaPHS1 for PHS susceptibility. Allele frequency analysis revealed low frequency of the T allele in wild diploid and tetraploid wheat progenitors, but very high frequency in modern wheat cultivars and breeding lines, indicating that artificial selection quickly enriched the T allele during modern breeding. The T allele was significantly associated with short SD in both T. aestivum and T. durum, the two most cultivated species of wheat. This variation together with previously reported functional sequence variations co-regulated TaPHS1 expression levels and PHS resistance in different germplasms. Haplotype analysis of the four functional variations identified the best PHS resistance haplotype of TaPHS1. The resistance haplotype can be used in marker-assisted selection to transfer TaPHS1 to new wheat cultivars.

SNPs in Sites for DNA Methylation, Transcription Factor Binding, and miRNA Targets Leading to Allele-Specific Gene Expression and Contributing to Complex Disease Risk: A Systematic Review

INTRODUCTION

The complex genetic diversity among human populations results from an assortment of factors acting at various sequential levels, including mutations, population migrations, genetic drift, and selection. Although there are a plethora of DNA sequence variations identified through genome-wide association studies (GWAS), the challenge remains to explain the mechanisms underlying interindividual phenotypic disparity accounting for disease susceptibility. Single nucleotide polymorphisms (SNPs) present in the sites for DNA methylation, transcription factor (TF) binding, or miRNA targets can alter the gene expression. The systematic review aimed to evaluate the complex crosstalk among SNPs, miRNAs, DNA methylation, and TFs for complex multifactorial disease risk.

METHODS

PubMed and Scopus databases were used from inception until May 15, 2019. Initially, screening of articles involved studies assessing the interaction of SNPs with TFs, DNA methylation, or miRNAs resulting in allele-specific gene expression in complex multifactorial diseases. We also included the studies which provided experimental validation of the interaction of SNPs with each of these factors. The results from various studies on multifactorial diseases were assessed.

RESULTS

A total of 11 articles for SNPs interacting with DNA methylation, 30 articles for SNPs interacting with TFs, and 11 articles for SNPs in miRNA binding sites were selected. The interactions of SNPs with epigenetic factors were found to be implicated in different types of cancers, autoimmune diseases, cardiovascular diseases, diabetes, and asthma.

CONCLUSION

The systematic review provides evidence for the interplay between genetic and epigenetic risk factors through allele-specific gene expression in various complex multifactorial diseases.

Identification of microRNAs Targeting the Transporter Associated with Antigen Processing TAP1 in Melanoma

The underlying molecular mechanisms of the aberrant expression of components of the HLA class I antigen processing and presentation machinery (APM) in tumors leading to evasion from T cell-mediated immune surveillance could be due to posttranscriptional regulation mediated by microRNAs (miRs). So far, some miRs controlling the expression of different APM components have been identified. Using in silico analysis and an miR enrichment protocol in combination with small RNA sequencing, miR-26b-5p and miR-21-3p were postulated to target the 3′ untranslated region (UTR) of the peptide transporter TAP1, which was confirmed by high free binding energy and dual luciferase reporter assays. Overexpression of miR-26b-5p and miR-21-3p in melanoma cells downregulated the TAP1 protein and reduced expression of HLA class I cell surface antigens, which could be reverted by miR inhibitors. Moreover, miR-26b-5p overexpression induced a decreased T cell recognition. Furthermore, an inverse expression of miR-26b-5p and miR-21-3p with TAP1 was found in primary melanoma lesions, which was linked with the frequency of CD8⁺ T cell infiltration. Thus, miR-26-5p and miR-21-3p are involved in the HLA class I-mediated immune escape and might be used as biomarkers or therapeutic targets for HLA class I^low melanoma cells.

Expression quantitative trait loci in ABC transporters are associated with survival in 5-FU treated colorectal cancer patients

The chemotherapeutic efficacy in colorectal cancer (CRC) is limited due to the inter-individual variability in drug response and the development of tumour resistance. ATP-binding cassette (ABC) transporters are crucial in the development of resistance by the efflux of anticancer agents from cancer cells. In this study, we identified 14 single nucleotide polymorphisms (SNPs) in 11 ABC transporter genes acting as an expression of quantitative trait loci (eQTLs), i.e. whose variation influence the expression of many downstream genes. These SNPs were genotyped in a case–control study comprising 1098 cases and 1442 healthy controls and analysed in relation to CRC development risk and patient survival. Considering a strict correction for multiple tests, we did not observe any significant association between SNPs and CRC risk. The rs3819720 polymorphism in the ABCB3/TAP2 gene was statistically significantly associated with shorter overall survival (OS) in the codominant, and dominant models [GA vs. GG, hazard ratio (HR) = 1.48; P = 0.002; AA vs. GG, HR = 1.70; P = 0.004 and GA + AA vs. GG, HR = 1.52; P = 0.0006]. Additionally, GA carriers of the same SNP displayed worse OS after receiving 5-FU based chemotherapy. The variant allele of rs3819720 polymorphism statistically significantly affected the expression of 36 downstream genes. Screening for eQTL polymorphisms in relevant genes such as ABC transporters that can regulate the expression of several other genes may help to identify the genetic background involved in the individual response to the treatment of CRC patients.

A SNP in the 3'UTR of the porcine IGF-1 gene interacts with miR-new14 to affect IGF-1 expression, proliferation and apoptosis of PK-15 cells

The kidney of miniature pigs has been considered the most likely potential kidney source for patients needing kidney transplantation. Insulin-like growth factor 1 (IGF-1) is involved in regulating the growth of miniature pigs and inducing growth of kidneys. There are evidences showing that the SNPs in the 3'UTR of a gene may affect the gene expression by affecting the binding to a miRNA target site. In this study, one SNP (rs34142920) was screened in the IGF-1 3'UTR between 2 different body types of porcine breeds, Bama Xiang (BX) pigs, a miniature pig breed, and Large White (LW) pigs by sequencing. The secondary structure of the IGF-1 3'UTR mRNA containing the SNP in BX pigs is different from that of LW pigs. We then verified that there was a porcine miRNA (miR-new14) binding to this SNP in the 3'UTR of IGF-1 via cotransfecting the 3'UTR from the 2 breeds and miR-new14. We further found that the SNP downregulated mRNA and protein levels of IGF-1 by affecting the binding of miR-new14. To understand the function of miR-new14 in porcine kidney (PK-15) cells and its mechanism, cell proliferation and cell apoptosis assays were employed and results showed that proliferation viability of PK-15 cells was weakened and the apoptotic percentage of PK-15 cells was higher in the miR-new14 group. Porcine miRNA reduced the mRNA expression of AKT/ERK and protein levels of p-AKT/p-ERK. These results suggested that the expression of IGF-1 is influenced by this SNP and miR-new14 and that miR-new14 may suppress cell proliferation and promote cell apoptosis in PK-15 cells through regulating AKT and ERK signaling pathways, in which IGF-1 is involved.

MicroRNA hsa-miR-1301-3p Regulates Human ADH6, ALDH5A1 and ALDH8A1 in the Ethanol-Acetaldehyde-Acetate Metabolic Pathway

Alcohol dehydrogenases (ADHs) and aldehyde dehydrogenases (ALDHs) are vital enzymes involved in the metabolism of a variety of alcohols. Differences in the expression and enzymatic activity of human ADHs and ALDHs correlate with individual variability in metabolizing alcohols and drugs and in the susceptibility to alcoholic liver disease. MicroRNAs (miRNAs) function as epigenetic modulators to regulate the expression of drug-metabolizing enzymes. To characterize miRNAs that target ADHs and ALDHs in human liver cells, we carried out a systematic bioinformatics analysis to analyze free energies of the interaction between miRNAs and their cognate sequences in ADH and ALDH transcripts and then calculated expression correlations between miRNAs and their targeting ADH and ALDH genes using a public data base. Candidate miRNAs were selected to evaluate bioinformatic predictions using a series of biochemical assays. Our results showed that 11 miRNAs have the potential to modulate the expression of two ADH and seven ALDH genes in the human liver. We found that hsa-miR-1301-3p suppressed the expression of ADH6, ALDH5A1, and ALDH8A1 in liver cells and blocked their induction by ethanol. In summary, our results revealed that hsa-miR-1301-3p plays an important role in ethanol metabolism by regulating ADH and ALDH gene expression. SIGNIFICANCE STATEMENT: Systematic bioinformatics analysis showed that 11 microRNAs might play regulatory roles in the expression of two alcohol dehydrogenase (ADH) and seven aldehyde dehydrogenase (ALDH) genes in the human liver. Experimental evidences proved that hsa-miR-1301-3p suppressed the expression of ADH6, ALDH5A1, and ALDH8A1 in liver cells and decreased their inducibility by ethanol.

Research on promoting liver fibrosis injury by the targeted regulation of miR-202 for HGF to activate HSC

BACKGROUND

Liver fibrosis is the primary cause of liver cirrhosis and hepatocellular carcinoma and leads to considerable morbidity and mortality. Recent studies have shown that microRNAs are associated with fibrotic processes in liver disorders, but the exact role of miR-202 is still unclear, and its related mechanisms are not fully understood.

AIMS

The aim of this research is to analyze the regarded regulation of miR-202 on HGF and its role in the pathological progress of liver fibrosis.

METHODS

In the present study, qRT-PCR was used to detect the expression level of miR-202 in serum of patients with liver fibrosis and to compare its expression in patients with different pathological stages. HGF was predicted to be the target gene of miR-202 by TargetScan and was verified by Dual-luciferase reporter gene assay. qRT-PCR and western blot were used to detect the regulatory effect of mir-202 on the mRNA and protein of HGF; effect of miR-202 on the expression of fibrosis factors α-smooth muscle actin (α-SMA), FSP1, and collagen was detected; effect of miR-202 on liver fibrosis in mice was detected by establishing CCL4-induced mouse model.

RESULTS

We found that the expression level of miR-202 in serum of patients with liver fibrosis was significantly higher than that of healthy people, and increased with the increase of fibrosis; miR-202 inhibited the expression level of mRNA and protein of HGF by combining with the 3'-UTR of HGF; the expression level of miR-202 significantly increased after hepatic stellate cells (HSC) were stimulated by AngII; the overexpression of miR-202 could up-regulate the expression of fibrotic factors α-SMA, FSP1, and collagen I. In addition, miR-202 up-regulated the expression of collagen I and collagen III in liver tissue of mice with liver fibrosis and promoted the progress of liver fibrosis.

CONCLUSIONS

miR-202 could negatively regulate the expression of target gene HGF, activated HSC, and increased the expression levels of various fibrosis factors, and the pathological process of liver fibrosis injury was promoted.

Tumor-induced escape mechanisms and their association with resistance to checkpoint inhibitor therapy

Immunotherapy aims to activate the immune system to fight cancer in a very specific and targeted manner. Despite the success of different immunotherapeutic strategies, in particular antibodies directed against checkpoints as well as adoptive T-cell therapy, the response of patients is limited in different types of cancers. This attributes to escape of the tumor from immune surveillance and development of acquired resistances during therapy. In this review, the different evasion and resistance mechanisms that limit the efficacy of immunotherapies targeting tumor-associated antigens presented by major histocompatibility complex molecules on the surface of the malignant cells are summarized. Overcoming these escape mechanisms is a great challenge, but might lead to a better clinical outcome of patients and is therefore currently a major focus of research.

Circular RNA Cdr1as sensitizes bladder cancer to cisplatin by upregulating APAF1 expression through miR-1270 inhibition

Circular RNAs (circRNAs) have recently emerged as essential regulators in carcinogenesis and cancer progression. Previous studies have shown that Cdr1as functions as a microRNA (miRNA) sponge in various cancer types. However, the role of Cdr1as in cisplatin chemosensitivity in bladder cancer remains unclear. Here, we used real‐time PCR to examine miRNA and gene expression in bladder cancer tissues and cell lines. The abilities of Cdr1as and its downstream regulatory molecules to induce apoptosis and promote cisplatin‐induced chemosensitivity of bladder cancer cells were determined by flow cytometry and cell counting kit. Bioinformatic analysis was utilized to predict potential miRNA target sites, and biotin‐coupled miRNA capture, biotin‐coupled probe pull‐down assay, and RNA fluorescent in situ hybridization were used to study the interaction between Cdr1as and target miRNAs. Dual‐luciferase reporter assay was also used to validate the target genes of miRNAs. The expression level of apoptotic protease‐activating factor 1 (APAF1) in bladder cancer cells was identified via western blot. Finally, the sensitivity of Cdr1as to cisplatin chemotherapy in nude mice xenografts was evaluated in terms of the size, volume of tumors, and the survival of mice. We report that Cdr1as induced the apoptosis and enhanced the cisplatin chemosensitivity of bladder cancer cells both in vitro and in vivo. Silencing of APAF1 reduced the sensitivity of bladder cancer cells to cisplatin chemotherapy. Furthermore, Cdr1as could directly sponge miR‐1270 and abolish its effect on APAF1. Our study verified that Cdr1as exerts a cisplatin‐chemosensitization effect on bladder cancer cells through the Cdr1as/miR‐1270/APAF1 axis. This newly identified axis may be a potential therapeutic target for bladder cancer patients.

Lack of association between PAX6/SOSTDC1/FAM20B gene polymorphisms and mesiodens

Background

The purpose of this study was to analyze the association between the genetic polymorphism of genes (PAX6, SOSTDC1and FAM20B) and the susceptibility to mesiodens.

Methods

This study was carried out on 50 patients with mesiodens and 50 controls. The family history of each patient with mesiodens were recorded. Genomic DNA was extracted from saliva samples, and single nucleotide polymorphisms were detected in all exons and exon/intron boundaries of PAX6, SOSTDC1 and FAM20B using Sanger sequencing. The data were analyzed using pearson chi-square test with theoretical frequency ≥ 5. For theoretical frequency less than 5 but at least 1 (≤20% cell), the data were analyzed by continuity correction. For the rest, Fisher’s Exact test was used. A P-value< 0.05 was considered statistically significant. The Odds ratio (OR) and confidence intervals (CI) were recorded.

Results

Three polymorphisms were detected in PAX6. Two polymorphisms were detected in SOSTDC1. Twenty-nine polymorphisms were detected in FAM20B. Although, the T allele of FAM20B (rs3766626) appears to be associated with mesiodens (P = 0.051), there were no significant differences of PAX6/SOSTDC1/FAM20B gene polymorphisms between the two groups. The T allele of FAM20B (rs3766626) was associated with susceptibility to two mesiodens (P < 0.001; OR = 8.333; CI = 2.516–27.600).

Conclusions

Lack of association between PAX6/SOSTDC1/FAM20B gene polymorphisms and mesiodens in the population studied was detected. Further studies with large samples on T allele of FAM20B (rs3766626) are needed.

Electronic supplementary material

The online version of this article (10.1186/s12903-019-0788-3) contains supplementary material, which is available to authorized users.

MicroRNA binding mediated Functional sequence variant in 3'-UTR of DNA repair Gene XPC in Age-related Cataract

DNA oxidative damage repair is strongly involved in the pathogenesis of age-related cataract (ARC). The sequence variants of in coding region of DNA repair genes have been shown to be associated with ARC. It is known that single nucleotide polymorphisms (SNPs) in the 3′-terminal untranslated region (3′-UTR) can alter the gene expression by binding with microRNAs (miRNAs). We hypothesize that SNP(s) in miRNA binding site of certain DNA oxidative damage repair genes might associate with ARC risk. We examined 10 miRNA binding SNPs in 3′-UTR of 7 oxidative damage genes and revealed the XPC- rs2229090 C allele was associated with nuclear type of ARC (ARNC) risk in Chinese population. The individuals with the variant G allele (CG and GG) of XPC- rs2229090 had higher XPC mRNA expression compared to individuals carrying CC genotype. The in vitro assay showed that luciferase reporter gene expression can be down regulated by hsa-miR-589-5p in cells transfected with rs2229090 C allele compared to G allele. These results suggested that the C allele of XPC-2229090 increase the risk with ARNC. The mechanism underlying might be due to the stronger interation of the C allele with hsa-miR-589-5p, resulting in lower XPC expression and DNA repair capability than the individuals carring G allele in lens.