Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study

GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma

BACKGROUND

The relationship between GEMIN4 genetic variants and cancer, especially bladder carcinoma (BLCA), has been explored without conclusive results. This study aims to elucidate the link between GEMIN4 polymorphisms and BLCA susceptibility through genetic analyses, bioinformatics, and molecular dynamics (MD) simulations.

METHODS

A cohort of 249 participants (121 BLCA patients and 128 unrelated controls) was enrolled. PCR was employed for allelic discrimination of GEMIN4 variants, followed by subgroup stratification, haplotype analyses, structural prediction using the AlphaFold2 prediction tool, subsequent MD simulations, structural analysis, and residue interaction mapping using Desmond, UCSF ChimeraX, and Cytoscape softwares.

RESULTS

The rs.2740348*G variant demonstrated a protective role against BLCA in allelic (OR = 0.55, p = 0.002) and recessive (OR = 0.54, p = 0.017) models, whereas the rs.7813*T variant increased BLCA risk under the recessive model (OR = 1.90, p = 0.019). Haplotype analysis revealed a significant association between GEMIN4 haplotype (rs.2740348*C/rs.7813*T) with increased BLCA risk (OR = 2.01, p = 0.004). Univariate analysis revealed associations of the variants with albumin levels and absolute neutrophil count in BLCA patients. Pathogenicity evaluation categorized p.Gln450Glu as neutral and p.Arg1033Cys as deleterious. MD simulations revealed structural alterations and conformational shifts in the GEMIN4 protein induced by the Glu450 and Cys1033 mutations.

CONCLUSIONS

The study highlights the dual role of GEMIN4 variants in BLCA susceptibility, with rs.2740348 conferring protection and rs.7813 increasing risk. The Glu450 residue positively impacted protein stability, while Cys1033 had a detrimental effect on protein function. These findings underscore the significance of GEMIN4 variants in BLCA susceptibility and pave the way for future diagnostic and therapeutic initiatives.

Pan-Cancer Study on Variants of Canonical miRNA Biogenesis Pathway Components: A Pooled Analysis

Single nucleotide polymorphisms in genes involved in microRNA processing/maturation and release may deregulate the microRNAome expression levels. We aimed to assess the relationship between miRNA machinery genetic variants and human cancer risk using integrative bioinformatics analyses to identify the role of these genes in cancer aggressiveness. Mutations of 8176 pan-cancer samples were retrieved from 33 studies in "TCGA" database, and a Cox regression model for survival was performed. Next, 22 computationally identified variants within 11 genes were selected based on their high citation rate and MAF. Relevant articles through March 2020 were included. Pooled estimates under the five genetic association models were calculated. Publication bias and heterogeneity between articles were evaluated. Trial Sequential Analysis (TSA) was applied to assess the power and reliability of the draw conclusions. TCGA patients with different cancer types revealed significant alterations in miRNA machinery genes, with mutation frequency ranging from 0.6-13% of samples. RAN was associated with LN metastasis, while TARBP2 and PIWIL1 gene mutations exhibited better overall survival. In the meta-analysis, 45 articles (74,593 cases and 89,198 controls) met the eligibility criteria. Pooled analysis revealed an increased cancer risk with DROSHArs10719*G, RANrs3803012*G, DGCR8rs417309*A, and GEMIN3rs197414*A. In contrast, both DICER1rs1057035*T and GEMIN4rs2743048*G conferred protection against developing cancer. TSA showed the cumulative evidence is inadequate, and the addition of further primary studies is necessary. This study suggests a potential role of miRNA biogenesis genes in cancer development/prognosis. Further functional studies may reveal biological explanations for the differential risks of the machinery variants in different cancer types.

PACT promotes the metastasis of basal-like breast cancer through Rac1 SUMOylation and activation

Most basal-like breast cancers (BLBCs) are triple-negative breast cancers (TNBCs), which is associated with high malignancy, high rate of recurrence and distant metastasis, and poor prognosis among all types of breast cancer. However, there are currently no effective therapies for BLBC. Furthermore, chemoresistance limits the therapeutic options for BLBC treatment. In this study, we screen out protein activator of the interferon-induced protein kinase (PACT) as an essential gene in BLBC metastasis. We find that high PACT expression level was associated with poor prognosis among BLBC patients. In vivo and in vitro investigations indicated that PACT could regulate BLBC metastasis by interacting with SUMO-conjugating enzyme Ubc9 to stimulate the SUMOylation and thus consequently the activation of Rac1. BLBC patients receiving chemotherapy presents poorer prognosis with PACT high expression, and PACT disruption sensitizes experimental mammary tumor metastases to chemotherapy, thus providing insights to consider PACT as a potential therapeutic target to overcome acquired chemoresistance in BLBC.

Single Nucleotide Polymorphisms in microRNA Genes and Colorectal Cancer Risk and Prognosis

There is growing interest in single nucleotide polymorphisms (SNPs) in the genes of microRNAs (miRNAs), which could be associated with susceptibility to colorectal cancer (CRC) and therefore for prognosis of the disease and/or treatment response. Moreover, these miRNAs-SNPs could serve as new, low-invasive biomarkers for early detection of CRC. In the present article, we performed a thorough review of different SNPs, which were investigated for a correlation with the CRC risk, prognosis, and treatment response. We also analyzed the results from different meta-analyses and the possible reasons for reported contradictory findings, especially when different research groups investigated the same SNP in a gene for a particular miRNA. This illustrates the need for more case-control studies involving participants with different ethnic backgrounds. According to our review, three miRNAs-SNPs-miR-146a rs2910164, miR-27a rs895819 and miR-608 rs4919510-appear as promising prognostic, diagnostic and predictive biomarkers for CRC, respectively.

Association of GEMIN4 gene polymorphisms with the risk of colorectal cancer in the Polish population

<br><b>Aim:</b> Gem-associated protein 4 (GEMIN4), a member of the GEMIN gene family, is a key compound of the regulating factors responsible for miRNA biogenesis. Genetic variability within this gene can alter the risk for development of colorectal cancer (CRC) as was shown for other genes involved in miRNA biogenesis. Therefore, presented study was intended to identify genetic variants of three single nucleotide polymorphisms (SNPs) in the GEMIN4 gene (rs1062923, rs2740348 and rs910925) and their relationship with CRC.</br> <br><b>Methods:</b> The study comprised 203 patients and 179 age and sex matched controls. Genotyping of GEMIN4 gene variants was done using Taqman® assay. The association of GEMIN4 variants with CRC was done by odds ratio analysis. Haplotype analysis was done to see the combined effect of studied variants on CRC.</br> <br><b>Results:</b> Patients carrying all variant genotypes for GEMIN4 rs1062923 (odds ratio [OR]= 0.205; 95% confidence interval [CI] = 0.1034–0.4065 for CC variant and [OR] = 0.1436; [CI] = 0.0869–0.2373 for CT variant, respectively) and GEMIN4 rs2740348 (odds ratio [OR] = 0.4498; 95% confidence interval [CI] = 0.2342–0.8637 for CC variant and [OR] = 0.3986; [CI] = 0.2043–0.7776 for CG variant, respectively) showed significant association in lower occurrence of cancer, whereas in case of GEMIN4 G/C rs910925 variant genotype, no significance correlation was found.</br> <br><b>Conclusion:</b> Our study gives a substantive support for the association between the GEMIN4 gene variants/miRNA biogenesis and CRC risk.</br>

Research progress in lncRNA and its action as ceRNA in ovarian function as well as the relevant diseases

Long chain non-encoding RNA (lncRNA) can affect gene expression through transcription, post transcriptional regulation and epigenetic modification, and it is involved in regulating ovarian physiological function. LncRNA, as a competitive endogenous RNA, can affect the expression of target gene mRNA by competitively binding microRNA (miRNA), which are called lncRNA/miRNA/mRNA regulatory network. It plays an important role in the regulation of ovarian physiological function and the occurrence and development of ovarian reproductive disorders, expecting to become a new target and diagnostic index for the treatment of reproductive disorders.

A pan-cancer atlas of somatic mutations in miRNA biogenesis genes

It is a well-known and intensively studied phenomenon that the levels of many miRNAs are differentiated in cancer. miRNA biogenesis and functional expression are complex processes orchestrated by many proteins cumulatively called miRNA biogenesis proteins. To characterize cancer somatic mutations in the miRNA biogenesis genes and investigate their potential impact on the levels of miRNAs, we analyzed whole-exome sequencing datasets of over 10 000 cancer/normal sample pairs deposited within the TCGA repository. We identified and characterized over 3600 somatic mutations in 29 miRNA biogenesis genes and showed that some of the genes are overmutated in specific cancers and/or have recurrent hotspot mutations (e.g. SMAD4 in PAAD, COAD and READ; DICER1 in UCEC; PRKRA in OV and LIN28B in SKCM). We identified a list of miRNAs whose level is affected by particular types of mutations in either SMAD4, SMAD2 or DICER1 and showed that hotspot mutations in the RNase domains in DICER1 not only decrease the level of 5p-miRNAs but also increase the level of 3p-miRNAs, including many well-known cancer-related miRNAs. We also showed an association of the mutations with patient survival. Eventually, we created an atlas/compendium of miRNA biogenesis alterations providing a useful resource for different aspects of biomedical research.

Association between genetic variants in DICER1 and cancer risk: An updated meta-analysis

Dysfunctions in mechanisms of gene regulation based on RNA interference are recognized as a common feature of the molecular basis of cancer pathogenesis. Therefore, as one of the crucial components of the machinery involved in the biogenesis of both siRNAs and microRNA molecules, DICER was recognized as one of the candidates for the research in the field of carcinogenesis. Due to their potential functional properties, several genetic variants located within DICER1 gene were analyzed for their possible association with the susceptibility to cancer through case-control studies. In order to elucidate their effect on the overall cancer risk, we conducted an updated meta-analysis of all eligible association studies. The publications were selected based on PubMed database search, while OpenMeta-analyst and MetaGenyo software were used for quantitative data synthesis. Statistically significant results were found for the association of rs1057035 with the overall cancer risk under multiple genetic models (P_{CT vs. TT} < 0.001, OR_{CT vs. TT} = 0.870, 95% CI = 0.812-0.933; P_allelic = 0.009, OR_allelic = 0.896, 95% CI = 0.825-0.973; P_dom < 0.001, OR_dom = 0.874, 95% CI = 0.817-0.934; P_overdom = 0.004, OR_overdom = 0.858, 95% CI = 0.773-0.953). Other selected genetic variants within DICER1, rs13078, rs1209904 and rs3742330, did not show the association with the overall susceptibility to malignant diseases. We conclude that rs1057035 may represent a potential biomarker associated with the risk of developing cancer, which requires a confirmation in a larger set of studies.

The prognostic value of microRNA-biogenesis genes Argonaute 1 and 2 variants in breast cancer patients

MicroRNA machinery genes Argonaute 1 (AGO1) and 2 (AGO2) are associated with several hallmarks of cancer. They play a key role in transcriptomic silencing, regulation of the immune system, cell differentiation, and angiogenesis processes. The present pilot study aims to explore the impact of genetic variants rs636832 and rs2977490 of AGO1 and AGO2, respectively, on breast cancer (BC) risk in a sample of Mediterranean population. TaqMan genotyping assay of 93 consecutive breast cancer female patients and age- as well as ethnicity-matched controls, was done by Real-Time allele discrimination polymerase chain reaction. Association with the available clinical, histopathological and immunohistochemistry assessments was applied. In silico data analysis was also executed. Although allele and genotype frequencies distribution of both study variants were comparable in BC and healthy control cohorts, AGO1*G variant conferred a significant BC risk under recessive model [adjusted odds ratio (95% confidence interval); 4.90 (1.03-23.39), P = 0.024], and was significantly associated with lymph node infiltration (P = 0.037), distant metastasis (P = 0.019), advanced clinical stage (P < 0.001), recurrence (P = 0.032), and shorter overall survival (P = 0.001). Furthermore, AGO2*G/G genotype showed an association with poor pathological grade (P = 0.029). Our results suggested for the first time that rs636832 and rs2977490 variants of the miRNA-machinery genes AGO1 and 2, respectively, may impact susceptibility and/or clinical outcomes of BC patients in the study population.

Association between genetic variants in genes encoding Argonaute proteins and cancer risk: A meta-analysis

With the accumulation of evidence of the involvement of small-RNA-based regulatory mechanisms in carcinogenesis, genes encoding Ago proteins emerged as candidates for case-control studies on cancer. Since the data from association studies on various cancer types was not previously meta-analyzed, the potential effect of these variants on cancer risk in general was not previously evaluated. Therefore, we conducted a meta-analysis of all eligible studies, testing multiple genetic models of association. The identification of publication was based on PubMed database search, while OpenMeta-analyst, as well as MetaGenyo software, were used for quantitative data synthesis. AGO1 genetic variant rs636832 was found to associate with the overall cancer risk, assuming the overdominant genetic model (P =  0.030; OR_overdom = 0.865, 95%CI 0.759-0.986). For the same genetic variant, statistical significance was reached for the association with solid tumors, as well as with lung cancer susceptibility. Similar results were found in the Asians cohort for another AGO1 variant, rs595961. For rs4961280, none of the meta-analyses yielded statistically significant results. We conclude that genetic variants rs636832 and rs595961 located within AGO1 may represent susceptibility variants for specific types of cancer, while the association with malignant diseases was not determined for AGO2 variant rs4961280.

The association of AGO1 (rs595961G>A, rs636832A>G) and AGO2 (rs11996715C>A, rs2292779C>G, rs4961280C>A) polymorphisms and risk of recurrent implantation failure

Recurrent implantation failure (RIF) is a common reproductive clinical condition treated by fertility specialists at in vitro fertilization (IVF) clinics. Several factors affect embryo implantation including the age of the female, the quality of embryos and the sperm, genetics, immunologic factors. Here, we investigated the association of Argonaute 1 (AGO1) and Argonaute 2 (AGO2) polymorphisms and RIF. We collected blood samples from 167 patients with RIF and 211 controls. Genetic polymorphisms were detected by polymerase chain reaction (PCR) – restriction fragment length polymorphism analysis and real-time PCR. We found that the AGO2 rs4961280C>A polymorphism (adjusted odds ratio [AOR] = 1.984; P = 0.023) was significantly associated with RIF. Furthermore, in RIF patients with three or more consecutive implantation failure, the AGO2 rs4961280C>A CA genotype (AOR = 2.133; P = 0.013) and dominant model (AOR = 2.272; P = 0.006) were both significantly associated with prevalence of RIF. An analysis of variance revealed that patients with the AGO2 rs2292779C>G genotypes (CC: 6.52 ± 2.55; CG: 7.46 ± 3.02; GG: 8.42 ± 2.74; P = 0.044) and the dominant model (CC: 6.52 ± 2.55; CG+GG: 7.70 ± 2.97; P = 0.029) exhibited significantly increased white blood cell levels. Furthermore, patients with the AGO1 rs595961G>A dominant model (GG: 36.81 ± 8.69; GA+AA: 31.58 ± 9.17; P = 0.006) and the AGO2 rs4961280C>A recessive model (CC+CA: 35.42 ± 8.77; AA: 22.00 ± 4.24; P = 0.035) exhibited a significantly decreased number of CD4⁺ helper T cells. Our study showed that AGO1 and AGO2 polymorphisms are associated with the prevalence of RIF. Hence, the results suggest that variations in AGO1 and AGO2 genotypes may be useful clinical biomarkers for the development and prognosis of RIF.

Genetic polymorphism in DGCR8 is associated with late onset of preeclampsia

Background

PE (preeclampsia) is a heterogeneous disorder with early onset PE (EOPE) and late onset PE (LOPE) subtypes. Associations between maternal miRNAs biosynthesis genes polymorphisms and risk of PE have been previously observed. However, the impact of polymorphisms in DGCR8 which is indispensable in miRNA maturing processing on the susceptibility to preeclampsia (PE) has not been elucidated yet. We, therefore, conducted a case-control study to evaluate the impact of polymorphisms in DGCR8 on the risk of EOPE and LOPE.

Methods

A total of 66 patients diagnosed with EOPE, 206 with LOPE and 330 healthy controls were recruited. Five SNPs in DGCR8 were genotyped including rs1558496, rs1640299, rs720012, rs720014, and rs9606241. Logistic regression was used to estimate the OR and the 95% CI for the associations.

Results

Increased risk of LOPE has been observed among patients with rs1640299 TG genotype (OR = 1.98 (95%CI: 1.38, 2.87), p = 2.32e-4) and rs720014 TC genotype (OR = 2.49 (95%CI: 1.72, 3.60), p = 1.40e-7). The DGCR8 rs1558496/ rs1640299/ rs720012/ rs720014/ rs9606241 haplotype T-G-A-C-A and T-G-A-C-G were associated with increased risk of LOPE (OR = 2.20 (95%CI: 1.49, 3.25), p = 5.90e-5, and 1.58 (95%CI: 1.06, 2.36), p = 0.024, respectively). And the haplotype T-T-G-T-A was associated with lower risk of LOPE (OR = 0.74 (95%CI: 0.58, 0.95), p = 0.018). These significant associations retained after false-positive discovery rate correction. However, none of the tested SNPs or haplotypes in DGCR8 gene is associated with risk of EOPE (p > 0.05).

Conclusions

Polymorphisms in DGCR8 might participate in the pathological process of preeclampsia. The rs1640299 T > G and rs720014 T > C polymorphisms are associated with late onset preeclampsia susceptibility.

Electronic supplementary material

The online version of this article (10.1186/s12881-019-0887-7) contains supplementary material, which is available to authorized users.

A Sex-Stratified Genome-Wide Association Study of Tuberculosis Using a Multi-Ethnic Genotyping Array

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. A total of 810 individuals (410 cases and 405 controls) from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome (8,27,386 variants) and X chromosome (20,939 variants) in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.

The role of microRNAs involved in PI3-kinase signaling pathway in colorectal cancer

In recent decades, cancer has been one of the most important concerns of the human community, which affects human life from many different ways, such as breast, lung, colorectal, prostate, and other cancers. Colorectal cancer is one of the most commonly diagnosed cancers in the world that has recently been introduced as the third leading cause of cancer deaths in the world. microRNAs have a very crucial role in tumorgenesis and prevention of cancer, which plays a significant role with influencing various factors through different signaling pathways. Phosphoinositide 3 (PI3)-kinase/AKT is one of the most important signaling pathways involved in the control and growth of tumor in colorectal cancer, through important proteins of this pathway, such as PTEN and AKT, that they can perform specific influence on this process. Our effort in this study is to collect microRNAs that act as tumor suppressors and oncomirs in this cancer through PI3-kinase/AKT signaling pathway.

Polymorphisms in non-coding RNAs and risk of colorectal cancer: A systematic review and meta-analysis

Colorectal cancer (CRC) has been regarded as a common cancer due to its prevailing incidence in both males and females. Recently, non-coding RNAs used as biomarkers for screening, diagnosis and prognosis of different cancers have been under the focus of attention. As a result of this, the aim of this study was to systematically review articles that investigated the SNPs in genes related to microRNAs and long non-coding RNAs to assess the genetic susceptibility of colorectal cancer risk. The outcome is presented as the results of a meta-analysis. We systematically searched PubMed, Web of Science, and Scopus to identify relevant studies published up to 20/5/2017. These included eligible studies consisting of 23,581 patients and 22,697 controls. The conferred risk was estimated and presented using odds ratios (ORs) and 95% confidence intervals (CI). The Hardy-Weinberg equilibrium (HWE) was assessed by the goodness-of-fit chi-square test in all studies. The power of each study was also calculated based on the available results. Out of 27 different microRNAs which had published results, although most of the studies were under powered, miR-146a and miR-196a were amongst the most studied microRNAs. For five miRNAs (miR-196a, miR-146a, miR-27a, miR-499 and miR-149) which we performed a meta-analysis, miR-27a and miR-149 gene polymorphisms were associated with susceptibility to CRC. Other miRNAs did not show any effect on the CRC risk. Overall, significant association between miR-149 rs2292832 and susceptibility to cancer was identified in a recessive genetic model, TT/ (TC + CC) (OR = 1.19, 95% CI = 1.02-1.39, P = 0.02). On the other hand, rs895819 (miR-27a) GG carriers were more susceptible to CRC (OR = 1.47, 95% CI = 1.21-1.78, P = <0.05) in a recessive genetic model. Analysis of the data based on race revealed that rs2910164 (miR-146a) polymorphism may decrease the risk of CRC among Europeans, in a co dominant model [OR = 0.81, 95% CI 0.66-0.99, p = 0.04], but not among Asians. In conclusion, certain miRNAs (miR-27a and miR-149) may affect the CRC risk and can be regarded as genetic markers amongst different populations. LncRNAs still have to be studied more to reach a conclusion for their association with CRC risk.

The association of polymorphisms in miRNAs with nonsmall cell lung cancer in a Han Chinese population

Background

MicroRNAs (miRNAs) have been demonstrated to play important roles in cancer progression. Recently, studies have revealed that polymorphisms in miRNAs might be associated with cancer susceptibility.

Materials and methods

In the current study, we investigated the associations of single nucleotide polymorphisms (SNPs) in miRNAs (rs11134527 in pri-miR-218-2, rs74693964 in pri-miR-145, rs6062251 in pri-miR-133a-2, and rs4705343 in pri-miR-143) with nonsmall cell lung cancer (NSCLC) in a Han population from Yunnan Province, Southwest China using a binary logistic regression analysis. A total of 452 patients with NSCLC and 452 healthy individuals were recruited for polymorphism genotyping using the TaqMan assay.

Results

Our results showed that the allelic frequencies of rs11134527 and rs4705343 were significantly different between the NSCLC and control groups (P=0.025 and 0.029). Additionally, the genotypic frequencies of rs11134527 were significantly different between the NSCLC and control groups (P=0.045). The mode of inheritance analysis showed that genotypes A/G+G/G of rs11134527 were associated with a lower risk of NSCLC under the dominant model (OR=0.69; 95% CI: 0.51–0.94). In addition, genotypes 2C/C+C/T of rs4705343 were associated with an increased risk of NSCLC under the log-additive model (OR=1.25; 95% CI: 1.01–1.53). However, there was no significant difference in the other SNPs between the NSCLC and control groups (P>0.05). Moreover, the association analysis of these SNPs between adenocarcinoma and squamous cell carcinoma (SCC) showed that allele A of rs11134527 was associated with SCC (OR=0.65; 95% CI: 0.48–0.88).

Conclusion

Our results indicated that the A allele of rs11134527 might be a risk factor (OR=1.24; 95% CI: 1.03–1.50) and that the T allele of rs4705343 might be a protective factor (OR=0.80; 95% CI: 0.66–0.98) for NSCLC in a Han Chinese population.

miRNA processing gene polymorphisms, blood DNA methylation age and long-term ambient PM2.5 exposure in elderly men

AIM

We tested whether genetic variation in miRNA processing genes modified the association of PM2.5 with DNA methylation (DNAm) age.

PATIENTS & METHODS

We conducted a repeated measures study based on 552 participants from the Normative Aging Study with multiple visits between 2000 and 2011 (n = 940 visits). Address-level 1-year PM2.5 exposures were estimated using the GEOS-chem model. DNAm-age and a panel of 14 SNPs in miRNA processing genes were measured from participant blood samples.

RESULTS & CONCLUSION

In fully adjusted linear mixed-effects models, having at least one copy of the minor rs4961280 [AGO2] allele was associated with a lower DNAm-age (β = -1.13; 95% CI: -2.26 to -0.002). However, the association of PM2.5 with DNAm-age was significantly (Pinteraction  = 0.01) weaker in homozygous carriers of the major rs4961280 [AGO2] allele (β = 0.38; 95% CI: -0.20 to 0.96) when compared with all other participants (β = 1.58; 95% CI: 0.76 to 2.39). Our results suggest that miRNA processing impacts DNAm-age relationships. Graphical abstract: miRNA processing AGO2 polymorphism (rs4961280) modifies the association of long-term ambient fine particle exposure with blood DNA methylation age [Formula: see text] The graph depicts lines from a fully adjusted linear regression model with fine particle exposure levels ranging from the tenth to the ninetieth percentile, all other continuous variables held constant at their means, and all other categorical variables held at their most frequent level.

Association of GEMIN4 gene polymorphism and the risk of cancer: a meta-analysis

Gem-associated protein 4 (GEMIN4) gene is a key regulator for the miRNA biogenesis processes. Recent studies have demonstrated that some single-nucleotide polymorphisms (SNPs) in GEMIN4 gene are associated with the risk of cancer, but the results are still controversial. Therefore, we conducted a meta-analysis to analyze the association between three major SNPs (rs2740348, rs7813, and rs3744741) in the GEMIN4 gene and the risk of cancer. Relevant articles were searched in Web of Science, PubMed, Cochrane Library, Chinese Wan Fang, and Chinese National Knowledge Infrastructure databases. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to quantitatively estimate the association. Publication bias and sensitivity analyses were undertaken to evaluate the stability of the results. Overall, the pooled results showed that rs2740348 involving 3,604 cases and 3,770 controls was significantly associated with increased cancer risk (GG vs GC/CC: OR =1.16, 95% CI =1.05-1.29, P=0.004) and rs7813 involving 4,729 cases and 4,562 controls was also related to increased cancer risk (TT vs TC/CC: OR =1.12, 95% CI =1.03-1.22, P=0.009). However, there was no significant association between rs3744741 and cancer risk under overall genetic models. In conclusion, our study has demonstrated that rs2740348 and rs7813 are associated with increased risk of cancer, and they may be new biomarkers for predicting cancer risk.

MicroRNA‑27a promotes tumorigenesis via targeting AKT in triple negative breast cancer

Altered microRNA (miRNA/miR) expression regulates tumor development and progression in triple‑negative breast cancer (TNBC). The present study examined the effect of miR‑27a on proliferation, migration and invasion of TNBC cells in vitro and in vivo. An MTT assay was performed to examine the proliferation of MDA‑MB‑231 and MDA‑MB‑468 breast cancer cells with either overexpression of miR‑27a or downregulation of miR‑27a, in the presence or absence of radiation. The migratory and invasive abilities of MDA‑MB‑231 and MDA‑MB‑468 breast cancer cells were assessed by Transwell migration and Matrigel invasion assays. The protein expression levels were examined by western blotting. The caspase‑Glo3/7 assay was performed to examine the effect of miR‑27a on radiation‑induced apoptosis in MDA‑MB‑231 and MDA‑MB‑468 breast cancer cells. A luciferase assay was performed to evaluate the effect of miR‑27a on phosphatase and tensin homolog (PTEN) and B cell lymphoma (Bcl)‑2 associated X, apoptosis regulator (BAX) expression. Immunodeficient nude mice were used to examine tumor growth following injection of MDA‑MB‑231 breast cancer cells. miR‑27a promoted proliferation in vitro and in vivo, and enhanced migration and invasion in TNBC cells. miR‑27a improved the survival of TNBC cells following irradiation. miR‑27a inhibited radiation‑induced apoptosis in TNBC cells by regulation of caspase 3/7 and Bcl‑2 expression. Furthermore, the expression levels of PTEN and phosphorylated protein kinase B in MDA‑MB‑231 and MDA‑MB‑468 cells was altered following overexpression of miR‑27a. The luciferase assay demonstrated that miR‑27a regulated PTEN and BAX expression by binding to 3'‑untranslated regions. Overall, miR‑27a exhibits an essential role in tumor development and progression in TNBC and may be used as a potential biomarker to predict radiotherapy response and prognosis for the disease.

MicroRNA-455-3p promotes invasion and migration in triple negative breast cancer by targeting tumor suppressor EI24

Lacking of treatment methods for the patients with triple negative breast cancer (TNBC) underscores the pivotal needs to further understand its biology as well as to find better biomarkers and develop novel therapeutic strategies. Increasing evidences support that aberrantly expressed microRNAs (miRNAs) are involved in tumorigenesis and may serve as biomarkers for diagnostic and prognostic purposes of various cancers. In current study, we found that miR-455-3p and miR-196a-5p were intensively overexpressed in TNBC compared with the hormone receptor (HR) positive breast cancer whereas miR-425-5p was down-regulated by miRNA microarray analysis. qRT-PCR analysis confirmed that the expression of miR-455-3p in TNBC cell lines MDA-MB-231 and MDA-MB-468 was higher than that in HR positive breast cancer cell line MCF-7(p<0.01). Functional experiments in vitro showed that miR-455-3p enhanced cell proliferative, invasive and migrational abilities in TNBC cell lines. miRNA targets prediction showed SMAD2, LTBR and etoposide induced 2.4 (EI24) were potential target genes of miR-455-3p, and then it was confirmed by qRT-PCR assay. Dual luciferase reporter assay showed the specific binding of miR-455-3p to 3′ UTR of EI24 in TNBC. Then we found miR-455-3p inhibited the EI24 expression at the levels of mRNA and protein. Through small interfering RNA (siRNA) targeting EI24 gene, there were strengthened capabilities of invasion and migration of TNBC cells, and increased expression of EI24 had the inverse effects. In conclusion, the data suggest that miRNA455-3p promotes invasion and migration by targeting tumor suppressor EI24 and might be a potential prognostic biomarker and therapeutic target in TNBC.

ADAR1 polymorphisms are related to severity of liver fibrosis in HIV/HCV-coinfected patients

The adenosine deaminase acting on RNA (ADAR1) gene is an interferon-stimulated gene involved in liver injury protection. Our aim was to analyze the association of polymorphisms within this gene with the severity of liver disease in European HIV/HCV-coinfected patients. We performed a cross-sectional study in 220 patients that underwent a liver biopsy. Five SNPs in the ADAR1 gene (rs1127326, rs1127317, rs1127314, rs1127313, rs2229857) were genotyped by GoldenGate assay. The outcome variables were fibrosis stage and necroinflammatory activity grade by METAVIR-score, aspartate aminotransferase to platelet ratio index (APRI), FIB-4 index, and fibrosis progression rate (FPR). In multivariate analysis, fibrosis progression rate (FPR) (aAMRs = 0.97) decreased in a dose-dependent manner with the presence of rs2229857_T, rs1127313_G, rs1127314_G and rs1127317_G; while rs1127326_T allele had only significant associations with FIB-4 (aAMRs ≤ 0.63) and FPR (aAMRs ≤ 0.97). Moreover, carriers of rs2229857_T, rs1127314_G, rs1127317_G, and rs1127326_T alleles were protected against advanced fibrosis (F ≥ 3) (adjusted ORs (aORs) ≤ 0.44), APRI ≥ 1.5 (aORs ≤ 0.33), and FPR ≥ 0.075 (aORs ≤ 0.45). rs1127313_G carriers showed lower odds of having F ≥ 3 (aORs = 0.39), FIB4 ≥ 3.25 (aOR = 0.22) and FPR ≥ 0.075 (aORs = 0.44). In conclusion, ADAR1 polymorphisms protected against severe liver disease in HIV/HCV-coinfected patients. These results could be used to improve therapeutic decision-making in clinical practice.

microRNAs Make the Call in Cancer Personalized Medicine

Since their discovery and the advent of RNA interference, microRNAs have drawn enormous attention because of their ubiquitous involvement in cellular pathways from life to death, from metabolism to communication. It is also widely accepted that they possess an undeniable role in cancer both as tumor suppressors and tumor promoters modulating cell proliferation and migration, epithelial-mesenchymal transition and tumor cell invasion and metastasis. Moreover, microRNAs can even affect the tumor surrounding environment influencing angiogenesis and immune system activation and recruitment. The tight association of microRNAs with several cancer-related processes makes them undoubtedly connected to the effect of specific cancer drugs inducing either resistance or sensitization. In this context, personalized medicine through microRNAs arose recently with the discovery of single nucleotide polymorphisms in the target binding sites, in the sequence of the microRNA itself or in microRNA biogenesis related genes, increasing risk, susceptibility and progression of multiple types of cancer in different sets of the population. The depicted scenario implies that the overall variation displayed by these small non-coding RNAs have an impact on patient-specific pharmacokinetics and pharmacodynamics of cancer drugs, pushing on a rising need of personalized treatment. Indeed, microRNAs from either tissues or liquid biopsies are also extensively studied as valuable biomarkers for disease early recognition, progression and prognosis. Despite microRNAs being intensively studied in recent years, a comprehensive review describing these topics all in one is missing. Here we report an up-to-date and critical summary of microRNAs as tools for better understanding personalized cancer biogenesis, evolution, diagnosis and treatment.

microRNAs in Cancer Susceptibility

microRNAs (miRNAs) are a small RNA species without protein-coding potential. However, they are key modulators of protein translation. Many studies have linked miRNAs with cancer initiation, progression, diagnosis, and prognosis, and recent studies have also linked them with cancer etiology and susceptibility, especially through single-nucleotide polymorphisms (SNPs). This review discusses some of the recent advances in miRNA-SNP literature-including SNPs in miRNA genes, miRNA target sites, and the processing machinery. In addition, we highlight some emerging areas of interest, including isomiRs and non-3'UTR focused miRNA-binding mechanisms that could provide further novel insight into the relationship between miR-SNPs and cancer. Finally, we note that additional epidemiological and experimental research is needed to close the gap in our understanding of the genotype-phenotype relationship between miRNA-SNPs and cancer.

Targeting miRNAs by polyphenols: Novel therapeutic strategy for cancer

In the recent years, polyphenols have gained significant attention in scientific community owing to their potential anticancer effects against a wide range of human malignancies. Epidemiological, clinical and preclinical studies have supported that daily intake of polyphenol-rich dietary fruits have a strong co-relationship in the prevention of different types of cancer. In addition to direct antioxidant mechanisms, they also regulate several therapeutically important oncogenic signaling and transcription factors. However, after the discovery of microRNA (miRNA), numerous studies have identified that polyphenols, including epigallocatechin-3-gallate, genistein, resveratrol and curcumin exert their anticancer effects by regulating different miRNAs which are implicated in all the stages of cancer. MiRNAs are short, non-coding endogenous RNA, which silence the gene functions by targeting messenger RNA (mRNA) through degradation or translation repression. However, cancer associated miRNAs has emerged only in recent years to support its applications in cancer therapy. Preclinical experiments have suggested that deregulation of single miRNA is sufficient for neoplastic transformation of cells. Indeed, the widespread deregulation of several miRNA profiles of tumor and healthy tissue samples revealed the involvement of many types of miRNA in the development of numerous cancers. Hence, targeting the miRNAs using polyphenols will be a novel and promising strategy in anticancer chemotherapy. Herein, we have critically reviewed the potential applications of polyphenols on various human miRNAs, especially which are involved in oncogenic and tumor suppressor pathways.

Single nucleotide polymorphisms within MicroRNAs, MicroRNA targets, and MicroRNA biogenesis genes and their impact on colorectal cancer survival

We have shown that single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, miRNA target genes, and miRNA biogenesis genes minimally contribute to colon cancer risk. It is possible that these SNPs alter survival. We analyzed 565 SNPs in or adjacent to microRNAs, target genes, or biogenesis genes, using 1,115 cases and 1,173 controls; 837 cases had survival information. We tested SNPs for associations with colorectal cancer (CRC) survival using a Cox proportional hazard model adjusting for age, study center, gender, AJCC disease stage, and MSI tumor status. Multiple comparison adjustments were made using the step-down Bonferroni correction. SNPs associated with survival (P_raw  < 0.05) also were assessed with messenger RNA (mRNA). Seven of the 565 SNPs analyzed were associated significantly with CRC survival after adjustment for multiple comparisons. Six of these increased risk of dying, and one, rs12140 (ADAMTS1) decreased risk of dying from CRC (HRR = 0.44, 95% CI (0.24, 0.83; P_Holm  = 0.011). Six SNPs altered colon cancer risk and five were associated with altered mRNA expression across genotypes. One SNP, rs2059691 (PRKRA), was associated with increased mRNA expression and worse survival, and one SNP, rs6598964 (LIN28A), decreased risk of developing colon cancer [OR = 0.77 95% CI (0.61, 0.98)] and increased risk of dying from CRC (HRR = 2.26 95% CI (1.52, 3.36). P_Holm  = 0.003). The few SNPs associated with CRC survival, colon cancer risk, or with mRNA expression, resided in genes that influence metastasis and angiogenesis. © 2017 Wiley Periodicals, Inc.

Evaluation of miR-506 and miR-4316 expression in early and non-invasive diagnosis of colorectal cancer

PURPOSE

Examination of the entire colon by colonoscopy remains the golden standard for screening of colorectal cancer (CRC). However, patients are reluctant to perform invasive colonoscopies because of interference with their intimacy. Therefore, the potential use of non-invasive analysis of microRNAs expression in liquid biopsy as a novel biomarker for early CRC has investigated in several studies. In this study, we analyzed the expression of two novel microRNAs: miR-506 and miR-4316, which have never been examined in CRC.

METHODS

Plasma samples were collected from 56 patients (median age of 68 years) with operable colorectal cancer and from 70 healthy individuals (median age of 59 years). Expression of plasma microRNAs was evaluated by quantitative reverse transcription polymerase chain reaction using Eco real-time PCR device (Illumina, USA).

RESULTS

We found a significant elevated expression of both examined microRNAs in early CRC patients when compared to those in healthy individuals (p = 0.0054 for miR-506 and p = 0.0025 for miR-4316). The expression of miR-506 and miR-4316 did not depend on gender, age, disease stage, and tumor localization of CRC patients. ROC curve analysis showed that both examined microRNAs could differentiate early stage colorectal cancer from healthy individuals with 76.8% specificity and 60.7% sensitivity for miR-506 analysis and 76.8% specificity and 75% specificity for miR-4316 analysis.

CONCLUSION

Our study revealed that elevated expression of miR-506 and miR-4316 in peripheral blood were potential molecular markers for early colorectal cancer.