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.

The Impact of microRNA SNPS on Breast Cancer: Potential Biomarkers for Disease Detection

Breast cancer is considered a significant health concern worldwide, with genetic predisposition playing a critical role in its etiology. Single nucleotide polymorphisms (SNPs), particularly those within the 3' untranslated regions (3'UTRs) of target genes, are emerging as key factors in breast cancer susceptibility. Specifically, miRNAs have been recognized as possible novel approach for biomarkers discovery for both prognosis and diagnosis due to their direct association with cancer progression. Regional disparities in breast cancer incidence underscore the need for precise interventions, considering socio-cultural and economic factors. This review explores into the differential effects of SNP-miRNA interactions on breast cancer risk, emphasizing both risk-enhancing and protective associations across diverse populations. Furthermore, it explores the clinical implications of these findings, highlighting the potential of personalized approaches in breast cancer management. Additionally, it reviews the evolving therapeutic prospect of microRNAs (miRNAs), extending beyond cancer therapeutics to encompass various diseases, indicative of their versatility as therapeutic agents.

A case–control study of single-nucleotide variants in microRNA biogenesis genes (AGO1 and GEMIN4) in people with primary immune thrombocytopenia

Background

The role of microRNA (miRNA) is to regulate the translation of genes involved in a variety of diseases.

Aim of the work

This study investigated the relation between the rs636832 and rs2740348 single-nucleotide polymorphisms (SNPs) of the AGO1 gene and the GEMIN4 gene of miRNA biogenesis genes and the risk for primary ITP and the response to therapy.

Patients and methods

In this case–control study, 100 patients with immune thrombocytopenic purpura from the clinical hematology department and outpatient clinic were compared to 100 control subjects. Patients' blood samples are taken, and DNA extraction and PCR amplification of rs636832 A/G of AGO1 and rs2740348 G/C of GEMIN4 were done on sera and compared to the clinical status of the patients.

Results

According to statistical analysis, the genotype and allele frequencies of both variants did not differ significantly between cases and controls. The GG genotype was found to be more prevalent in the chronic phase of ITP than the AA and AG genotypes, with a significance level of p 0.05. The GG genotype was found to be more prevalent in the chronic phase of ITP than the AA and AG genotypes, with a significance level of p 0.05. In addition, the GG genotype was more prevalent in ITP patients who did not respond to treatment compared to the AA and AG genotypes, although this difference was not statistically significant. Concerning rs2740348: the CC genotype was more common than the GC genotype in ITP cases that did not respond to treatment and needed a second line of therapy like splenectomy or TPO-RA, but this did not reach statistical significance.

Conclusion

The rs636832 and rs2740348 SNPs did not appear to be risk factors for ITP; however, the rs636832:GG genotype was more prevalent in older patients, who tend to have the chronic phase of the disease. Although this distinction was not statistically significant, they were less responsive to therapy than the AA and AG genotypes. Concerning rs2740348: the CC genotype was more common than the GC genotype in ITP cases that did not respond to treatment and needed a second line of therapy like splenectomy or TPO-RA, but this did not reach statistical significance.

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.

Association of DROSHA rs6877842, rs642321 and rs10719 polymorphisms with increased susceptibility to breast cancer: A case-control study with genotype and haplotype analysis

BACKGROUND

Multiple lines of evidence suggest that single nucleotide polymorphisms (SNPs) in genes encoding components of the microRNA processing machinery may underlie susceptibility to various human diseases, including cancer.

OBJECTIVE

The present study aimed to investigate whether rs6877842, rs642321 and rs10719 SNPs of DROSHA, a key component of the miRNA biogenesis pathway, are associated with increased risk of breast cancer.

METHODS

A total of 100 patients diagnosed with breast cancer and 100 healthy women were included. Following extraction of DNA, genotyping was performed by tetra primer- amplification refractory mutation system-PCR (T-ARMS-PCR) technique. Under the co-dominant, dominant and recessive inheritance models, the association between DROSHA SNPs and breast cancer risk was determined by logistic regression analysis. The association of DROSHA SNPs with patients' clinicopathological parameters was assessed. Also, haplotype analysis was performed to evaluate the combined effect of DROSHA SNPs on breast cancer risk.

RESULTS

We observed a statistically significant association between DROSHA rs642321 polymorphism and breast cancer susceptibility (P < 0.05). Under the dominant inheritance model, DROSHA rs642321 polymorphism was significantly associated with increased risk of breast cancer (OR: 6.091; 95% CI: 3.291-11.26; P = 0.0001). Our findings demonstrated that DROSHA rs642321 T allele can contribute to the development of breast cancer (OR: 3.125; 95% CI: 1.984-4.923; P = 0.0001). We also found that GTC and GTT haplotypes conferred significant risk for breast cancer (OR: 2.367; 95% CI: 1.453-3.856; P = 0.0001 and OR: 7.944; 95% CI: 2.073-30.43; P = 0.0001, respectively).

CONCLUSIONS

These results provide the first evidence that DROSHA rs642321 polymorphism is associated with increased risk of breast cancer. However, further studies are needed to firmly validate these findings.

Micro-RNA Biogenesis Genes (AGO1 and GEMIN4) Single Nucleotide Variants of Bad Prognosis and Poor Therapeutic Response in Egyptian Chronic Myeloid Leukemia Patients: Case–control Study

BACKGROUND: Chronic myeloid leukemia (CML) is one of the most common hematological tumors. Gene candidate studies cleared the association of single genetic variants (SNVs) to the risk and progression in CML. MicroRNA biogenesis genes disruption contributes a fundamental role in carcinogenesis. AIM: We aimed to determine the association between rs636832 and rs2740348 SNVs of AGO1 gene and GEMIN4 gene, respectively, and the risk and prognosis in CML Egyptian patients with 5 years survival estimation. METHODS: The study was conducted on 110 newly diagnosed CML patients and 110 age and sex healthy matched controls. Real-time polymerase chain reaction utilizing TaqMan probes was operated to demonstrate genetic modalities of rs636832 and rs2740348. RESULTS: No significance difference was observed between the cases and controls regarding the genotypic and allelic frequencies for both variants. On the other hand, the rs636832 GG genotype was more evident at a younger age of diagnosis and associated with the poor grades of the Sokal and Eutos scores. As well, rs2740348 CC genotype was encountered in high Eutos score levels. Regarding the response therapy, rs636832 GG genotype was overrepresented in the resistance to Imatinib while rs2740348 CC genotype was prevalent in the resistance to both Imatinib and Nilotinib. Overall survival was of no statistical significance for both variants. CONCLUSION: Our study revealed that the major homozygous genotypes of both variants were associated with bad prognostic clinical scores and poor response to therapy but with no role in CML risk.

Argonaute Proteins Take Center Stage in Cancers

Simple Summary

The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies.

Abstract

Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.

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.

From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies

Regulation of gene expression has emerged as a fundamental element of transcript homeostasis. Key effectors in this process are the Argonautes (AGOs), highly specialized RNA-binding proteins (RBPs) that form complexes, such as the RNA-Induced Silencing Complex (RISC). AGOs dictate post-transcriptional gene-silencing by directly loading small RNAs and repressing their mRNA targets through small RNA-sequence complementarity. The four human highly-conserved family-members (AGO1, AGO2, AGO3, and AGO4) demonstrate multi-faceted and versatile roles in transcriptome’s stability, plasticity, and functionality. The post-translational modifications of AGOs in critical amino acid residues, the nucleotide polymorphisms and mutations, and the deregulation of expression and interactions are tightly associated with aberrant activities, which are observed in a wide spectrum of pathologies. Through constantly accumulating information, the AGOs’ fundamental engagement in multiple human diseases has recently emerged. The present review examines new insights into AGO-driven pathology and AGO-deregulation patterns in a variety of diseases such as in viral infections and propagations, autoimmune diseases, cancers, metabolic deficiencies, neuronal disorders, and human infertility. Altogether, AGO seems to be a crucial contributor to pathogenesis and its targeting may serve as a novel and powerful therapeutic tool for the successful management of diverse human diseases in the clinic.

MicroRNA-22 inhibits proliferation, invasion and metastasis of breast cancer cells through targeting truncated neurokinin-1 receptor and ERα

HEADING AIMS

This topic aims to clarify whether miR-22 directly targets and downregulates the expression of ERα and NK1R-Tr to inhibit the malignant behaviors of breast cancer cells.

MATERIALS AND METHODS

RT-PCR and Western Blotting were used to detect the expression profile of miR-22, NK1R-Tr and ERα. Luciferase reporter assay and CHIP experiment were conducted to investigate the regulation network between miR-22, NK1R-Tr and ERα. MCF-7-ERαI and MDA-MB-231-ERα cell lines were constructed to study the biological behaviors. The SP-NK1R-ERK1/2 signaling pathway was analyzed using Western Blotting. The subcutaneous and metastases tumor models were employed to study the effects of miR-22 on cell proliferation and metastasis of breast cancer cells in vivo.

KEY FINDINGS

MiR-22 expression level was significantly lower in breast cancerous tissues and cell lines than the adjacent normality, while that of NK1R-Tr increased. The ERα could positively regulate NK1R-Tr expression at DNA level. The descent degree of NK1R-Tr in MCF-7-ERαI cells was far less than that in wild MCF-7 cells, while the findings in MDA-MB-231-ERα cells was more apparent than wild MDA-MB-231 cells. The malignant phenotype was decreased in miR-22 overexpressing cells compared with the wild type. The peak of ERK1/2 phosphorylation was delayed and weakened in miR-22 overexpressing MCF-7 cells, which was agreed with the findings using NK1R-Tr antagonist. The size and number of metastatic tumors declined compared to the controls.

SIGNIFICANCE

MiR-22 downregulated the expression of NK1R-Tr and ERα to delay and weaken phosphorylation of ERK1/2 to inhibit proliferation and metastasis of breast cancer cells.