Association of microRNA biosynthesis genes XPO5 and RAN polymorphisms with cancer susceptibility: Bayesian hierarchical meta-analysis

Impact of pan-cancer analysis of the exportins family on prognosis, the tumor microenvironment and its potential therapeutic efficacy

This study aims to comprehensively analyze the role of the exportin (XPO) family in the development and progression of cancer. These nuclear transport proteins have been increasingly recognized for their involvement in oncogenic processes and tumor growth. We utilized updated public databases and bioinformatics tools to assess the expression levels of the XPO family and their associations with key oncological markers including patient survival, immune subtypes, tumor microenvironment, stemness scores, drug sensitivity, and DNA methylation across various cancers. Expression levels of XPO family proteins varied significantly across different cancer types, indicating cancer-specific roles. Specific XPO proteins were linked to adverse prognosis in particular cancers. Additionally, expression levels were correlated with classifications of immune subtypes and tumor purity; notably, lower expression levels were often found in tumors with elevated stromal and immune scores. A marked correlation was observed between XPO proteins and RNA stemness scores, whereas the correlation with DNA stemness scores varied. Furthermore, XPO expression levels significantly influenced cancer cell drug sensitivity and generally showed correlations with gene methylation patterns, although these correlations differed among cancer types. Our findings underscore the distinct roles of XPO family members in cancer, linking them to immune infiltration, the tumor microenvironment, and drug sensitivity. These insights not only enhance our understanding of the prognostic and therapeutic potentials of XPO proteins in cancer but also lay the groundwork for further studies into their mechanisms and applications in cancer diagnosis and treatment.

Prognostic significance of exportin-5 in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. As liver cancer often presents no noticeable symptoms in its early stages, most patients are diagnosed at an advanced stage, complicating treatment. Therefore, the identification of new biomarkers is crucial for the early detection and treatment of HCC. Research on exportin-5 (XPO5) could offer new avenues for early diagnosis and improve treatment strategies.

AIM

To explore the role of XPO5 in HCC progression and its potential as a prognostic biomarker.

METHODS

This study assessed XPO5 mRNA expression in HCC using The Cancer Genome Atlas, TIMER, and International Cancer Genome Consortium databases, correlating it with clinical profiles and disease progression. We performed in vitro experiments to examine the effect of XPO5 on liver cell growth. Gene Set Enrichment Analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were used to elucidate the biological roles and signaling pathways. We also evaluated XPO5's impact on immune cell infiltration and validated its prognostic potential using machine learning.

RESULTS

XPO5 was significantly upregulated in HCC tissues, correlating with tumor grade, T-stage, and overall survival, indicating poor prognosis. Enrichment analyses linked high XPO5 expression with tumor immunity, particularly CD4 T cell memory activation and macrophage M0 infiltration. Drug sensitivity tests identified potential therapeutic agents such as MG-132, paclitaxel, and WH-4-023. Overexpression of XPO5 in HCC cells, compared to normal liver cells, was confirmed by western blotting and quantitative real-time polymerase chain reaction. The lentiviral transduction-mediated knockdown of XPO5 significantly reduced cell proliferation and metastasis. Among the various machine learning algorithms, the C5.0 decision tree algorithm achieved accuracy rates of 95.5% in the training set and 92.0% in the validation set.

CONCLUSION

Our analysis shows that XPO5 expression is a reliable prognostic indicator for patients with HCC and is significantly associated with immune cell infiltration.

Investigation of the association of the RAN (rs14035) and XPO5 (rs11077) polymorphisms with venous thromboembolism

INTRODUCTION

Venous thromboembolism (VTE) is the third most common hemostatic disease worldwide. Studies have reported a role for microRNA (miRNA) in the homeostasis and development of VTE. The ras-related nuclear protein (RAN) and exportin 5 (XPO5) genes are involved in miRNA biogenesis, as both regulate the transport of pre-miRNA from the nucleus to the cytoplasm. Therefore, the aim of the current study is to examine the association between RAN (rs14035) and XPO5 (rs11077) single nucleotide polymorphisms (SNPs) and VTE.

METHODS

The study sample consisted of 300 subjects (150 patients and 150 age and sex matched controls). The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and tetra-primer amplification refractory mutation system (T-ARMS) techniques were used to genotype rs14035 and rs11077, respectively.

RESULTS

The results showed that there was a significant association between the XPO5 rs11077 and the risk of VTE (P < 0.05). Subjects with AC (OR: 2.08, CI:1.26-3.44) and CC (OR: 1.77, CI: 0.88-3.55) genotypes were at increased risk of the developing VTE. Regarding RAN gene, no association was found between rs14035 and VTE (P > 0.05). In addition, no associations were found between XPO5 rs11077 and RAN rs14035 genotypes with blood cell parameters (P > 0.05). As for the demographic characteristics, the results indicated a strong association between family history and body mass index (BMI) with the risk of VTE (P < 0.01).

CONCLUSION

The XPO5 rs11077, BMI and family history might contribute to the development of VTE in Jordan.

Unleash Multifunctional Role of miRNA Biogenesis Gene Variants (XPO5*rs34324334 and RAN*rs14035) with Susceptibility to Hepatocellular Carcinoma

Numerous reports have explored the roles of different genetic variants in miRNA biogenesis mechanisms and the progression of various types of carcinomas. The goal of this study is to explore the association between XPO5*rs34324334 and RAN*rs14035 gene variants and susceptibility to hepatocellular carcinoma (HCC). In a cohort of 234 participants (107 HCC patients and 127 unrelated cancer-free controls) from the same geographic region, we characterized allelic discrimination using PCR-RFLP and performed subgroup analysis and multivariate regression. We found that the frequency of the XPO5*rs34324334 (A) variant was correlated with elevated risk of HCC under allelic (OR = 10.09, p-value < 0.001), recessive (OR = 24.1, p-value < 0.001), and dominant (OR = 10.1, p-value < 0.001) models. A/A genotype was associated with hepatitis C cirrhosis (p-value = 0.012), ascites (p-value = 0.003), and higher levels of alpha-fetoproteins (p-value = 0.011). Carriers of the RAN*rs14035 (T) variant were more likely to develop HCC under allelic (OR = 1.76, p-value = 0.003) and recessive (OR = 3.27, p-value < 0.001) models. Our results suggest that XPO5*rs34324334 and RAN*rs14035 variants are independent risk factors for developing HCC.

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.

Effects of Knockdown of XPO5 by siRNA on the Biological Behavior of Head and Neck Cancer Cells

OBJECTIVES/HYPOTHESIS

Dysregulated expression of microRNAs (miRNAs) and dysregulation of the mechanisms that regulate them are associated with carcinogenesis. Exportin-5 (XPO5), a member of the Karyopherin family, is responsible for the transfer of pre-miRNAs from the nucleus to the cytoplasm. Despite the high oncogenic potential of XPO5 as a critical regulator of the biogenesis of miRNAs, its role in head and neck squamous cell carcinoma (HNSCC) biology has not been explained yet.

STUDY DESIGN

In-vitro translational.

METHODS

The expression of XPO5 at the mRNA, protein, and intracellular level in SCC-9, FaDu SCC-90, and Detroit-562 cell lines were evaluated with quantitative reverse transcription polymerase chain reaction, Western-blot analysis, and immunofluorescence staining, respectively. The functional role of XPO5 in HNSCC was analyzed by silencing the gene expression with XPO5-small interfering RNA (siRNA) in the in vitro model. Cell proliferation, migration capacity, and apoptosis in XPO5 knockdown HNSCC cell lines were evaluated by MTT, wound-healing, and caspase-3 assay, respectively.

RESULTS

Expression of XPO5 was determined to be upregulated at mRNA, protein, and intracellular level in metastatic cells compared to primary cells in HNSCC. XPO5 gene expression was knockdown by XPO5-siRNA transfection, verifying that it was suppressed at the mRNA, protein, and intracellular level. Silencing XPO5 caused a decrease in cell proliferation, delay in wound healing, and increase in Caspase-3 enzyme activity in HNSCC cell lines compared to control.

CONCLUSIONS

This report is the first to describe the oncogenic role of XPO5 in HNSCC biology by in vitro experiments. Consequently, XPO5 can be used as a potential biomarker and therapeutic target molecule against the disease in the diagnosis-treatment-follow-up of HNSCC.

LEVEL OF EVIDENCE

N/A Laryngoscope, 2021.

Individual and joint effects of genetic polymorphisms in microRNA-machinery genes on congenital heart disease susceptibility

Single-nucleotide polymorphisms in miRNA-machinery genes may alter the biogenesis of miRNAs affecting disease susceptibility. In this case-control study, we aimed to evaluate the impact of three single-nucleotide polymorphisms (DICER rs1057035, DROSHA rs10719, and XPO5 rs11077) and their combined effect in a genetic risk score model on congenital heart disease (CHD) risk. A total of 639 participants was recruited, including 125 patients with CHD (65 males; age 9.2 ± 10 years) and 514 healthy controls (289 males; age 15.8 ± 18 years). Genotyping of polymorphisms in miRNA-machinery genes was performed using a TaqMan®SNP genotyping assay. A genetic risk score was calculated by summing the number of risk alleles of selected single-nucleotide polymorphisms. There was a significantly increased risk of CHD in patients with XPO5 rs11077 CC genotype as compared to AC heterozygote and AA homozygote patients (ORadjusted = 1.7; 95% CI: 1.1-2.8; p = 0.018). A clear tendency to significance was also found for DROSHA rs10719 AA genotype and CHD risk for both codominant and recessive models (ORadjusted = 1.8; 95% CI: 0.91-3.8; p = 0.09 and ORadjusted = 1.9; 95% CI: 0.92-4; p = 0.08, respectively). The resulting genetic risk score predicted a 1.73 risk for CHD per risk allele (95% CI: 1.2-2.5; p = 0.002). Subjects in the top tertile of genetic risk score were estimated to have more than three-fold increased risk of CHD compared with those in the bottom tertile (ORadjusted = 3.52; 95% CI: 1.4-9; p = 0.009). Our findings show that the genetic variants in miRNA-machinery genes might participate in the development of CHD.

Key Regulatory miRNAs and their Interplay with Mechanosensing and Mechanotransduction Signaling Pathways in Breast Cancer Progression

According to the WHO, breast cancer is the most common cancer in women worldwide. Identification of underlying mechanisms in breast cancer progression is the main concerns of researches. The mechanical forces within the tumor microenvironment, in addition to biochemical stimuli such as different growth factors and cytokines, activate signaling cascades, resulting in various changes in cancer cell physiology. Cancer cell proliferation, invasiveness, migration, and, even, resistance to cancer therapeutic agents are changed due to activation of mechanotransduction signaling. The mechanotransduction signaling is frequently dysregulated in breast cancer, indicating its important role in cancer cell features. So far, a variety of experimental investigations have been conducted to determine the main regulators of the mechanotransduction signaling. Currently, the role of miRNAs has been well-defined in the cancer process through advances in molecular-based approaches. miRNAs are small groups of RNAs (∼22 nucleotides) that contribute to various biological events in cells. The central role of miRNAs in the regulation of various mediators involved in the mechanotransduction signaling has been well clarified over the last decade. Unbalanced expression of miRNAs is associated with different pathologic conditions. Overexpression and downregulation of certain miRNAs were found to be along with dysregulation of mechanotransduction signaling effectors. This study aimed to critically review the role of miRNAs in the regulation of mediators involved in the mechanosensing pathways and clarify how the cross-talk between miRNAs and their targets affect the cell behavior and physiology of breast cancer cells.