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Background: The contribution of MTHFR and TP53 genetic variants to breast carcinoma (BC) susceptibility has been examined, but their findings have been inconclusive. This work is designed to explore the potential roles of the MTHFR (rs1801131, rs1801133) and TP53 (rs1042522) variants with increased risk of BC using genetic and bioinformatic approaches.

Methods: This work included a total of 242 female participants [142 BCE patients and 100 healthy controls]. We genotyped the allelic discrimination analysis for these genetic variants using the T-ARMS-PCR technique. Logistic regression, haplotype analysis, genetic association models, and multivariate clustering were executed.

Results: The rs1801131*C allele revealed a significant association with elevated risk of breast carcinoma compared to healthy controls under allelic (OR = 2.02, p-value < 0.001) and recessive (OR = 3.26, p-value < 0.001) models. Moreover, the rs1801133*T allele was correlated to cancer susceptibility under allelic (OR = 1.81, p-value = 0.002) and dominant (OR = 3.33, p-value < 0.001) models, while the rs1042522*G allele was associated with increased risk of BC under allelic (OR = 2.98, p-value < 0.001) and recessive (OR = 3.21, p-value < 0.001) models. BC women carrying the rs1801131*C/C genotype were associated with histological grade III, while those with the rs1801133*T/T and rs1042522*G/G genotypes were correlated with a moderate/poor NPI score (p-value < 0.05).

Conclusions: The rs1801131*C, rs1801133*T, and rs1042522*G alleles are associated with an increased risk of BC. The rs1801133*T and rs1042522*G alleles correlated with moderate/poor NPI score. These findings pave the way for the diagnostic functions of these genetic variants as potential prognostic biomarkers.

Background: P-element-induced wimpy testis (PIWI) proteins bind to PIWI-interactingRNAs (piRNAs) to form the piRNA/PIWI complex, which affects protein regulation. PIWIL4, a member of the PIWI family, has been demonstrated in recent studies to promote the migration of triple-negative breast cancer (TNBC) cell line MDA-MB-231. However, the molecular mechanisms underlying cell migration remain obscure.

Methods: RNA immunoprecipitation and real-time PCR assays were conducted to detect piRNAs binding to PIWIL4. piRNA mimics and inhibitors were employed to modify piRNA expression in MDA-MB-231 cells. Cell migration assays were carried out using transwell inserts. Co-immunoprecipitation (co-IP) combined with mass spectrometry (MS) was performed to identify the proteins that interacted with PIWIL4 under the regulation of piRNA. Western blotting (WB) was utilised to detect the regulatory relationship between the piRNA/PIWIL4 complexes and the mutually-binding proteins.

Results: RNA Immunoprecipitation (RIP) results revealed that PIWIL4 bound to piR-31115 in the MDA-MB-231 cells. Transwell assays demonstrated that piR-31115 promoted the migration of MDA-MB-231 cells via PIWIL4. Co-IP coupled with MS results showed that piR-31115 promoted the binding of PIWIL4 to HSP90AA1 in MDA-MB-231 cells, and this interaction protected HSP90AA1 from degradation. Knockdown of HSP90AA1 in MDA-MB-231 cells attenuated the promoting effects of piR-31115/PIWIL4 on cell migration.

Conclusions: Our findings cast light on a novel molecular pathway through which piR-31115 promotes the migration of MDA-MB-231 TNBC cells by regulating the interaction between PIWIL4 and HSP90AA1.

Aim: The objective of this study was to examine the transcriptomic profile changes in hyperuricemia (HUA) and to investigate the pathogenic mechanisms and biomarkers of HUA from a transcriptomic perspective.

Methods: In this study, three patients with HUA were randomly selected and matched with three healthy controls. Six participants provided peripheral blood mononuclear cells (PBMCs) for analysis. RNA sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) and alternative splicing events (ASEs). Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to identify the functions and pathways of the DEGs and ASEs. Additionally, a co-expression network was constructed to analyze the regulation of DEGs and ASEs by RNA-binding protein (RBP) genes. In addition, important DEGs and ASEs were validated using quantitative real-time PCR (qPCR).

Results: There were 633 DEGs identified, 348 up-regulated DEGs and 285 down-regulated DEGs, including RGS18, CAVIN2, GZMH, GNLY and MT-TV, which were mainly enriched in inflammatory and immune-related biological processes. A total of 1542 ASEs were significantly differentially expressed in HUA, of which LTB4R and ENTPD4 were closely associated with the development of HUA. In addition, 15 RBP genes were detected to be differentially expressed in HUA. Three RBP genes (IFIT1, IFFIT2, and IFIT3) were highly associated with immunoinflammation and affected HUA by modulating downstream immune responses, inflammatory response-associated DEGs, and ASEs. The selected five DEGs and two ASEs were verified by qPCR, which was consistent with the results of RNA sequencing.

Conclusions: In summary, the findings indicate that HUA is associated with significant changes in inflammatory and immune response-related genes (RGS18, CAVIN2, GZMH, GNLY, MT-TV, LTB4R, ENTPD4, IFIT1, IFFIT2, and IFIT3). These findings suggest potential biomarkers and therapeutic targets.

Advances in molecular medicine and biotechnology have demonstrated messenger RNA (mRNA)-based therapies to be a promising therapeutic modality for infectious diseases, genetic disorders, and cancers. However, key challenges persist, including low translation efficiency and short half-life of exogenous mRNA. The untranslated regions (UTRs) influence important parameters like mRNA stability and translation efficiency. This study adopted a combinatorial screening strategy to enhance exogenous mRNA translation efficiency by de novo designing 5'UTRs and combining them with multiple potential 3'UTRs. We designed a novel 5'UTR, 5UTR05, which exhibited comparable protein expression levels to the reference mRNA-1273 5'UTR that has been found to exhibit high expression in the COVID-19 vaccine development. Furthermore, the screening experiments found that combining 5UTR05 with both the 3'UTR of immunoglobulin heavy constant gamma 2 (IGHG2) and the 3'UTR of mitochondrially encoded 12S ribosomal RNA (mtRNR1) significantly improved mRNA translation efficiency, compared to individual 3'UTRs. Collectively, these findings provide valuable insights for UTR optimization strategies aimed at augmenting exogenous mRNA therapeutic translation. Continuing exploration of synergistic UTR combinations offers promise to advance customized mRNA constructs with optimized expression profiles tailored for diverse applications.

Background: It is largely unidentified concerning the underlying genetic causes responsible for triple-negative breast cancers (TNBC), with unpredictable disease recurrence. This study aimed to examine the role of ZNF703 (Zinc finger 703) in the malignant behaviors of TNBC and its role in predicting disease-free survival (DFS).

Methods: After downregulation of ZNF703 with short interfering RNA (siRNA), we examined the proliferation of TNBC cell line MDA-MB-231 by sulforhodamine B (SRB) assay, the invasion of cells by a transwell invasion model, and the migration of cells by the monolayer wound-healing experiment. mRNA-sequencing data of ZNF703, BRCA1, BRCA2, PALB2, CHEK2, CDH1, PTEN, STK11, ATM, and TP53, and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA) dataset for a total of 157 stage I-III TNBC samples. The selection of modeling features was executed using the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm to avoid model overfitting. The TIMER 2.0 algorithm determined the associations between immune score and gene expressions. Kaplan-Meier analysis was conducted to plot survival analyses.

Results: The aggressive tumor morphology, cell proliferation, cell migration, and cell invasion were partly reversed by the siRNA knockdown of ZNF703 in MDA-MB-231 cells. ZNF703 knockdown markedly enhanced the killing ability of cisplatin These phenomena were verified by another TNBC cell line BT-549. Patients with high expression of ZNF703 had an inferior DFS for TNBC patients at 8 years [Hazard ratio (HR) for high expression vs. low expression was 2.71; 95 %CI, 1.03 to 7.14, P = 0.044]. Receiver Operating Characteristic (ROC) curve was also developed, indicating the area under the curve (AUC) was 0.744 (95 %CI, 0.628 to 0.861) at 5 years and 0.738 (95 %CI, 0.552 to 0.924) at 8 years, respectively. In addition, LASSO regression results showed that the optimal penalization parameter corresponds to two prognostic genes - ZNF703 and STK11. The risk score was computed as Risk Score (RS) = 0.1033*ZNF703 + 0.2131*STK11 (named "ZS -TNBC model"). The high expression of both ZNF703 and STK11 had as high as 7.035 HR in comparison to the low-expression category (95 %CI, 2.044 to 24.206, P = 0.00197).

Conclusion: ZNF703 is required for the growth, invasion, and migratory behavior of TNBC cells. Downregulation of ZNF703 increases cisplatin efficacy. This study suggests that either ZNF703 alone or in conjunction with STK11 can be utilized to predict DFS in TNBC.

Emerging evidence suggests that circular RNAs (circRNAs), a class of non-coding RNAs, play a critical role in the progression of several cancers, including osteosarcoma (OS). In this study, we focused on a specific circRNA, hsa_circ_0002005, derived from the mesoderm-induced early response 1 family member 2 (MIER2) gene. We determined the expression levels of hsa_circ_0002005 in OS samples through the use of real-time quantitative polymerase chain reaction (RT-qPCR). To assess the effect of hsa_circ_0002005, we used lentiviral analysis and performed several assays including transwell migration, cell invasion, 5-ethynyl-2'-deoxyuridine assay (EdU), cell counting kit-8 (CCK-8), proliferation, colony formation, and western blotting. In addition, we investigated the delivery mechanism of hsa_circ_0002005 in nude mice and predicted the interaction network involving hsa_circ_0002005, microRNA (miRNA), and mRNAs through bioinformatics analysis. The results showed that hsa_circ_0002005 is overexpressed in OS tissues and cells and is derived from exons 2 to 7 of the MIER2 gene. Knockdown of hsa_circ_0002005 markedly reduced the proliferation, migration, and invasive capabilities of cells, as well as their metastatic potential. We discovered miRNAs that may engage with hsa_circ_0002005. Further mechanistic studies indicated that the suppression of hsa_circ_0002005 influenced the expression levels of proteins associated with the epithelial-mesenchymal transition (EMT), suggesting its regulatory role in EMT progression through modulation of cell proliferation, migration, and invasion.

Background: The precise role of Galectin-9, an immune checkpoint protein involved in immune responses, in hepatocellular carcinoma (HCC) remains elusive. Importantly, the prognostic value of serum Galectin-9 has not been clarified, and its association with infiltrating immune characteristics was unclear.

Methods: The association between serum Galectin-9 concentration and HCC recurrence was analyzed in two cohorts of HCC patients (training 133; validation 97) who received curative resection during 2018 and 2019. Bioinformatic analyses, including WGCNA, GSEA, GO, KEGG, Hallmark, CIBERSORT, QUANTISEQ, ssGSEA and TISIDB, were performed to systematically demonstrate the expression pattern, immunomodulation role, and prognostic value of Galectin-9 in HCC. These findings were further validated by immunohistochemistry staining.

Results: Patients with high serum Galectin-9 levels had significantly shorter time to tumor recurrence (TTR; P < 0.001) in both cohorts, and serum Galectin-9 was identified as an independent predictor of HCC recurrence, even in patients with low-AFP or early-stage. Bioinformatic analyzes revealed high Galectin-9 expression is involved in immune-evasive and inflammatory signaling pathways. It correlated with increased infiltration of exhausted CD8 + T cells, Tregs, TAMs and MDSCs. Interestingly, we found Galectin-9 was predominantly expressed on macrophages rather than malignant cells, and showed positively association with serum Galectin-9 concentration according to IHC results. Concordantly, high serum Galectin-9 levels also reflected an immune-evasive microenvironment composed by extensive CD163 + and FOXP3 + cell infiltrates.

Conclusions: Elevated serum Galectin-9 was a novel indicator for worse prognosis in HCC. The high expression of Galectin-9 may reflect the immunosuppressive environment by increasing CD163 + and FOXP3 + cell infiltrates.

CRISPR-Cas9 technology has revolutionized genetic engineering, offering precise and efficient genome editing capabilities. This review explores the application of CRISPR-Cas9 for cystic fibrosis (CF), particularly targeting mutations in the CFTR gene. CF is a multiorgan disease primarily affecting the lungs, gastrointestinal system (e.g., CF-related diabetes (CFRD), CF-associated liver disease (CFLD)), bones (CF-bone disease), and the reproductive system. CF, a genetic disorder characterized by defective ion transport leading to thick mucus accumulation, is often caused by mutations like ΔF508 in the CFTR gene. This review employs a systematic methodology, incorporating an extensive literature search across multiple academic databases, including PubMed, Web of Science, and ScienceDirect, to identify 40 high-quality studies focused on CRISPR-Cas9 applications for CFTR gene editing. The data collection process involved predefined inclusion criteria targeting experimental approaches, gene-editing outcomes, delivery methods, and verification techniques. Data analysis synthesized findings on editing efficiency, off-target effects, and delivery system optimization to present a comprehensive overview of the field. The review highlights the historical development of CRISPR-Cas9, its mechanism, and its transformative role in genetic engineering and medicine. A detailed examination of CRISPR-Cas9's application in CFTR gene correction emphasizes the potential for therapeutic interventions while addressing challenges such as off-target effects, delivery efficiency, and ethical considerations. Future directions include optimizing delivery systems, integrating advanced editing tools like prime and base editing, and expanding personalized medicine approaches to improve treatment outcomes. By systematically analyzing the current landscape, this review provides a foundation for advancing CRISPR-Cas9 technologies for cystic fibrosis treatment and related disorders.

Background: Ischemic stroke (IS) is an important disease causing death and disability worldwide, and further investigation of IS-related genes through genome-wide association study (GWAS) data is valuable.

Methods: The study included GWAS data from 62,100 IS patients of European origin and 1,234,808 controls in a cross-tissue transcriptome association study (TWAS). A joint analysis was first performed by the Unified Test for Molecular Markers (UTMOST) and FUSION methods. The results of the joint analysis were also validated by fine-mapping through FOCUS. Mendelian randomisation analysis was performed to determine whether the obtained genes were causally related to IS. Genome Annotated Multiple Marker Analysis (MAGMA) explored which biological functions the genes associated with IS. We used Coloc to co-localise GWAS and eQTL of the genes. We also biologically validated the results by Western blotting and immunofluorescence staining in the middle cerebral artery occlusion/reperfusion (MCAO/R) mouse model.

Results: Four TWAS methods identified only one new susceptibility gene (USP38) associated with IS risk. Mendelian randomization and colocalization analysis found that USP38 may be protective against IS development. Functional enrichment analysis indicated IS-related genes were mainly associated with the intrinsic fibrinogen activation, acute myocardial infarction, exogenous fibrinogen activation, coagulation cascade response, TNF signalling pathway and GRB2 signalling pathway. Western blotting and immunofluorescence staining demonstrated a reduction in USP38 expression in MCAO/R mice.

Conclusion: Our research indicates that USP38 is an essential gene related to IS, with its expression strongly connected with IS risk, thus providing new perspectives on the genetic framework of IS.

Background: Methyltransferase-like 3 (METTL3) regulates numerous biological processes and diverse cancers.

Objective: To explore the frequency distribution of METTL3 rs1061026, rs1139130, and rs1263801 polymorphisms, and their potential impacts on clinical outcomes and chemotherapy-induced toxicities in a cohort of Chinese pediatric patients diagnosed with primary brain tumors (PBTs).

Methods: Genotyping for three investigated SNPs was performed in 107 pediatric patients with PBTs using the Sequenom MassARRAY iPLEX platform. Serum METTL3 levels were determined by Enzyme-Linked Immunosorbent Assay. Serum methotrexate (MTX) concentrations were quantified utilizing fluorescence polarization immunoassay.

Results: The three investigated SNPs were not significantly associated with the risks of relapse and metastasis after adjusting all confounders. Compared to individuals with the rs1139130 GG genotype, GA genotype carriers exhibited a significantly higher risk of oral mucositis (adjusted OR: 7.504; 95 % CI, 1.931-29.436; P = 0.004). The rs1139130 GA (adjusted OR: 5.091; 95 % CI, 1.351-19.176; P = 0.016) and AA (adjusted OR: 9.588; 95 % CI, 1.769-51.949; P = 0.009) genotype carriers exhibited a significantly lower risk of fever than GG genotype carriers. The median dose-normalized MTX concentrations at 42 h were lower with borderline significance in children with rs1061026 GT and GG genotypes (0.004 μmol/L per g/m²) than the TT genotype carriers (0.006 μmol/L per g/m², P = 0.048). Patients with the rs1139130 GA genotype had significantly higher median serum METTL3 protein levels (59.91 ng/mL) than GG genotype carriers (44.57 ng/mL, P = 0.015).

Conclusion: This study demonstrated the association of the rs1139130 polymorphism with the development of oral mucositis and fever and the rs1061026 polymorphism with MTX exposure.