FOXM1-induced TYMS upregulation promotes the progression of hepatocellular carcinoma

Machine learning-based algorithm identifies key mitochondria-related genes in non-alcoholic steatohepatitis

BACKGROUND

Evidence suggests that hepatocyte mitochondrial dysfunction leads to abnormal lipid metabolism, redox imbalance, and programmed cell death, driving the onset and progression of non-alcoholic steatohepatitis (NASH). Identifying hub mitochondrial genes linked to NASH may unveil potential therapeutic targets.

METHODS

Mitochondrial hub genes implicated in NASH were identified via analysis using 134 algorithms.

RESULTS

The Random Forest algorithm (RF), the most effective among the 134 algorithms, identified three genes: Aldo-keto reductase family 1 member B10 (AKR1B10), thymidylate synthase (TYMS), and triggering receptor expressed in myeloid cell 2 (TREM2). They were upregulated and positively associated with genes promoting inflammation, genes involved in lipid synthesis, fibrosis, and nonalcoholic steatohepatitis activity scores in patients with NASH. Moreover, using these three genes, patients with NASH were accurately categorized into cluster 1, exhibiting heightened disease severity, and cluster 2, distinguished by milder disease activity.

CONCLUSION

These three genes are pivotal mitochondrial genes implicated in NASH progression.

DNMT3L inhibits hepatocellular carcinoma progression through DNA methylation of CDO1: insights from big data to basic research

BACKGROUND

DNMT3L is a crucial DNA methylation regulatory factor, yet its function and mechanism in hepatocellular carcinoma (HCC) remain poorly understood. Bioinformatics-based big data analysis has increasingly gained significance in cancer research. Therefore, this study aims to elucidate the role of DNMT3L in HCC by integrating big data analysis with experimental validation.

METHODS

Dozens of HCC datasets were collected to analyze the expression of DNMT3L and its relationship with prognostic indicators, and were used for molecular regulatory relationship evaluation. The effects of DNMT3L on the malignant phenotypes of hepatoma cells were confirmed in vitro and in vivo. The regulatory mechanisms of DNMT3L were explored through MSP, western blot, and dual-luciferase assays.

RESULTS

DNMT3L was found to be downregulated in HCC tissues and associated with better prognosis. Overexpression of DNMT3L inhibits cell proliferation and metastasis. Additionally, CDO1 was identified as a target gene of DNMT3L and also exhibits anti-cancer effects. DNMT3L upregulates CDO1 expression by competitively inhibiting DNMT3A-mediated methylation of CDO1 promoter.

CONCLUSIONS

Our study revealed the role and epi-transcriptomic regulatory mechanism of DNMT3L in HCC, and underscored the essential role and applicability of big data analysis in elucidating complex biological processes.

Abnormal expression of FOXM1 in carcinogenesis of renal cell carcinoma: From experimental findings to clinical applications

Renal cell carcinoma (RCC) is a prevalent malignancy within the genitourinary system. At present, patients with high-grade or advanced RCC continue to have a bleak prognosis. Mounting research have emphasized the significant involvement of Forkhead box M1 (FOXM1) in RCC development and progression. Therefore, it is imperative to consolidate the existing evidence regarding the contributions of FOXM1 to RCC tumorigenesis through a comprehensive review. This study elucidated the essential functions of FOXM1 in promoting RCC growth, invasion, and metastasis by regulating cell cycle progression, DNA repair, angiogenesis, and epithelial-mesenchymal transition (EMT). Also, FOXM1 might serve as a novel diagnostic and prognostic biomarker as well as a therapeutic target for RCC. Clinical findings demonstrated that the expression of FOXM1 was markedly upregulated in RCC samples, while a high level of FOXM1 was found to be associated with a poor overall survival rate of RCC. Furthermore, it is worth noting that FOXM1 may have a significant impact on the resistance of renal cell carcinoma (RCC) to radiotherapy. This observation suggests that inhibiting FOXM1 could be a promising strategy to impede the progression of RCC and enhance its sensitivity to radiotherapy. The present review highlighted the pivotal role of FOXM1 in RCC development. FOXM1 has the capacity to emerge as not only a valuable diagnostic and prognostic tool but also a viable therapeutic option for unresectable RCC.

SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common form of liver cancer and the 5-year relative overall survival (OS) rate is less than 20%. Since there are no specific symptoms, most patients with HCC are diagnosed in an advanced stage with poor prognosis. Therefore, identifying novel prognostic biomarkers to improve the survival of patients with HCC is urgently needed. In the present study, we attempted to identify SAMD13 (Sterile Alpha Motif Domain-Containing Protein 13) as a novel biomarker associated with the prognosis of HCC using various bioinformatics tools. SAMD13 was found to be highly expressed pan-cancer; however, the SAMD13 expression was significantly correlated with the worst prognosis in HCC. Clinicopathological analysis revealed that SAMD13 upregulation was significantly associated with advanced HCC stage and high-grade tumor type. Simultaneously, high SAMD13 expression resulted in association with various immune markers in the immune cell subsets by TIMER databases and efficacy of immunotherapy. Methylation analysis showed SAMD13 was remarkably associated with prognosis. Furthermore, a six-hub gene signature associated with poor prognosis was correlated with the cell cycle, transcription, and epigenetic regulation and this analysis may support the connection between SAMD13 expression and drug-resistance. Our study illustrated the characteristics of SAMD13 role in patients with HCC using various bioinformatics tools and highlights its potential role as a therapeutic target and promising biomarker for prognosis in HCC.

Evening Primrose Extract Modulates TYMS Expression via SP1 Transcription Factor in Malignant Pleural Mesothelioma

PURPOSE

To determine the mechanism of EPE in downregulating TYMS in MPM cancer.

METHODS

The TYMS mRNA expression with epithelial-to-mesenchymal transition biomarkers and nuclear factor SP1 was assessed using the GEO database in a data set of MPM patients (GSE51024). Invasive MPM cell lines were in vitro models for the investigation of TYMS expression after EPE treatment. The tyms promoter SP1 binding sequences were determined using Genomatix v 3.4 software Electrophoretic mobility shift and dual-luciferase reporter assays revealed specific SP1 motifs in the interaction of EPE and reference compounds. Chromatin immunoprecipitation and Re-ChIP were used for the co-occupancy study.

RESULTS

In MPM patients, a positive correlation of overexpressed TYMS with mesenchymal TWIST1, FN1 and N-cadherin was observed. EPE and its major components, gallic and ellagic acid (GA and EA, respectively), downregulated TYMS in invasive MPM cells by interacting with particular SP1 motifs on the tyms promoter. The luciferase constructs confirmed the occupation of two SP1 regulatory regions critical for the promotion of TYMS expression. Both EPE and reference standards influenced SP1 translocation into the nucleus.

CONCLUSION

EPE components reduced TYMS expression by occupation of SP1 motifs on the tyms promoter and reversed the EMT phenotype of invasive MPM cells. Further in-depth analysis of the molecular docking of polyphenol compounds with SP1 regulatory motifs is required.

Vital role of SHMT2 in diverse disease

One-carbon metabolism is essential for our human cells to carry out nucleotide synthesis, methylation, and reductive metabolism through one-carbon units, and these pathways ensure the high proliferation rate of cancer cells. Serine hydroxymethyltransferase 2 (SHMT2) is a key enzyme in one-carbon metabolism. This enzyme can convert serine into a one-carbon unit bound to tetrahydrofolate and glycine, ultimately supporting the synthesis of thymidine and purines and promoting the growth of cancer cells. Due to SHMT2's crucial role in the one-carbon cycle, it is ubiquitous in human cells and even in all organisms and highly conserved. Here, we summarize the impact of SHMT2 on the progression of various cancers to highlight its potential use in the development of cancer treatments.

Genomic Profiling of Lower-Grade Gliomas Subtype with Distinct Molecular and Clinicopathologic Characteristics via Altered DNA-Damage Repair Features

Lower WHO grade II and III gliomas (LGGs) exhibit significant genetic and transcriptional heterogeneity, and the heterogeneity of DNA damage repair (DDR) and its relationship to tumor biology, transcriptome, and tumor microenvironment (TME) remains poorly understood. In this study, we conducted multi-omics data integration to investigate DDR alterations in LGG. Based on clinical parameters and molecular characteristics, LGG patients were categorized into distinct DDR subtypes, namely, DDR-activated and DDR-suppressed subtypes. We compared gene mutation, immune spectrum, and immune cell infiltration between the two subtypes. DDR scores were generated to classify LGG patients based on DDR subtype features, and the results were validated using a multi-layer data cohort. We found that DDR activation was associated with poorer overall survival and that clinicopathological features of advanced age and higher grade were more common in the DDR-activated subtype. DDR-suppressed subtypes exhibited more frequent mutations in IDH1. In addition, we observed significant upregulation of activated immune cells in the DDR-activated subgroup, which suggests that immune cell infiltration significantly influences tumor progression and immunotherapeutic responses. Furthermore, we constructed a DDR signature for LGG using six DDR genes, which allowed for the division of patients into low- and high-risk groups. Quantitative real-time PCR results showed that CDK1, CDK2, TYMS, SMC4, and WEE1 were significantly upregulated in LGG samples compared to normal brain tissue samples. Overall, our study sheds light on DDR heterogeneity in LGG and provides insight into the molecular pathways of DDR involved in LGG development.

Predictive investigation of idiopathic pulmonary fibrosis subtypes based on cellular senescence-related genes for disease treatment and management

Background: Idiopathic pulmonary fibrosis (IPF), a chronic, progressive lung disease characterized by interstitial remodeling and tissue destruction, affects people worldwide and places a great burden on society. Cellular senescence is thought to be involved in the mechanisms and development of IPF. The aim of this study was to predictively investigate subtypes of IPF according to cellular senescence-related genes and their correlation with the outcome of patients with IPF, providing possible treatment and management options for disease control. Methods: Gene expression profiles and follow-up data were obtained from the GEO database. Senescence-related genes were obtained from the CSGene database and analyzed their correlation with the outcome of IPF. A consensus cluster was constructed to classify the samples based on correlated genes. The GSVA and WGCNA packages in R were used to calculate the immune-related enriched fractions and construct gene expression modules, respectively. Metascape and the clusterProfiler package in R were used to enrich gene functions. The ConnectivityMap was used to probe suitable drugs for potential treatment. Results: A total of 99 cellular senescence-related genes were associated with IPF prognosis. Patients with IPF were divided into two subtypes with significant prognostic differences. Subtype S2 was characterized by enhanced fibrotic progression and infection, leading to acute exacerbation of IPF and poor prognosis. Finally, five cellular senescence-related genes, TYMS, HJURP, UBE2C, BIRC5, and KIF2C, were identified as potential biomarkers in poor prognostic patients with IPF. Conclusion: The study findings indicate that cellular senescence-related genes can be used to distinguish the prognosis of patients with IPF. Among them, five genes can be used as candidate biomarkers to predict patients with a poor prognostic subtype for which anti-fibrosis and anti-infection treatments could be suitable.