Knockdown of DEAD-box RNA helicase 52 (DDX52) suppresses the proliferation of melanoma cells in vitro and of nude mouse xenografts by targeting c-Myc

Characterization of RNA Processing Genes in Colon Cancer for Predicting Clinical Outcomes

Objective

Colon cancer is associated with multiple levels of molecular heterogeneity. RNA processing converts primary transcriptional RNA to mature RNA, which drives tumourigenesis and its maintenance. The characterisation of RNA processing genes in colon cancer urgently needs to be elucidated.

Methods

In this study, we obtained 1033 relevant samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to explore the heterogeneity of RNA processing phenotypes in colon cancer. Firstly, Unsupervised hierarchical cluster analysis detected 4 subtypes with specific clinical outcomes and biological features via analysis of 485 RNA processing genes. Next, we adopted the least absolute shrinkage and selection operator (LASSO) as well as Cox regression model with penalty to characterise RNA processing-related prognostic features.

Results

An RNA processing-related prognostic risk model based on 10 genes including FXR1, MFAP1, RBM17, SAGE1, SNRPA1, SRRM4, ADAD1, DDX52, ERI1, and EXOSC7 was identified finally. A composite prognostic nomogram was constructed by combining this feature with the remaining clinical variables including TNM, age, sex, and stage. Genetic variation, pathway activation, and immune heterogeneity with risk signatures were also analysed via bioinformatics methods. The outcomes indicated that the high-risk subgroup was associated with higher genomic instability, increased proliferative and cycle characteristics, decreased tumour killer CD8+ T cells and poorer clinical prognosis than the low-risk group.

Conclusion

This prognostic classifier based on RNA-edited genes facilitates stratification of colon cancer into specific subgroups according to TNM and clinical outcomes, genetic variation, pathway activation, and immune heterogeneity. It can be used for diagnosis, classification and targeted treatment strategies comparable to current standards in precision medicine. It provides a rationale for elucidation of the role of RNA editing genes and their clinical significance in colon cancer as prognostic markers.

DDX52 gene expression in LUAD tissues indicates potential as a prognostic biomarker and therapeutic target

Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related morbidity and mortality globally. While DDX52, an ATP-dependent RNA helicase, plays a role in several biological processes, its specific involvement in LUAD is yet to be elucidated. We utilized ROC curves to determine DDX52's predictive potential for LUAD. Kaplan-Meier survival curves, along with univariate and multivariate Cox analyses, assessed the prognostic implications of DDX52 in LUAD. We constructed nomogram models to further delineate DDX52's influence on prognosis, employed GSEA for functional analysis, and used qRT-PCR to examine DDX52 expression in LUAD tissues. DDX52 expression was notably higher in LUAD tissues, suggesting its potential as a negative prognostic marker. We observed a direct relationship between DDX52 expression and advanced T and N stages, as well as higher grading and staging in LUAD patients. Cox analyses further underscored DDX52's role as an independent prognostic determinant for LUAD. GSEA insights indicated DDX52's influence on LUAD progression via multiple signaling pathways. Our nomogram, founded on DDX52 expression, effectively projected LUAD patient survival, as validated by calibration curves. Elevated DDX52 expression in LUAD tissues signals its potential as a poor prognostic marker. Our findings emphasize DDX52's role not only as an independent prognostic factor for LUAD but also as a significant influencer in its progression through diverse signaling pathways. The constructed nomogram also underscores the feasibility of predicting LUAD patient survival based on DDX52 expression.

TRIP13/FLNA Complex Promotes Tumor Progression and Is Associated with Unfavorable Outcomes in Melanoma

Cutaneous melanoma is a high-grade malignant tumor originating from skin melanocytes with high risk of recurrence and metastasis. Further study on the mechanism of melanoma development is urgently needed. Here, we performed a bioinformatic analysis to identify critical genes in melanoma using public datasets in the Gene Expression Omnibus database. Among these differentially expressed genes, thyroid hormone receptor interactor 13 (TRIP13) has been reported to exert an important role in the development of various tumors, while its role in melanoma remains unclear. We selected TRIP13 as a candidate gene for further study. TRIP13 expression in clinical specimens was evaluated by immunohistochemistry, and its association with patient prognosis was analyzed by the Kaplan-Meier method and log-rank test. MV3 and A2058 melanoma cells were transfected with lentiviral vector to overexpress or knockdown TRIP13 expression level, and then, its biological function was studied using a series of in vitro and in vivo assays. RNA sequencing, co-immunoprecipitation, and mass spectrometry were used to identify the underlying mechanism of TRIP13. The results of this study exhibited that TRIP13 expression was upregulated in melanoma tissue compared with normal tissues, and high levels of TRIP13 were closely correlated with poor prognoses of melanoma patients. Elevated TRIP13 promoted the invasion and migration of melanoma cells in vitro and enhanced lung metastasis in vivo, without an influence on tumor growth. Importantly, elevated TRIP13 promoted the epithelial-mesenchymal transition (EMT) of melanoma cells, indicating a higher metastatic potential of these cells. Mechanically, TRIP13 physically interacted with filamin A (FLNA) and then activated the PI3K/AKT pathway to transcriptional activation of EMT-related genes. The present study revealed that TRIP13 is a novel prognostic biomarker and potential therapeutic target for melanoma treatment.

DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism

In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.

Protein tyrosine phosphatase 1B(PTP1B) promotes melanoma cells progression through Src activation

Previous studies have demonstrated that protein tyrosine phosphatase 1B (PTP1B) can promote tumor progression in breast cancer, colon cancer and prostate cancer. Additionally, PTP1B also acts as a tumor suppressor in esophageal cancer and lymphoma. These findings suggest that PTP1B functions as a double-faceted molecule in tumors. However, the role of PTP1B in malignant melanoma (MM) is still unknown. PTP1B expression in normal and melanoma tissues was evaluated by GEO analysis and immunohistochemistry. The effects of PTP1B on cell migration and invasion were evaluated in melanoma cells with up – and downregulated PTP1B expression. In this study, we initially demonstrated that the expression of PTP1B in malignant melanoma tissue is significantly higher than its expression in benign nevus tissue and indicated poor survival of malignant melanoma patients. In vitro studies have demonstrated that inhibition of PTP1B suppresses and overexpression of PTP1B promotes migration and invasion of melanoma cells. Moreover, we found that PTP1B could interact with Src via coimmunoprecipitation and dephosphorylation of the Src at Tyr530 site. Collectively, our study revealed that PTP1B can promote melanoma cell metastasis by interacting with Src and provides a theoretical basis for future applications of PTP1B inhibitors in the treatment of malignant melanoma.

Fermitin family homolog 2 (Kindlin-2) affects vascularization during the wound healing process by regulating the Wnt/β-catenin signaling pathway in vascular endothelial cells

Kindlin-2 is a member of the FERM-containing cytoskeletal protein family that regulates cell–matrix interactions. Previous studies have shown that Kindlin-2 recruits focal adhesion proteins and regulates integration by binding to the focal adhesion region of the integrin β-segment. Although Kindlin-2 has been reported to be involved in various skin diseases and many kinds of tumors, its role in the skin wound healing process remains unclear. The aim of the present study was to investigate the role of Kindlin-2 in the regulation of wound healing. The effects of Kindlin-2 on wound healing were studied by a wound healing model, kindlin-2 (±) mice. The effects of Kindlin-2 on cell migration, cellular tube formation, and cell adhesion and spreading were evaluated in human umbilical vein endothelial cells (HUVECs) with downregulated Kindlin-2 expression. We found that the expression of kindlin-2 was elevated in wound healing tissues and that interfering with the expression of Kindlin-2 delayed the wound healing process and reduced neovascularization. We found that the wound healing of kindlin-2 (±) mice was delayed, with a decreased number of new blood vessels. Furthermore, depletion of Kindlin-2 impaired HUVEC spreading, migration and tube formation. Intriguingly, we found that kindlin-2 binds to β-catenin in the Wnt/β-catenin signaling pathway and cooperates with β-catenin to enter the nucleus from the cytoplasm, activating the downstream Wnt/β-catenin signaling pathway. Taken together, these results help to elucidate the mechanism of Kindlin-2 in the regulation of the wound healing process and provide a theoretical basis for further study of wound healing and abnormal healing.