The RNA-helicase DDX21 upregulates CEP55 expression and promotes neuroblastoma

m6A-induced DEAD-box RNA helicase 21 enhances lipid metabolism via 3‑hydroxy-3-methylglutaryl-CoA synthases 1 in colorectal cancer

BACKGROUND

Altered lipid metabolism is a well-known hallmark of cancer. However, the underlying mechanisms of altered lipid metabolism in colorectal cancer (CRC) progression requires further investigation. Previously we have revealed that DEAD-box RNA helicase 21 (DDX21) promotes CRC metastasis via liquid-liquid phase separation. In this study, we identify DDX21 as a novel regulator of lipid metabolism in CRC.

METHODS

In vitro and in vivo assays illustrated the biological role of DDX21 and YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) in CRC lipid metabolism and progression. Bioinformatics analysis, ChIP, meRIP, RIP, RNA stability assay and dual-luciferase reporter assay were applied to explore the underlying molecular mechanisms. The expression levels and prognostic role of YTHDF1/DDX21/HMGCS1 axis in CRC patients were analyzed by immunohistochemical staining and Kaplan-Meier plotter.

RESULTS

DDX21 enhanced CRC progression via promoting lipid metabolism. Mechanistically, YTHDF1 enhanced DDX21 mRNA stability by recognizing its m6A-modified sites. DDX21 further binded to 3‑hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) promoter region and directly activated HMGCS1 transcription. Moreover, our clinical data showed that a simultaneously high expression of YTHDF1, DDX21 and HMGCS1 predicted an unfavorable overall survival in CRC patients.

CONCLUSIONS

Our study demonstrates that the YTHDF1/DDX21/HMGCS1 axis promotes CRC progression via regulating lipid metabolism and DDX21 might be a promising target for CRC therapy.

Competitive binding between DDX21 and SIRT7 enhances NAT10-mediated ac4C modification to promote colorectal cancer metastasis and angiogenesis- DDX21 promotes colorectal cancer metastasis

DExD- box helicase 21 (DDX21) is overexpressed in colorectal cancer (CRC) and is positively correlated with poor prognosis and the malignant phenotype of CRC. Functional characterization indicated that DDX21 promotes CRC metastasis and angiogenesis both in vitro and in vivo. N-acetyltransferase 10 (NAT10) is a key regulator of the N4-acetylcytidine (ac4C) modification of mRNA, regulating the stabilization of mRNA via ac4C modification. Here, we identified that DDX21 competitive binding with sirtuin 7 (SIRT7), inducing the overexpression of NAT10. Furthermore, DDX21 upregulates NAT10 expression to enhance ac4C modification and the stability of ATAD2, SOX4 and SNX5 mRNAs, which mediate CRC metastasis and angiogenesis. Overall, the present study revealed a mechanism of DDX21/NAT10-mediated mRNA stability in CRC, laying the foundation for the use of DDX21 as a therapeutic target to overcome metastasis and angiogenesis in CRC. DDX21 competitive binding with sirtuin 7 (SIRT7), inducing the overexpression of NAT10. Furthermore, DDX21 upregulates NAT10 expression to enhance ac4C modification and the stability of ATAD2, SOX4 and SNX5 mRNAs, which mediate CRC metastasis and angiogenesis.

The liver-specific long noncoding RNA FAM99B inhibits ribosome biogenesis and cancer progression through cleavage of dead-box Helicase 21

Emerging evidence has demonstrated that long noncoding RNAs (lncRNAs) are promising targets or agents for the treatment of human cancers. Most liver-specific lncRNAs exhibit loss of expression and act as tumor suppressors in liver cancer. Modulating the expression of these liver-specific lncRNAs is a potential approach for lncRNA-based gene therapy for hepatocellular carcinoma (HCC). Here, we report that the expression of the liver-specific lncRNA FAM99B is significantly decreased in HCC tissues and that FAM99B suppresses HCC cell proliferation and metastasis both in vitro and in vivo. FAM99B promotes the nuclear export of DDX21 through XPO1, leading to further cleavage of DDX21 by caspase3/6 in the cytoplasm. FAM99B inhibits ribosome biogenesis by inhibiting ribosomal RNA (rRNA) processing and RPS29/RPL38 transcription, thereby reducing global protein synthesis through downregulation of DDX21 in HCC cells. Interestingly, the FAM99B65-146 truncation exhibits tumor-suppressive effects in vivo and in vitro. Moreover, GalNAc-conjugated FAM99B65-146 inhibits the growth and metastasis of orthotopic HCC xenografts, providing a new strategy for the treatment of HCC. This is the first report of the use of a lncRNA as an agent rather than a target in tumor treatment. Graphical illustration of the mechanism of FAM99B in HCC.

DDX21 Is a Potential Biomarker for Predicting Recurrence and Prognosis in Hepatocellular Carcinoma

DEAD-box helicase 21 (DDX21) is a conserved Asp-Glu-Ala-Asp (DEAD) box RNA helicase with multiple functions that is involved in various cellular processes and diseases. However, the role of DDX21 in the recurrence and prognosis of hepatocellular carcinoma (HCC) patients remains unknown. In the current study, we examined the protein expression of DDX21 in HCC tissues through immunohistochemical staining and analyzed the correlation between DDX21 protein expression and clinical outcome via Kaplan-Meier survival analysis. The Cox proportional hazards regression model was used to assess the interrelationships between the outcome and variable over time. Our results showed that increased expression of DDX21 protein was observed in HCC tissues compared with paracancerous tissues and was associated with advanced BCLC stage. Recurrent HCC patients had higher levels of DDX21 protein than nonrecurrent cases. Notably, DDX21 was an independent risk factor for predicting worse overall survival and recurrence-free survival in HCC patients. Furthermore, lack of DDX21 abated the growth and mobility of Hep3B cells. Taken together, our data highlight the clinical significance of DDX21 in the recurrence and prognosis of HCC patients and indicate that targeting DDX21 may represent an effective therapeutic strategy for the treatment of HCC.

Prognostic assessment value of immune escape-related genes in patients with acute myeloid leukemia

This study explores the prognostic value of immune escape-related genes in acute myeloid leukemia (AML) patients. Using TARGET_AML and GSE37642 datasets, we identified CEP55, DNAJC13, and EMC2 as significant prognostic indicators, with high transcript abundance correlating with poor outcomes. Consensus clustering divided patients into two groups, with Cluster 1 showing worse prognosis. A prognostic signature based on these genes stratified patients into high- and low-risk groups, with the high-risk group experiencing worse outcomes. The risk score was an independent prognostic factor. Functional analysis revealed that high-risk genes could promote cell cycle progression. The selected genes were strongly associated with immune cells, particularly mast cells and CD8+ T cells. This study enriches the prognostic evaluation system for AML and suggests a new therapeutic direction.

DDX21 at the Nexus of RNA Metabolism, Cancer Oncogenesis, and Host-Virus Crosstalk: Decoding Its Biomarker Potential and Therapeutic Implications

DDX21, a member of the DEAD-box RNA helicase family, plays a pivotal role in various aspects of RNA metabolism, including ribosomal RNA (rRNA) processing, transcription, and translation. Its diverse functions in cancer progression and viral infections have attracted considerable attention. DDX21 exerts a pivotal function through ribosomal DNA (rDNA) transcription and rRNA processing. DDX21 is involved in different biological processes of mRNA transcription. It interacts with transcription factors, modulates RNA polymerase II elongation, binds R-loops to regulate transcription, and participates in alternative splicing. The elevated expression of DDX21 has been observed in most cancers, where it influences tumorigenesis by affecting ribosome biogenesis, transcription, genome stability, and cell cycle regulation. Additionally, DDX21 plays a key role in the antiviral defense of host by interacting with viral proteins to regulate essential stages of the infection process. This review provides a thorough examination of the biological functions of DDX21, its involvement in cancer progression and viral infections, and its potential as both a biomarker and a therapeutic target. Future studies should aim to clarify the specific mechanisms of the activity of DDX21, advance the development of targeted therapies, and assess its clinical relevance across various cancer types and stages.

Current understanding of the role of DDX21 in orchestrating gene expression in health and diseases

RNA helicases are involved in almost all biological events, and the DDXs family is one of the largest subfamilies of RNA helicases. Recently, studies have reported that RNA helicase DDX21 is involved in several biological events, specifically in orchestrating gene expression. Hence, in this review, we provide a comprehensive overview of the function of DDX21 in health and diseases. In the genome, DDX21 contributes to genome stability by promoting DNA damage repair and resolving R-loops. It also facilitates transcriptional regulation by directly binding to promoter regions, interacting with transcription factors, and enhancing transcription through non-coding RNA. Moreover, DDX21 is involved in various RNA metabolism such as RNA processing, translation, and decay. Interestingly, the activity and function of DDX21 are regulated by post-translational modifications, which affect the localization and degradation of DDX21. Except for its role of RNA helicase, DDX21 also acts as a non-enzymatic function in unwinding RNA, regulating transcriptional modifications and promoting transcription. Next, we discuss the potential application of DDX21 as a clinical predictor for diseases, which may facilitate providing novel pharmacological targets for molecular therapy.

Lnc-PLCB1 is stabilized by METTL14 induced m6A modification and inhibits Helicobacter pylori mediated gastric cancer by destabilizing DDX21

Helicobacter pylori (H. pylori) infection is considered to be an important factor in gastric cancer (GC). Long noncoding RNA (lncRNA) and m6A modification are involved in the occurrence and development of GC, but the role of lncRNA m6A modification in the development of GC mediated by H. pylori is still unclear. Here, we found that H. pylori infection downregulated the expression of lnc-PLCB1 through METTL14-mediated m6A modification and IRF2-mediated transcriptional regulation. Overexpression of lnc-PLCB1 inhibited the proliferation and migration of GC cells, while downregulation of lnc-PLCB1 promoted the proliferation and migration ability of GC cells. In addition, clinical analysis showed that lnc-PLCB1 is lower in GC tissues than in normal tissues. Further study found that lnc-PLCB1 reduced the protein stability of its binding protein DEAD-box helicase 21 (DDX21) and then downregulated the expression of CCND1 and Slug, thereby playing tumour suppressing role in the occurrence and development of GC. In conclusion, the METTL14/lnc-PLCB1/DDX21 axis plays an important role in H. pylori-mediated GC, and lnc-PLCB1 can be used as a new target for GC treatment.

Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid

BACKGROUND

Colorectal cancer (CRC) is a common malignancy in the gastrointestinal tract. Keloid refers to abnormal scar tissue that forms on the skin or mucous membrane. The relationship between RRP9 and DDX21 and the two diseases is unclear.

METHODS

Download the colorectal cancer dataset GSE134834, GSE206800, GSE209892 and keloid dataset GSE44270 from the GEO database. Differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. The construction and analysis of protein-protein interaction (PPI) network, functional enrichment analysis, gene set enrichment analysis (GSEA). Gene expression heat map was drawn. The comparative toxicogenomics database (CTD) analysis was performed to find diseases most related to core genes. TargetScan screened miRNAs that regulated central DEGs. We conducted experimental validation using Western blotting and Polymerase Chain Reaction (PCR).

RESULTS

In the colorectal cancer dataset and the scar tissue dataset, we identified 1380 DEGs and 1000 DEGs, respectively. The enrichment pattern for scar tissue was similar to that of colorectal cancer. We identified two core genes, RRP9 and DDX21. CTD analysis indicated that RRP9 and DDX21 are associated with proliferation, scar tissue, colorectal tumors, scleroderma, and inflammation. We found that the core genes (RRP9 and DDX21) were highly expressed in colorectal cancer and scar tissue samples, while their expression was lower in normal samples. This was further validated through Western blotting (WB) and Polymerase Chain Reaction (PCR).

CONCLUSIONS

The higher the expression of RRP9 and DDX21 in colorectal cancer and keloid, the worse the prognosis.

CEP55 as a promising biomarker and therapeutic target on gallbladder cancer

Introduction

Gallbladder cancer (GBC) is a highly malignant biliary tumor with a poor prognosis. As existing therapies for advanced metastatic GBC are rarely effective, there is an urgent need to identify more effective targets for treatment.

Methods

Hub genes of GBC were identified by bioinformatics analysis and their expression in GBC was analyzed by tissue validation. The biological role of CEP55 in GBC cell and the underlying mechanism of the anticancer effect of CEP55 knockdown were evaluated via CCK8, colony formation assay, EDU staining, flow cytometry, western blot, immunofluorescence, and an alkaline comet assay.

Results

We screened out five hub genes of GBC, namely PLK1, CEP55, FANCI, NEK2 and PTTG1. CEP55 is not only overexpressed in the GBC but also correlated with advanced TNM stage, differentiation grade and poorer survival. After CEP55 knockdown, the proliferation of GBC cells was inhibited with cell cycle arrest in G2/M phase and DNA damage. There was a marked increase in the apoptosis of GBC cells in the siCEP55 group. Besides, in vivo, CEP55 inhibition attenuated the growth and promoted apoptosis of GBC cells. Mechanically, the tumor suppressor effect of CEP55 knockdown is associated with dysregulation of the AKT and ERK signaling networks.

Discussion

These data not only demonstrate that CEP55 is identified as a potential independent predictor crucial to the diagnosis and prognosis of gallbladder cancer but also reveal the possibility for CEP55 to be used as a promising target in the treatment of GBC.

MiRNA and Potential Prognostic Value in Non-Smoking Females with Lung Adenocarcinoma by High-Throughput Sequencing

Background

Non-smoking females with lung adenocarcinoma (LUAD) account for a unique disease entity and miRNA play critical roles in cancer development and progression. The purpose of this study is to explore prognosis-related differentially expressed miRNA (DEmiRNA) and establish a prognostic model for non-smoking females with LUAD.

Methods

Eight specimens were collected from thoracic surgery of non-smoking females with LUAD and implemented the miRNA sequencing. The intersection of our miRNA sequencing data and TCGA database were identified as common DEmiRNA. Then, we predicted the target genes of the common DEmiRNAs (DETGs) and explored the functional enrichment and prognosis of DETGs. A risk model by overall survival (OS)-related DEmiRNA was constructed based on multivariate Cox regression analyses.

Results

A total of 34 overlapping DEmiRNA were obtained. The DETGs were enriched in pathways including "Cell cycle" and "miRNAs in cancer". The DETGs (KPNA2, CEP55, TRIP13, MYBL2) were risk factors, significantly related to OS, progression-free survival (PFS), and were also hub genes. ScRNA-seq data also validated the expression of the four DETGs. Hsa-mir-200a, hsa-mir-21, and hsa-mir-584 were significantly associated with OS. The prognostic prediction model constructed by the 3 DEmiRNA could effectively predict OS and can be used as an independent prognostic factor of non-smoking females with LUAD.

Conclusion

Hsa-mir-200a, hsa-mir-21, and hsa-mir-584 can serve as potential prognostic predictors in non-smoking females with LUAD. A novel prognostic model based on the three DEmiRNAs was also constructed to predict the survival of non-smoking females with LUAD and showed good performance. The result of our paper can be helpful for treatment and prognosis prediction for non-smoking females with LUAD.

Synthetic lethal interactions of DEAD/H-box helicases as targets for cancer therapy

DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.

Pan-cancer analysis reveals DDX21 as a potential biomarker for the prognosis of multiple tumor types

Background

DExD-box helicase 21 (DDX21) is an essential member of the RNA helicase family. DDX21 is involved in the carcinogenesis of various malignancies, but there has been no comprehensive research on its involvement in different types of cancer.

Method

This study used TCGA, CPTAC, GTEx, GEO, FANTOM5, BioGRID, TIMER2, GEPIA2, cBioPortal, STRING, and Metascape databases and Survival ROC software to evaluate DDX21 gene expression, protein expression, immunohistochemistry, gene mutation, immune infiltration, and protein phosphorylation in 33 TCGA tumor types, as well as the prognostic relationship between DDX21 and different tumors, by survival analysis and similar gene enrichment analysis. Furthermore, Cell Counting Kit-8 (CCK-8) and Transwell studies were employed to assess the effect of DDX21 expression on lung adenocarcinoma (LUAD) cell proliferation and migration.

Result

The DDX21 gene was highly expressed in most cancers, and overexpression was associated with poor overall survival (OS) and disease-free survival (DFS). DDX21 mutations were most common in uterine corpus endometrial carcinoma (UCEC; >5%), and DDX21 expression was positively correlated with the degree of infiltration of CAF and CD8+ cells in several tumor types. Numerous genes were co-expressed with DDX21. Gene enrichment analysis revealed close links between DDX21, RNA metabolism, and ribosomal protein production. In vitro analysis of LUAD cells showed that DDX21 expression was positively correlated with cell proliferation and migration capacity, consistent with prior bioinformatics studies.

Conclusions

DDX21 is overexpressed in a variety of cancers, and overexpression in some cancers is associated with poor prognosis. Immune infiltration and DDX21-related gene enrichment analyses indicated that DDX21 may affect cancer development through mechanisms that regulate tumor immunity, RNA metabolism, and ribosomal protein synthesis. This pan-cancer study revealed the prognostic value and the oncogenic role of DDX21.

Nanotechnology-Based Diagnostic and Therapeutic Strategies for Neuroblastoma

Neuroblastoma (NB), as the most common extracranial solid tumor in childhood, is one of the critical culprits affecting children's health. Given the heterogeneity and invisibility of NB tumors, the existing diagnostic and therapeutic approaches are inadequate and ineffective in early screening and prognostic improvement. With the rapid innovation and development of nanotechnology, nanomedicines have attracted widespread attention in the field of oncology research for their excellent physiological and chemical properties. In this review, we first explored the current common obstacles in the diagnosis and treatment of NB. Then we comprehensively summarized the advancements in nanotechnology-based multimodal synergistic diagnosis and treatment of NB and elucidate the underlying mechanisms. In addition, a discussion of the pending challenges in biocompatibility and toxicity of nanomedicine was conducted. Finally, we described the development and application status of nanomaterials against some of the recognized targets in the field of NB research, and pointed out prospects for nanomedicine-based precision diagnosis and therapy of NB.

DDX55 promotes HCC progression via interacting with BRD4 and participating in exosome-mediated cell-cell communication

The involvement of DEAD‐box helicase 55 (DDX55) in oncogenesis has been suggested, but its biological role in hepatocellular carcinoma (HCC) remains unknown. The present study verified the upregulation of DDX55 in HCC tissues compared with non‐tumor controls. DDX55 displayed the highest prognostic values among the DEAD‐box protein family for recurrence‐free survival and overall survival of HCC patients. In addition, the effects of DDX55 in the promotion of HCC cell proliferation, migration, and invasion were determined ex vivo and in vivo. Mechanistically, we revealed that DDX55 could interact with BRD4 to form a transcriptional regulatory complex that positively regulated PIK3CA transcription. Following that, β‐catenin signaling was activated in a PI3K/Akt/GSK‐3β dependent manner, thus inducing cell cycle progression and epithelial–mesenchymal transition. Intriguingly, both DDX55 mRNA and protein were identified in the exosomes derived from HCC cells. Exosomal DDX55 was implicated in intercellular communication between HCC cells with high or low DDX55 levels and between HCC cells and endothelial cells, thereby promoting the malignant phenotype of HCC cells and angiogenesis. In conclusion, DDX55 may be a valuable prognostic biomarker and therapeutic target in HCC.

Inhibition of miR-144-3p exacerbates non-small cell lung cancer progression by targeting CEP55

Increasing evidence has indicated that microRNA dysregulation is closely related to the occurrence and development of cancers. Herein, we investigated the relationship between miR-144-3p and CEP55 expression. We then evaluated the association between miR-144-3p and CEP55 expression and proliferation, invasion and apoptosis of non-small cell lung cancer (NSCLC) cells. Real-time quantitative PCR results revealed that CEP55 was over-expressed whereas miR-144-3p was under-expressed in NSCLC tissues. CCK-8 assay, wound healing assay, and flow cytometry further revealed that overexpression of miR-144-3p significantly inhibited proliferation and migration, but promoted apoptosis of A549 cells. Conversely, inhibition of miR-144-3p promoted proliferation and migration but suppressed apoptosis of H460 cells. Dual-luciferase reporter assay revealed that miR-144-3p modulated malignant properties of cancer cells by targeting CEP55. Overexpression of CEP55 partially blocked the inhibitory effect of miR-144-3p on proliferation and migration of A549 cells and induced apoptosis of A549 cells. CEP55 knockdown modulated the increase in proliferation and migration and the decrease in apoptosis of H460 cells following miR-144-3p inhibition. These findings demonstrated that miR-144-3p suppresses NSCLC development by inhibiting CEP55 expression.

DEAD-Box RNA Helicases in Cell Cycle Control and Clinical Therapy

Cell cycle is regulated through numerous signaling pathways that determine whether cells will proliferate, remain quiescent, arrest, or undergo apoptosis. Abnormal cell cycle regulation has been linked to many diseases. Thus, there is an urgent need to understand the diverse molecular mechanisms of how the cell cycle is controlled. RNA helicases constitute a large family of proteins with functions in all aspects of RNA metabolism, including unwinding or annealing of RNA molecules to regulate pre-mRNA, rRNA and miRNA processing, clamping protein complexes on RNA, or remodeling ribonucleoprotein complexes, to regulate gene expression. RNA helicases also regulate the activity of specific proteins through direct interaction. Abnormal expression of RNA helicases has been associated with different diseases, including cancer, neurological disorders, aging, and autosomal dominant polycystic kidney disease (ADPKD) via regulation of a diverse range of cellular processes such as cell proliferation, cell cycle arrest, and apoptosis. Recent studies showed that RNA helicases participate in the regulation of the cell cycle progression at each cell cycle phase, including G1-S transition, S phase, G2-M transition, mitosis, and cytokinesis. In this review, we discuss the essential roles and mechanisms of RNA helicases in the regulation of the cell cycle at different phases. For that, RNA helicases provide a rich source of targets for the development of therapeutic or prophylactic drugs. We also discuss the different targeting strategies against RNA helicases, the different types of compounds explored, the proposed inhibitory mechanisms of the compounds on specific RNA helicases, and the therapeutic potential of these compounds in the treatment of various disorders.