Construction of a potential microRNA, transcription factor and mRNA regulatory network in hepatocellular carcinoma

Li, Ning; Jiang, Shaotao; Shi, Jinhua; Fu, Rongdang; Wu, Huihui; Lu, Min-qiang

doi:10.21037/tcr-20-686

Cited by 6 publications

(6 citation statements)

References 54 publications

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“…Furthermore, they found that increased expression of CCNF mRNA was associated with worse OS, relapse free survival (RFS), distant metastasis free survival (DMFS), and post progression survival (PPS), and further demonstrated the elevated levels of cyclin F protein in BC tissues using IHC [ 15 ]. Similar studies of Wang et al [ 16 ] have also revealed that high mRNA expression levels of CCNF denote a poor prognosis in BC patients, whereas Li et al [ 17 ] have reported corresponding findings for hepatocellular carcinoma (HCC). Conversely, CCNF mRNA levels correlated with better survival outcome in colorectal cancer (CRC), as it has been presented by Chen et al [ 18 ] based on the in silico analysis.…”

Section: Discussionsupporting

confidence: 54%

“…Conversely, CCNF mRNA levels correlated with better survival outcome in colorectal cancer (CRC), as it has been presented by Chen et al [ 18 ] based on the in silico analysis. In contrast to the study by Li et al [ 17 ], Fu et al [ 19 ] have provided evidence for high expression of cyclin F mRNA and protein being correlated with better survival of HCC patients. Here, we also observed that patients with tumors that express more cyclin F protein survived longer than those with its low expression, though our results were not statistically significant (606 days vs. 314 days; p = 0.14).…”

Section: Discussionmentioning

confidence: 68%

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Expression of Genomic Instability-Related Molecules: Cyclin F, RRM2 and SPDL1 and Their Prognostic Significance in Pancreatic Adenocarcinoma

Klimaszewska‐Wiśniewska

Buchholz

Neska-Długosz

et al. 2021

Cancers

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In the present study, we aimed to assess the selected components of cell cycle machinery, checkpoint, DNA repair, and synthesis, namely RRM2, cyclin F, and SPDL1 in pancreatic adenocarcinomas (PAC) by in-house immunohistochemistry (IHC) and bioinformatic analysis of public datasets, in terms of expression, correlation with clinicopathological parameters, and patient survival. Sixty eight patients with pancreatic ductal adenocarcinoma (PDAC) were included in our cohort study, and IHC was performed on tissue macroarrays. RNA-Seq-based transcriptome data for 177 PACs were retrieved from the Cancer Genome Atlas (TCGA). We found cyclin F, RRM2, and SPDL1 to be overexpressed at both protein and mRNA levels in tumor tissues compared to respective controls. Based on TCGA dataset, we have demonstrated that CCNF, RRM2, and SPDL1 are potent independent prognostic markers for poor overall survival, both by themselves and even more in combination with each other. Furthermore, high CCNF mRNA expression was associated with features of cancer progression. By contrast, overexpression of cyclin F or SPDL1 proteins denoted a good prognosis in PDAC patients; however, in the case of the former protein, the results did not reach statistical significance. Specifically, high levels of SPDL1 protein emerged as the most powerful independent prognostic factor associated with a better outcome. If validated, the CCNF/RRM2/SPDL1 three-gene panel developed in this study, as well as SPDL1 protein, may provide significant clinical implications for the prognosis prediction of PAC patients.

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 68%

Expression of Genomic Instability-Related Molecules: Cyclin F, RRM2 and SPDL1 and Their Prognostic Significance in Pancreatic Adenocarcinoma

Klimaszewska‐Wiśniewska

Buchholz

Neska-Długosz

et al. 2021

Cancers

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“…Since miRNAs are strictly regulated by different transcription factors, altered expression of miRNAs in cancer may be caused by dysregulation of some transcription factors, such as c-Myc and p53 [ 48 ]. The proto-oncogene c-Myc plays a fundamental regulatory role in growth control, cell proliferation, differentiation, and apoptosis, and alterations in its expression are associated with many tumors.…”

Section: Mirnas In Cancermentioning

confidence: 99%

Recent insights into the microRNA-dependent modulation of gliomas from pathogenesis to diagnosis and treatment

et al. 2022

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Gliomas are the most lethal primary brain tumors in adults. These highly invasive tumors have poor 5-year survival for patients. Gliomas are principally characterized by rapid diffusion as well as high levels of cellular heterogeneity. However, to date, the exact pathogenic mechanisms, contributing to gliomas remain ambiguous. MicroRNAs (miRNAs), as small noncoding RNAs of about 20 nucleotides in length, are known as chief modulators of different biological processes at both transcriptional and posttranscriptional levels. More recently, it has been revealed that these noncoding RNA molecules have essential roles in tumorigenesis and progression of multiple cancers, including gliomas. Interestingly, miRNAs are able to modulate diverse cancer-related processes such as cell proliferation and apoptosis, invasion and migration, differentiation and stemness, angiogenesis, and drug resistance; thus, impaired miRNAs may result in deterioration of gliomas. Additionally, miRNAs can be secreted into cerebrospinal fluid (CSF), as well as the bloodstream, and transported between normal and tumor cells freely or by exosomes, converting them into potential diagnostic and/or prognostic biomarkers for gliomas. They would also be great therapeutic agents, especially if they could cross the blood–brain barrier (BBB). Accordingly, in the current review, the contribution of miRNAs to glioma pathogenesis is first discussed, then their glioma-related diagnostic/prognostic and therapeutic potential is highlighted briefly.

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“… Ouimet et al (2016) reported that induction of miR-33 inhibited autophagy and lipid catabolism, promoted M. tuberculosis replication, and led to the bacteria survival in host cells. In addition, Lin et al (2017) demonstrated that multiple miRNAs could simultaneously interact with the transcription factor CEBPB to regulate the expression of FCGR1A, a gene associated with TB, which in turn affects TB development. Increasing evidence in recent years has also shown that M. tuberculosis has evolved various strategies to impair host autophagy mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Identification of Hub Genes and Typing of Tuberculosis Infections Based on Autophagy-Related Genes

Sheng,

Hua,

Yong

et al. 2023

Polish Journal of Microbiology

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Tuberculosis (TB) caused by Mycobacterium tuberculosis is one of the leading causes of morbidity and death in humans worldwide. Some autophagy genes associated with TB and some miRNAs regulating TB have been found, but the identification of autophagy-related genes in M. tuberculosis remains to be explored. Forty-seven autophagy-related genes differentially expressed in TB were identified in this study by analysis of TB-related datasets in the Gene Expression Omnibus (GEO) and autophagy-related genes in the Human Autophagy Database. The potential crucial genes affecting TB were found through the protein-protein interaction (PPI) network, and the possible pathways affected by these genes were verified. Analysis of the PPI network of miRNAs associated with M. tuberculosis infection and their target genes revealed that hsa-let-7, hsa-mir-155, hsa-mir-206, hsa-mir-26a, hsa-mir-30a, and hsa-mir-32 may regulate the expression of multiple autophagy-related genes (MAPK8, UVRAG, UKL2, and GABARAPL1) alone or in combination. Subsequently, Cytoscape was utilized to screen the differentially expressed genes related to autophagy. The hub genes (GABARAPL1 and ULK2) affecting TB were identified. Combined with Gene Set Enrichment Analysis (GSEA), the signaling pathways affected by the hub genes were verified. Finally, we divided TB patients into two subgroups based on autophagy-related genes, and the immune microenvironment of patients in different subgroups was significantly different. Our study found two autophagy-related hub genes that could affect TB and divide TB samples into two subgroups. This finding is of great significance for TB treatment and provides new ideas for exploring the pathogenesis of M. tuberculosis.

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Construction of a potential microRNA, transcription factor and mRNA regulatory network in hepatocellular carcinoma

Cited by 6 publications

References 54 publications

Expression of Genomic Instability-Related Molecules: Cyclin F, RRM2 and SPDL1 and Their Prognostic Significance in Pancreatic Adenocarcinoma

Expression of Genomic Instability-Related Molecules: Cyclin F, RRM2 and SPDL1 and Their Prognostic Significance in Pancreatic Adenocarcinoma

Recent insights into the microRNA-dependent modulation of gliomas from pathogenesis to diagnosis and treatment

Identification of Hub Genes and Typing of Tuberculosis Infections Based on Autophagy-Related Genes

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