Investigation of miRNA and mRNA Co-expression Network in Ependymoma

Liu, Feili; Dong, Hang; Mei, Zi; Huang, Tao

doi:10.3389/fbioe.2020.00177

Cited by 16 publications

(13 citation statements)

References 71 publications

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“…In this study, we fitted a recurrence model consisting of 6 genes, including ELMSAN1, KRT33B, NDRG1, PPP1R13L, PPP2R1B, and WDYHV1 [ 27 – 31 ]. A majority of genes have been reported to be involved in the initiation and progression of tumor.…”

Section: Discussionmentioning

confidence: 99%

Development and clinical validation of a novel six-gene signature for accurately predicting the recurrence risk of patients with stage II/III colorectal cancer

Wang

et al. 2021

Cancer Cell Int

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Background A large number of patients with stage II/III colorectal cancer (CRC) have a high recurrence rate after radical resection. We aimed to develop a novel tool to stratify patients with different recurrence-risk for optimizing decision-making in post-operative surveillance and therapeutic regimens. Methods We retrospectively enrolled four independent cohorts from the Gene Expression Omnibus and 66 CRC tissues from our hospital. The initial signature discovery was conducted in GSE143985 (n = 91). This was followed by independent validation of this signature in GSE17536 (n = 111), GSE29621 (n = 40), and GSE92921 (n = 59). Further experimental validation using qRT-PCR assays (n = 66) was performed to ensure the robustness and clinical feasible of this signature. Results We developed a novel recurrence-related signature consisting of six genes. This signature was validated to be significantly associated with dismal recurrence-free survival in five cohorts GSE143985 (HR: 4.296 [2.612–7.065], P < 0.0001), GSE17536 (HR: 2.354 [1.662–3.334], P < 0.0001), GSE29621 (HR: 3.934 [1.622–9.539], P = 0.0024), GSE92921 (HR: 7.080 [2.011–24.924], P = 0.0023), and qPCR assays (HR: 3.654 [2.217–6.020], P < 0.0001). This signature was also proven to be an independent recurrent factor. More importantly, this signature displayed excellent discrimination and calibration in predicting the recurrence-risk at 1–5 years, with most AUCs were above 0.9, average C-index for the five cohorts was 0.8795, and near-perfect calibration. Conclusions We discovered and experimental validated a novel gene signature with stable and powerful performance for identifying patients at high recurrence-risk in stage II/III CRC.

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Section: Discussionmentioning

confidence: 99%

Development and clinical validation of a novel six-gene signature for accurately predicting the recurrence risk of patients with stage II/III colorectal cancer

Wang

et al. 2021

Cancer Cell Int

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“…Recently, dysregulated expression of RNAs (lncRNAs, circRNAs, miRNAs, and mRNAs) and regulation of their networks have been confirmed to affect the pathogenesis and progression of various tumors, such as endometrial carcinoma [ 23 ], ovarian cancer [ 24 ], and ependymoma [ 25 ]. In the cardiovascular system, several novel serum RNAs have been found to be associated with CHD [ 8 , 26 ].…”

Section: Discussionmentioning

confidence: 99%

Identifying a Serum Exosomal-Associated lncRNA/circRNA-miRNA-mRNA Network in Coronary Heart Disease

Jia

Zhou

et al. 2021

Cardiology Research and Practice

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Background. Accumulating evidence supports the importance of noncoding RNAs and exosomes in coronary heart disease (CHD). However, exosomal-associated competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms in CHD are largely unexplored. The present study aimed to explore exosomal-associated ceRNA networks in CHD. Methods. Data from 6 CHD patients and 32 normal controls were downloaded from the ExoRBase database. CHD and normal controls were compared by screening differentially expressed mRNAs (DEMs), lncRNAs (DELs), and circRNAs (DECs) in serum exosomes. MicroRNAs (miRNAs) targeting DEMs were predicted using the Targetscan and miRanda databases, and miRNAs targeted by DELs and DECs were predicted using the miRcode and starBase databases, respectively. The biological functions and related signaling pathways of DEMs were analyzed using the David and KOBAS databases. Subsequently, a protein-protein interaction (PPI) network was established to screen out on which hub genes enrichment analyses should be performed, and a ceRNA network (lncRNA/circRNA-miRNA-mRNA) was constructed to elucidate ceRNA axes in CHD. Results. A total of 312 DEMs, 43 DELs, and 85 DECs were identified between CHD patients and normal controls. Functional enrichment analysis showed that DEMs were significantly enriched in “chromatin silencing at rDNA,” “telomere organization,” and “negative regulation of gene expression, epigenetic.” PPI network analysis showed that 25 hub DEMs were closely related to CHD, of which ubiquitin C (UBC) was the most important. Hub genes were mainly enriched in “cellular protein metabolic process” functions. The exosomal-associated ceRNA regulatory network incorporated 48 DEMs, 73 predicted miRNAs, 10 DELs, and 15 DECs. The LncRNA/circRNA-miRNA-mRNA interaction axes (RPL7AP11/hsa-miR-17-5p/UBC and RPL7AP11/hsa-miR-20b-5p/UBC) were obtained from the network. Conclusions. Our findings provide a novel perspective on the potential role of exosomal-associated ceRNA network regulation of the pathogenesis of CHD.

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“…But it can be analyzed by mRNA-miRNA network and through applying weighted co-expression network analysis (WGCNA), so as to collect seven pairs of key genes in the co-expressed gene network: CYP11B1, KRT33B, RUNx1t1, SIK1, MAP 3 K4, MLANA and SFRP5 that are regulated by miR-15 and miR-24-1. These 7 pairs of miRNA-mRNA play a key role in the growth and inhibition of ependymomas [ 41 ]. However, we believe that at this stage, the above findings can only be used as a reference, that is, the future studies suggest a direction, how to intervene in these genes, regulate their expression, and develop new therapeutic methods according to this method, these problems have not been solved, so gene therapy is not mature in this field.…”

Section: Mrna Plays a Role In Different Central Nervous System Tumorsmentioning

confidence: 99%

The role of mRNA in the development, diagnosis, treatment and prognosis of neural tumors

et al. 2021

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Neural tumors can generally be divided into central nervous system tumors and peripheral nervous tumors. Because this type of tumor is located in the nerve, even benign tumors are often difficult to remove by surgery. In addition, the majority of neural tumors are malignant, and it is particular the same for the central nervous system tumors. Even treated with the means such as chemotherapy and radiotherapy, they are also difficult to completely cure. In recent years, an increasingly number of studies have focused on the use of mRNA to treat tumors, representing an emerging gene therapy. The use of mRNA can use the expression of some functional proteins for the treatment of genetic disorders or tissue repair, and it can also be applied to immunotherapy through the expression of antigens, antibodies or receptors. Therefore, although these therapies are not fully-fledged enough, they have a broad research prospect. In addition, there are many ways to treat tumors using mRNA vaccines and exosomes carrying mRNA, which have drawn much attention. In this study, we reviewed the current research on the role of mRNA in the development, diagnosis, treatment and prognosis of neural tumors, and examine the future research prospects of mRNA in neural tumors and the opportunities and challenges that will arise in the future application of clinical treatment.

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Investigation of miRNA and mRNA Co-expression Network in Ependymoma

Cited by 16 publications

References 71 publications

Development and clinical validation of a novel six-gene signature for accurately predicting the recurrence risk of patients with stage II/III colorectal cancer

Development and clinical validation of a novel six-gene signature for accurately predicting the recurrence risk of patients with stage II/III colorectal cancer

Identifying a Serum Exosomal-Associated lncRNA/circRNA-miRNA-mRNA Network in Coronary Heart Disease

The role of mRNA in the development, diagnosis, treatment and prognosis of neural tumors

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