Predicting microRNA biological functions based on genes discriminant analysis

Ding, Tao; Xu, Junhua; Sun, Mengmeng; Zhu, Shanshan; Gao, Jie

doi:10.1016/j.compbiolchem.2017.09.008

Cited by 6 publications

(3 citation statements)

References 38 publications

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“…Their structures are highly conserved and regulate gene expression post-transcriptionally by inhibiting protein translation or promoting the degradation of target mRNAs (12,13). miRNAs abrogate the biological functions of their target genes (14). Over 2,500 human miRNAs have been identified to serve critical roles in various physiological and pathological processes, including embryonic development, angiogenesis, apoptosis, autophagy, cell cycle progression and cell proliferation (15–17).…”

Section: Introductionmentioning

confidence: 99%

miR‑30a‑3p inhibits the proliferation of liver cancer cells by targeting DNMT3a through the PI3K/AKT signaling pathway

Chen

Gao

et al. 2019

Oncol Lett

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MicroRNAs (miRNAs or miRs) are crucial for normal development and maintenance of homeostasis. Dysregulated miRNA expression contributes to numerous pathological conditions, including cancer tumorigenesis. However, a limited number of studies have examined the regulatory effects of miR-30a-3p in tumorigenesis. Therefore, the present study investigated the mechanistic process of tumorigenesis in liver cancer. The results revealed a high expression of DNA methyltransferase 3a (DNMT3a) and a low expression of miR-30a-3p in HepG2 cells compared with that in the L02 cell line. A luciferase reporter assay demonstrated that DNMT3a is a direct target of miR-30a-3p. In addition, DNMT3a overexpression significantly enhanced cell proliferation, which was reversed by a miR-30a-3p mimic. Similarly, the miR-30a-3p mimic blocked DNMT3a-triggered cell cycle processes and apoptosis by attenuating active p-AKT and p-PI3K in HepG2 cells. In summary, the results of the present study demonstrate that miR-30a-3p is essential for cell proliferation regulation via its association with AKT/PI3K signaling in liver cancer. These results provide insight into the molecular mechanism by which miR-30a-3p inhibits liver cancer cell proliferation and provides a foundation for its clinical development and application.

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Section: Introductionmentioning

confidence: 99%

miR‑30a‑3p inhibits the proliferation of liver cancer cells by targeting DNMT3a through the PI3K/AKT signaling pathway

Chen

Gao

et al. 2019

Oncol Lett

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“…It is well known that miRNAs significantly affect many biological processes, such as cell proliferation, apoptosis, differentiation, and metabolism [34,35]. An increasing body of evidence indicates that miR-218 is downregulated in various diseases.…”

Section: Discussionmentioning

confidence: 99%

Glucose-induced microRNA-218 suppresses the proliferation and promotes the apoptosis of human retinal pigment epithelium cells by targeting RUNX2

Yao

Liu

et al. 2019

Bioscience Reports

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Objective: MicroRNA-218 (miR-218) critical for preventing the progression of numerous diseases, including diseases of the retinal pigment epithelium (RPE). However, the mechanism by which miR-218 regulates the PRE in humans remains largely unknown. Our study investigated the effects of glucose-induced miR-218 expression on human RPE cells (ARPE-19), as well as its targeted regulatory effect. Methods: The levels of miR-218 and runt-related transcription factor 2 (RUNX2) expression were investigated by RT-qPCR or Western blot assays. Cell viability and apoptosis were assessed by CCK-8 assays, flow cytometry, and Hoechst staining. A luciferase reporter assay was performed to determine whether Runx2 is a target gene of miR-218. Results: Our results showed that glucose up-regulated miR-218 expression, suppressed proliferation, and induced the apoptosis of ARPE-19 cells. We verified that miR-218 could inhibit the proliferation and facilitate the apoptosis of ARPE-19 cells, while inhibition of miR-218 expression produced the opposite effects. In terms of mechanism, we demonstrated that RUNX2 was a direct target of miR-218. Functional experiments showed that Runx2 served as a miR-218 target to help inhibit the proliferation and induction of apoptosis in ARPE-19 cells. Conclusion: Our findings suggest the miR-218/Runx2 axis as a potential target for treating diabetic retinopathy (DR).

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“…More in-depth studies, including miRNA co-expression and primary transcript identification, suggest that the clusters of proximal miRNAs are typically expressed as polycistronic, coregulated units and shared common biological functions [16]. Meanwhile, miRNA gene families are highly conserved in nucleotide sequence and secondary structure among closely related species over evolutionary time [17,18]. Notably, miRNAs with similar sequences or highly conserved secondary structures tend to play roles in the similar biological process [2,19,20].…”

Section: Introductionmentioning

confidence: 99%

Predicting microRNA‐disease association based on microRNA structural and functional similarity network

et al. 2019

Self Cite

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Background: Increasing evidences indicate that microRNAs (miRNAs) are functionally related to the development and progression of various human diseases. Inferring disease-related miRNAs can be helpful in promoting disease biomarker detection for the treatment, diagnosis, and prevention of complex diseases. Methods: To improve the prediction accuracy of miRNA-disease association and capture more potential diseaserelated miRNAs, we constructed a precise miRNA global similarity network (MSFSN) via calculating the miRNA similarity based on secondary structures, families, and functions. Results: We tested the network on the classical algorithms: WBSMDA and RWRMDA through the method of leaveone-out cross-validation. Eventually, AUCs of 0.8212 and 0.9657 are obtained, respectively. Also, the proposed MSFSN is applied to three cancers for breast neoplasms, hepatocellular carcinoma, and prostate neoplasms. Consequently, 82%, 76%, and 82% of the top 50 potential miRNAs for these diseases are respectively validated by the miRNA-disease associations database miR2Disease and oncomiRDB. Conclusion: Therefore, MSFSN provides a novel miRNA similarity network combining precise function network with global structure network of miRNAs to predict the associations between miRNAs and diseases in various models.Author summary: microRNAs (miRNAs) are functionally related to the development and progression of various human diseases. To improve the prediction accuracy of miRNA-disease association and capture more potential disease-related miRNAs, we constructed a precise miRNA global similarity network via calculating the miRNA similarity of secondary structures, families, and functions. The novel miRNA similarity network combining precise function network with global structure network of miRNAs showed the better performance compared with others similarity network and could be used to predict the associations between miRNAs and diseases in various models.

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Predicting microRNA biological functions based on genes discriminant analysis

Cited by 6 publications

References 38 publications

miR‑30a‑3p inhibits the proliferation of liver cancer cells by targeting DNMT3a through the PI3K/AKT signaling pathway

miR‑30a‑3p inhibits the proliferation of liver cancer cells by targeting DNMT3a through the PI3K/AKT signaling pathway

Glucose-induced microRNA-218 suppresses the proliferation and promotes the apoptosis of human retinal pigment epithelium cells by targeting RUNX2

Predicting microRNA‐disease association based on microRNA structural and functional similarity network

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