Deregulation of microRNAs in oral squamous cell carcinoma, a bioinformatics analysis

Nuoroozi, Ghader; Mirmotalebisohi, Seyed Amir; Sameni, Marzieh; Arianmehr, Yousef; Zali, Hakimeh

doi:10.1016/j.genrep.2021.101241

Cited by 3 publications

(2 citation statements)

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“…Deciphering the pathophysiology of diseases or the action mechanism of therapeutics requires the application of systems biology and network analysis 27,28 . Topological examination of the node functions in gene regulatory and protein−protein interaction networks (PPI) (gene regulatory network [GRN] and PPIN) may illuminate critical molecular actors responsible for therapeutic effects 29–31 . In regulatory networks, motifs are the fundamental units, and the nodes that participate in motif subnetworks are presented as playing a crucial regulatory function in many therapeutic and disease‐related biological features 32–34 …”

Section: Introductionmentioning

confidence: 99%

“…27,28 Topological examination of the node functions in gene regulatory and protein−protein interaction networks (PPI) (gene regulatory network [GRN] and PPIN) may illuminate critical molecular actors responsible for therapeutic effects. [29][30][31] In regulatory networks, motifs are the fundamental units, and the nodes that participate in motif subnetworks are presented as playing a crucial regulatory function in many therapeutic and disease-related biological features. [32][33][34] The purpose of this research was to identify the defining factors and molecular processes that contribute to the subtype-specific effects of Rapamycin in BC.…”

Section: Introductionmentioning

confidence: 99%

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A systems biology approach and in vitro experiment indicated Rapamycin targets key cancer and cell cycle‐related genes and miRNAs in triple‐negative breast cancer cells

Tafti,

Shojaei,

Zali

et al. 2023

Molecular Carcinogenesis

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An anticancer drug known as Rapamycin acts by inhibiting the mammalian target of the Rapamycin pathway. This agent has recently been investigated for its potential therapeutic benefits in sensitizing drug‐resistant breast cancer (BC) treatment. The molecular mechanism underlying these effects, however, is still a mystery. Using a systems biology method and in vitro experiment, this study sought to discover essential genes and microRNAs (miRNAs) targeted by Rapamycin in triple‐negative BC (TNBC) cells to aid prospective new medications with less adverse effects in BC treatment. We developed the transcription factor‐miRNA‐gene and protein−protein interaction networks using the freely accessible microarray data sets. FANMOD and MCODE were utilized to identify critical regulatory motifs, clusters, and seeds. Then, functional enrichment analyses were conducted. Using topological analysis and motif detection, the most important genes and miRNAs were discovered. We used quantitative real‐time polymerase chain reaction (qRT‐PCR) to examine the effect of Rapamycin on the expression of the selected genes and miRNAs to verify our findings. We performed flow cytometry to investigate Rapamycin's impact on cell cycle and apoptosis. Furthermore, wound healing and migration assays were done. Three downregulated (PTGS2, EGFR, VEGFA) and three upregulated (c‐MYC, MAPK1, PIK3R1) genes were chosen as candidates for additional experimental verification. There were also three upregulated miRNAs (miR‐92a, miR‐16, miR‐20a) and three downregulated miRNAs (miR‐146a, miR‐145, miR‐27a) among the six selected miRNAs. The qRT‐PCR findings in MDA‐MB‐231 cells indicated that c‐MYC, MAPK1, PIK3R1, miR‐92a, miR‐16, and miR‐20a expression levels were considerably elevated following Rapamycin treatment, whereas PTGS2, EGFR, VEGFA, miR‐146a, and miR‐145 expression levels were dramatically lowered (p < 0.05). These genes are engaged in cancer pathways, transcriptional dysregulation in cancer, and cell cycle, according to the top pathway enrichment findings. Migration and wound healing abilities of the cells declined after Rapamycin treatment, and the number of apoptotic cells increased. We demonstrated that Rapamycin suppresses cell migration and metastasis in the TNBC cell line. In addition, our data indicated that Rapamycin induces apoptosis in this cell line. The discovered vital genes and miRNAs affected by Rapamycin are anticipated to have crucial roles in the pathogenesis of TNBC and its therapeutic resistance.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A systems biology approach and in vitro experiment indicated Rapamycin targets key cancer and cell cycle‐related genes and miRNAs in triple‐negative breast cancer cells

Tafti,

Shojaei,

Zali

et al. 2023

Molecular Carcinogenesis

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Hubs and Bottlenecks in Protein-Protein Interaction Networks

Nithya,

Kiran,

Nagarajaram

2023

Methods in Molecular Biology

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Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study

Mariam

Miller‐Atkins

Moro

et al. 2022

PeerJ

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Background Improved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC. Methods We performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC. Results A total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue. Conclusions This study demonstrates, for the first time, that miRNAs relevant to HCC are detectable in saliva, that salivary miRNA signatures show potential to be highly sensitive and specific non-invasive biomarkers of HCC, and that additional studies utilizing larger cohorts are needed.

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Deregulation of microRNAs in oral squamous cell carcinoma, a bioinformatics analysis

Cited by 3 publications

References 30 publications

A systems biology approach and in vitro experiment indicated Rapamycin targets key cancer and cell cycle‐related genes and miRNAs in triple‐negative breast cancer cells

A systems biology approach and in vitro experiment indicated Rapamycin targets key cancer and cell cycle‐related genes and miRNAs in triple‐negative breast cancer cells

Hubs and Bottlenecks in Protein-Protein Interaction Networks

Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study

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