MiR-330-3p and miR-485-5p as biomarkers for glioblastoma: An integrated bioinformatics and experimental study

Rahmati, Yazdan; Alivand, Mohammad Reza; Mollanoori, Hasan

doi:10.1016/j.compbiolchem.2021.107458

Cited by 7 publications

(3 citation statements)

References 38 publications

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“…In this regard, we downloaded the expression profiling array data of GSE38167 (67 samples, including 31 primary TNBC, 13 lymph node metastases BC, and 23 matched normal breast tissues), GSE38867 (28 samples, including 7 DCIS BC, 7 invasive BC, 7 metastatic BC, and 7 normal samples), GSE42128 ( 116 samples, including 68 serum samples, 28 BC tissue samples and 20 normal breast tissue samples), GSE45666 (116 samples, including 101 breast tumor samples and 15 from adjacent breast normal tissue samples) and GSE53179 (16 blood samples, including 11 samples from ER+/HER2− advanced breast cancer subjects and 5 age-matched control subjects) from GEO database ( https://www.ncbi.nlm.nih.gov/geo/ ). Then, we normalized the expression array using Quantile Normalization function in Limma package [ 36 ]. Using the aggregate function in the S4 Vectors package, which gives an average measure for the probes of each miRNA.…”

Section: Methodsmentioning

confidence: 99%

The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer

et al. 2021

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Background Breast cancer (BC) is the most invasive cancer with different subtypes that its metabolism is unique compared with normal cells. Glutamine is considered critical nutrition that many cancer cells, particularly BC cells, are dependent on it for growth and proliferation. Therefore, targeting glutamine metabolism, especially enzymes that are related to this pathway, can be beneficial to design anti-cancer agents. Recent evidence has shown that microRNAs (miRNAs), with a short length and single-strand properties, play a prominent role in regulating the genes related to glutamine metabolism, which may control the development of cancer. Methods In silico analysis confirmed that miR-513c and miR-3163 might be involved in glutamine metabolism. The expression level of these two miRNAs was evaluated in eighty BC tissues and normal adjacent tissues. Furthermore, GSE38167, GSE38867, GSE42128, GSE45666, and GSE53179 were employed from gene expression omnibus (GEO). The Limma package was utilized to identify differentially expressed miRNAs (DEMs) of mentioned datasets to evaluate miR-513c and miR-3163 expression. Further, in silico analysis was utilized to predict the potential biological processes and molecular pathways of miR-513c and miR-3163, based on their target genes. Results In silico studies revealed top categories of biological processes and cellular pathways that might play a critical role in metabolism reprogramming and cancer development and were target genes for miR-513c and miR-3163. The current study showed that miR-513c (p value = 0.02062 and FC = − 2.3801) and miR-3163 (p value = 0.02034 and FC = − 2.3792) were downregulated in tumor tissues compared to normal adjacent tissues. The analysis of GEO microarray datasets showed that miR-513c was downregulated in GSE38167, GSE38867, GSE42128, GSE45666 and GSE53179, whereas there was a significant downregulation of miR-3163 in only two studies, including GSE38867 and GSE42128 that they were in accordance with our experimental results. Furthermore, the subgroup analysis did not show any substantial relationship between expression levels of these two miRNAs and factors such as age, family history of cancer, and abortion history. Conclusion MiR-513c and miR-3163 were downregulated in BC tissues, which might serve as tumor suppressors. They are suggested as potential therapeutic targets for patients with BC.

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Section: Methodsmentioning

confidence: 99%

The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer

et al. 2021

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“… High levels of miRNA-582–5p (fold change 2.86, p < 0.0001) and miRNA-363 (fold change 3.51, p < 0.0001) were significantly associated with glioblastoma (GBM) miR-363 Overexpressed/Elevated Serum Diagnosis Vojdani et al ( Vojdani et al, 2021 ) 2021 miR-34a Underexpressed/Decreased Serum, Tissue Diagnosis Dysregulation of the EGFR gene and miR-34a in serum samples of GBM patients promises the emergence of non-invasive biomarkers for early detection of GBM. Rahmati et al ( Rahmati et al, 2021 ) 2021 miR-330–3p Decreased Tissue, Serum Prognostic biomarker mir-330–3p and mir-485–5p could be potential biomarkers in GBM. miR-485–5p Decreased Tissue, Serum Prognostic biomarker Swellam et al ( Swellam et al, 2021 ) 2021 miR-17–5p Decreased Serum Prognostic and treatment response marker Detection of serum miR-17–5p, miR-125 b, and miR-221 aids in the prediction of prognosis and response to treatment strategy for GBM patients.…”

Section: Overviewmentioning

confidence: 99%

The potential of miRNA-based approaches in glioblastoma: An update in current advances and future perspectives

Ordóñez-Rubiano,

Rincón-Arias,

Espinosa

et al. 2024

Current Research in Pharmacology and Drug Discovery

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“…MicroRNAs (miRNAs) have been reported to play essential roles in different pathological and physiological processes, including cancer development [5]. Many studies have used serum miRNAs as predictors for the diagnosis and prognosis of glioma, demonstrating the potential of serum miRNAs in serving as non-invasive biomarkers [6][7][8]. For example, the expression of serum miR-100 [6] and miR-29b [8] has been used to discriminate glioblastoma patients from healthy controls.…”

Section: Introductionmentioning

confidence: 99%

Construct of qualitative diagnostic biomarkers specific for glioma by pairing serum microRNAs

Luo

et al. 2023

BMC Genomics

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Background Serum microRNAs (miRNAs) are promising non-invasive biomarkers for diagnosing glioma. However, most reported predictive models are constructed without a large enough sample size, and quantitative expression levels of their constituent serum miRNAs are susceptible to batch effects, decreasing their clinical applicability. Methods We propose a general method for detecting qualitative serum predictive biomarkers using a large cohort of miRNA-profiled serum samples (n = 15,460) based on the within-sample relative expression orderings of miRNAs. Results Two panels of miRNA pairs (miRPairs) were developed. The first was composed of five serum miRPairs (5-miRPairs), reaching 100% diagnostic accuracy in three validation sets for distinguishing glioma and non-cancer controls (n = 436: glioma = 236, non-cancers = 200). An additional validation set without glioma samples (non-cancers = 2611) showed a predictive accuracy of 95.9%. The second panel included 32 serum miRPairs (32-miRPairs), reaching 100% diagnostic performance in training set on specifically discriminating glioma from other cancer types (sensitivity = 100%, specificity = 100%, accuracy = 100%), which was reproducible in five validation datasets (n = 3387: glioma = 236, non-glioma cancers = 3151, sensitivity> 97.9%, specificity> 99.5%, accuracy> 95.7%). In other brain diseases, the 5-miRPairs classified all non-neoplastic samples as non-cancer, including stroke (n = 165), Alzheimer’s disease (n = 973), and healthy samples (n = 1820), and all neoplastic samples as cancer, including meningioma (n = 16), and primary central nervous system lymphoma samples (n = 39). The 32-miRPairs predicted 82.2 and 92.3% of the two kinds of neoplastic samples as positive, respectively. Based on the Human miRNA tissue atlas database, the glioma-specific 32-miRPairs were significantly enriched in the spinal cord (p = 0.013) and brain (p = 0.015). Conclusions The identified 5-miRPairs and 32-miRPairs provide potential population screening and cancer-specific biomarkers for glioma clinical practice.

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MiR-330-3p and miR-485-5p as biomarkers for glioblastoma: An integrated bioinformatics and experimental study

Cited by 7 publications

References 38 publications

The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer

The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer

The potential of miRNA-based approaches in glioblastoma: An update in current advances and future perspectives

Construct of qualitative diagnostic biomarkers specific for glioma by pairing serum microRNAs

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