Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale

Sarkar, Jnanendra Prasad; Saha, Indrajit; Lancucki, Adrian; Ghosh, Nimisha; Wlasnowolski, Michał; Bokota, Grzegorz; Dey, Ashmita; Lipiński, Piotr; Plewczyński, Dariusz

doi:10.3389/fgene.2020.00982

Cited by 6 publications

(3 citation statements)

References 72 publications

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“…Identifying circulating RNA biomarkers is another challenge. It is necessary to integrate multiple datasets from different studies and to use complex statistical models to identify circulating RNA biomarkers [ 140 ]. Additionally, the lack of standardized pipelines for the analysis of circulating RNA sequencing data is a significant challenge.…”

Section: Challenges In Circulating Rna Sequencing In Plasmamentioning

confidence: 99%

Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer

Kan

Pei

Yeung

et al. 2023

IJMS

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Circulating tumor RNA (ctRNA) has recently emerged as a novel and attractive liquid biomarker. CtRNA is capable of providing important information about the expression of a variety of target genes noninvasively, without the need for biopsies, through the use of circulating RNA sequencing. The overexpression of cancer-specific transcripts increases the tumor-derived RNA signal, which overcomes limitations due to low quantities of circulating tumor DNA (ctDNA). The purpose of this work is to present an up-to-date review of current knowledge regarding ctRNAs and their status as biomarkers to address the diagnosis, prognosis, prediction, and drug resistance of colorectal cancer. The final section of the article discusses the practical aspects involved in analyzing plasma ctRNA, including storage and isolation, detection technologies, and their limitations in clinical applications.

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Section: Challenges In Circulating Rna Sequencing In Plasmamentioning

confidence: 99%

Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer

Kan

Pei

Yeung

et al. 2023

IJMS

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“…However, the average accuracies of other methods were from 67% to 88.7%, suggesting that the batch effects were not soundly addressed. Sarkar et al [55] selected 17 miRNAs from miRNA expression of 1,707 samples of 10 carefully selected cancer types and 333 normal samples, and normalized miRNA expression in reads per million to

scaled values, then 5 classification algorithm achieved average accuracies of 96%.…”

Section: Introductionmentioning

confidence: 99%

Improved lung cancer classification by employing diverse molecular features of microRNAs

Guo,

Mao,

Peng

et al. 2024

Heliyon

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“…In recent years, an increasing number of studies have shown that genes and microRNA (miRNA) can be regulated by circular RNA (circRNA) (Zeng et al, 2020) and that the aberrant expression of circRNA and miRNA contributes to human diseases, including cancer (Lin et al, 2020;Sarkar et al, 2020). With the emergence of high-throughput RNA sequencing and next-generation sequencing technology, circRNA has been increasingly studied (Lu and Thum, 2019).…”

Section: Introductionmentioning

confidence: 99%

Identification of Potential Genomic Alterations and the circRNA-miRNA-mRNA Regulatory Network in Primary and Recurrent Synovial Sarcomas

Yao

Wang

et al. 2021

Front. Mol. Biosci.

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Introduction: Synovial sarcoma (SS) is one of the most invasive soft tissue sarcomas, prone to recurrence and metastasis, and the efficacy of surgical treatment and chemotherapy for SS remains poor. Therefore, the diagnosis and treatment of SS remain a significant challenge. This study aimed to analyze the mutated genes of primary SS (PSS) and recurrent SS (RSS), discover whether these sarcomas exhibit some potential mutated genes, and then predict associated microRNAs (miRNA) and circular RNAs (circRNA) by analyzing the mutated genes. We focused on the regulation mechanism of the circRNA-miRNA-mutated hub gene in PSS and RSS.Methods: We performed a comprehensive genomic analysis of four pairs of formalin-fixed paraffin-embedded samples of PSS and RSS, using Illumina human exon microarrays. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) function, and pathway enrichment of the mutated genes were analyzed, and the protein-protein interaction (PPI) network was forecast using String software 11.0. The hub genes were then obtained using the Molecular Complex Detection (MCODE) plug-in for Cytoscape 3.7.2 and were used to analyze overall survival (OS) using the Gene Expression Profiling Interactive Analysis (GEPIA) database. The corresponding miRNAs were obtained from the miRDB 5.0 and TargetScan 7.2 databases. The corresponding circRNAs of the hub genes were found through the miRNAs from these databases: Circbank, CircInteractome, and StarBase v2.0. Thereafter we set up a competing endogenous RNA (ceRNA) network with circRNA-miRNA and miRNA-messenger RNA (mRNA) pairs.Results: Using the chi-squared test, 391 mutated genes were screened using a significance level of p-values < 0.01 from the four pairs of PSS and RSS samples. A GO pathway analysis of 391 mutated genes demonstrated that differential expression mRNAs (DEmRNAs) might be bound up with the “positive regulation of neurogenesis,” “cell growth,” “axon part,” “cell−substrate junction,” or “protein phosphatase binding” of SS. The PPI network was constructed using 391 mutated genes, and 53 hub genes were identified (p < 0.05). Eight variant hub genes were discovered to be statistically significant using the OS analysis (p < 0.05). The circRNA-miRNA-mRNA (ceRNA) network was constructed, and it identified two circRNAs (hsa_circ_0070557 and hsa_circ_0070558), 10 miRNAs (hsa-let-7a-3p, hsa-let-7b-3p, hsa-let-7f-1-3p, hsa-let-7f-2-3p, hsa-mir-1244, hsa-mir-1197, hsa-mir-124-3p, hsa-mir-1249-5p, hsa-mir-1253, and hsa-mir-1271-5p) and five hub genes (CENPE, ENPP3, GPR18, MDC1, and PLOD2).Conclusion: This study screened novel biological markers and investigated the differentiated circRNA-miRNA-mutated hub gene axis, which may play a pivotal role in the nosogenesis of PSS and RSS. Some circRNAs may be deemed new diagnostic or therapeutic targets that could be conducive to the future clinical treatment of SS.

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Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale

Cited by 6 publications

References 72 publications

Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer

Exploring the Role of Circulating Cell-Free RNA in the Development of Colorectal Cancer

Improved lung cancer classification by employing diverse molecular features of microRNAs

Identification of Potential Genomic Alterations and the circRNA-miRNA-mRNA Regulatory Network in Primary and Recurrent Synovial Sarcomas

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