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336613

In silico analysis revealed the prognostic potential of a miRNA panel in lung carcinoma

Article

Last updated: 29 Dec 2024

Subjects

-

Tags

Pharmacology, Toxicology, and Biochemistry.

Abstract

Background. This research aims to identify potential prognostic biomarkers for squamous cell lung carcinoma (LUSC) by implementing bioinformatics tools to unveil the relationship between microRNAs (miRNAs) and LUSC, specifically by identifying the miRNAs and their critical target genes. Methods. We employed the Cancer Genome Atlas (TCGA)-LUSC dataset to identify differentially expressed miRNAs (DEmiRs) and genes (DEGs) utilizing R software. Subsequently, a lasso Cox regression survival model was developed to predict key prognostic DEmiRs. Their target genes were predicted using miRDB repository. Venn diagram was employed to identify the consensus genes shared between these target genes and DEGs in the TCGA-LUSC dataset. ClusetrProfiler analyzed Gene Ontology (GO) and KEGG pathways to comprehend these genes' biological functions. The STRING database and Cytoscape applications constructed the consensus gene protein-protein interactions network. Results. Lasso model predicted 6 prognostic DEmiRs (hsa-miR1270, hsa-miR-1291, hsa-19b-2, hsa-miR-2277, hsa-miR-4791, hsa-miR-485) for LUSC with 96.67% sensitivity and 68.54% specificity. Venn diagram retrieved 906 consensus genes shared between DEGs and these 6 prognostic DEmiRs. These genes were mainly related to protein-binding, neuroactive ligand receptor interaction, retinoid metabolism, carcinogenesis, cell cycle, and system development. Network analysis in Cytoscape STRING applications identified 19 crucial genes (SDC4, VCAN, BCAN, XYLT2, GPC1, GPC5, EGFR, EDNRA, EDN1, EDNRB, ERBB4, GNA14, GNAQ, CACNA1C, KCNQ1, KCND2, KCNH5, KCNB2, KCNQ5) linked to lung carcinogenesis. Conclusion. We developed a prognostic model reliant on 6 miRNAs that accurately predicted LUSC survival. These findings provide novel insights into lung carcinogenesis' underlying molecular mechanisms and potential biomarkers for prognosis and treatment.

DOI

10.21608/jpsdm.2024.257221.1007

Keywords

Differentially expressed miRNAs, prognosis, Lung carcinoma, Bioinformatics, Lasso model

Authors

First Name

Marwa

Last Name

Mohanad

MiddleName

-

Affiliation

Department of Biochemistry, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt.

Email

marwa.almarzouky@must.edu.eg

City

-

Orcid

-

First Name

Rasha

Last Name

Fakhr Eldeen

MiddleName

R.

Affiliation

Department of Biochemistry, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology

Email

rasha.rashid@must.edu.eg

City

-

Orcid

-

First Name

Hoda

Last Name

Shamloula

MiddleName

K.

Affiliation

Department of Biochemistry, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt.

Email

hoda.shamloula@must.edu.eg

City

-

Orcid

-

Volume

1

Article Issue

1

Related Issue

45797

Issue Date

2024-01-01

Receive Date

2023-12-21

Publish Date

2024-01-01

Page Start

6

Page End

20

Print ISSN

3009-6553

Online ISSN

3009-6677

Link

https://jpsdm.journals.ekb.eg/article_336613.html

Detail API

https://jpsdm.journals.ekb.eg/service?article_code=336613

Order

336,613

Type

Research articles

Type Code

2,973

Publication Type

Journal

Publication Title

Journal of Pharmaceutical Sciences and Drug Manufacturing-Misr University for Science and Technology

Publication Link

https://jpsdm.journals.ekb.eg/

MainTitle

In silico analysis revealed the prognostic potential of a miRNA panel in lung carcinoma

Details

Type

Article

Created At

20 Dec 2024