Differential gene expression and network analysis in head and neck squamous cell carcinoma

Habib, Insan; Anjum, Farah; Sulaimani, Md Nayab; Shafie, Alaa; Almehmadi, Mazen; Yadav, Dharmendra Kumar; Sohal, Sukhwinder Singh; Hassan, Md. Imtaiyaz

doi:10.1007/s11010-022-04379-3

Cited by 6 publications

(2 citation statements)

References 76 publications

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“…The biological role of bitter melon’s anti-BRCA targets was hypothesized using GO and KEGG pathway enrichment analysis. The GO analysis included molecular function, biological processes, and cellular components[ 37 ]. The anti-BRCA targets of bitter melon were uploaded to the DAVID platform ( ) to access the database of GO functions and KEGG pathways[ 38 ].…”

Section: Methodsmentioning

confidence: 99%

Exploring the mechanism of action bitter melon in the treatment of breast cancer by network pharmacology

Panchal,

Nihalani,

Oza

et al. 2023

World J Exp Med

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BACKGROUND Bitter melon has been used to stop the growth of breast cancer (BRCA) cells. However, the underlying mechanism is still unclear. AIM To predict the therapeutic effect of bitter melon against BRCA using network pharmacology and to explore the underlying pharmacological mechanisms. METHODS The active ingredients of bitter melon and the related protein targets were taken from the Indian Medicinal Plants, Phytochemistry and Therapeutics and SuperPred databases, respectively. The GeneCards database has been searched for BRCA-related targets. Through an intersection of the drug’s targets and the disease’s objectives, prospective bitter melon anti-BRCA targets were discovered. Gene ontology and kyoto encyclopedia of genes and genomes enrichment analyses were carried out to comprehend the biological roles of the target proteins. The binding relationship between bitter melon’s active ingredients and the suggested target proteins was verified using molecular docking techniques. RESULTS Three key substances, momordicoside K, kaempferol, and quercetin, were identified as being important in mediating the putative anti-BRCA effects of bitter melon through the active ingredient-anti-BRCA target network study. Heat shock protein 90 AA, proto-oncogene tyrosine-protein kinase, and signal transducer and activator of transcription 3 were found to be the top three proteins in the protein-protein interaction network study. The several pathways implicated in the anti-BRCA strategy for an active component include phosphatidylinositol 3-kinase/protein kinase B signaling, transcriptional dysregulation, axon guidance, calcium signaling, focal adhesion, janus kinase-signal transducer and activator of transcription signaling, cyclic adenosine monophosphate signaling, mammalian target of rapamycin signaling, and phospholipase D signaling. CONCLUSION Overall, the integration of network pharmacology, molecular docking, and functional enrichment analyses shed light on potential mechanisms underlying bitter melon’s ability to fight BRCA, implicating active ingredients and protein targets, as well as highlighting the major signaling pathways that may be altered by this natural product for therapeutic benefit.

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Section: Methodsmentioning

confidence: 99%

Exploring the mechanism of action bitter melon in the treatment of breast cancer by network pharmacology

Panchal,

Nihalani,

Oza

et al. 2023

World J Exp Med

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show abstract

“…The standards for determining the differentially expressed genes (DEGs) were de ned as an |log2(fold change) |>2 and an adjusted p-value < 0.05. Filtering of DEGs was performed using the criteria log2(fold change) > 2 for the up-regulated and log2(fold change) <-2 for the downregulated genes, respectively (Habib et al, 2022). The cut-off for the log2 fold change was set ± 2 to obtain a moderate number of DEGSs.…”

Section: Differential Expression Analysismentioning

confidence: 99%

Deciphering hub genes as potential therapeutic target involved in progression of Glioblastoma multiforme disease: A multi-omics approach

Saeed,

Choudhury,

Alajmi

et al. 2024

Preprint

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Glioblastoma multiforme (GBM) is a highly aggressive primary brain tumor associated with high fatality rates, poor prognosis, and limited treatment options. To enhance our understanding of the disease and pave the way for targeted therapies, it is imperative to identify key genes influencing GBM progression. In this study, we harnessed RNA-Seq gene count data from GBM patients sourced from the GEO database, conducting an in-depth analysis of gene expression patterns. Our investigation involved the stratification of samples into two distinct sets, Group I and Group II, comparing low-grade and GBM tumor samples, respectively. Subsequently, we performed differential expression analysis and enrichment analysis to uncover significant gene signatures. To elucidate the protein-protein interactions that underlie GBM, we leveraged the STRING plugin within Cytoscape for comprehensive network visualization and analysis. By applying Maximal clique centrality (MCC) scores, we identified a set of 10 hub genes in each group. These hub genes were subjected to survival analysis, highlighting their prognostic relevance. In Group I, comprising BUB1, DLGAP5, BUB1B, CDK1, TOP2A, CDC20, KIF20A, ASPM, BIRC5, and CCNB2, these genes emerged as potential biomarkers associated with the transition to low-grade tumors. In Group II, encompassing LIF, LBP, CSF3, IL6, CCL2, SAA1, CCL20, MMP9, CXCL10, and MMP1, these genes were implicated in transforming adult glioblastoma. Kaplan–Meier's overall survival analysis of these hub genes revealed that modifications, particularly upregulation of these candidate genes, were associated with reduced survival in GBM patients. The findings underscore the significance of genomic alterations and differential gene expression in GBM, presenting opportunities for early diagnosis and targeted therapeutic interventions. This study offers valuable insights into the potential avenues for improving the clinical management of GBM.

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Unveiling Potential Targeted Therapeutic Opportunities for Co-Overexpressed Targeting Protein for Xklp2 and Aurora-A Kinase in Lung Adenocarcinoma

Mukherjee,

Yadav,

Mukunthan

2023

Mol Biotechnol

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Lung adenocarcinoma (LUAD) is one of the most prevalent and leading causes of cancer deaths globally, with limited diagnostic and clinically significant therapeutic targets. Identifying the genes and processes involved in developing and progressing LUAD is crucial for developing effective targeted therapeutics and improving patient outcomes. Therefore, the study aimed to explore the RNA sequencing data of LUAD from The Cancer Genome Atlas (TCGA) and gene expression profile datasets involving GSE10072, GSE31210, and GSE32863 from the Gene Expression Omnibus (GEO) databases. The differential gene expression and the downstream analysis determined clinically significant biomarkers using a network-based approach. These therapeutic targets predominantly enriched the dysregulation of mitotic cell cycle regulation and revealed the co-overexpression of Aurora-A Kinase (AURKA) and Targeting Protein for Xklp2 (TPX2) with high survival risk in LUAD patients. The hydrophobic residues of the AURKA–TPX2 interaction were considered as the target site to block the autophosphorylation of AURKA during the mitotic cell cycle. The tyrosine kinase inhibitor (TKI) dacomitinib demonstrated the strong binding potential to hinder TPX2, shielding the AURKA destabilization. This in silico study lays the foundation for repurposing targeted therapeutic options to impede the Protein–Protein Interactions (PPIs) in LUAD progression and aid in future translational investigations.

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Differential gene expression and network analysis in head and neck squamous cell carcinoma

Cited by 6 publications

References 76 publications

Exploring the mechanism of action bitter melon in the treatment of breast cancer by network pharmacology

Exploring the mechanism of action bitter melon in the treatment of breast cancer by network pharmacology

Deciphering hub genes as potential therapeutic target involved in progression of Glioblastoma multiforme disease: A multi-omics approach

Unveiling Potential Targeted Therapeutic Opportunities for Co-Overexpressed Targeting Protein for Xklp2 and Aurora-A Kinase in Lung Adenocarcinoma

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