In Silico Identification of Hub Genes as Observing Biomarkers for Gastric Cancer Metastasis

Arulprakasam, Ajucarmelprecilla; Pandi, Jhansi; Dhandapani, Ranjithkumar; Ramanathan, Saikishore; Chinnappan, Jayaprakash; Paramasivam, Ragul; Thangavelu, Sathiamoorthi; Ghilan, Abdul-Kareem Mohammed; Aljohani, Saad Ali S.; Oyouni, Atif Abdulwahab A.; Farasani, Abdullah; Altayar, Malik A.; Althagafi, Hussam Awwadh E.; Alzahrani, Othman R.; Durairaj, Kaliannan; Shrestha, Ashwinee Kumar

doi:10.1155/2022/6316158

Cited by 12 publications

(6 citation statements)

References 35 publications

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“…An in silico analysis identified APE1 as a central hub gene for gastric cancer, as its overexpression had a great prognostic value in two analyzed datasets (GSE1611533 and GSE54129) [64]. Indeed, APE1 is overexpressed at both transcriptional and translational levels in gastric cancer [65,66].…”

mentioning

confidence: 99%

Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons

Malfatti,

Bellina,

Antoniali

et al. 2023

Cells

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APE1 is an essential endodeoxyribonuclease of the base excision repair pathway that maintains genome stability. It was identified as a pivotal factor favoring tumor progression and chemoresistance through the control of gene expression by a redox-based mechanism. APE1 is overexpressed and serum-secreted in different cancers, representing a prognostic and predictive factor and a promising non-invasive biomarker. Strategies directly targeting APE1 functions led to the identification of inhibitors showing potential therapeutic value, some of which are currently in clinical trials. Interestingly, evidence indicates novel roles of APE1 in RNA metabolism that are still not fully understood, including its activity in processing damaged RNA in chemoresistant phenotypes, regulating onco-miRNA maturation, and oxidized RNA decay. Recent data point out a control role for APE1 in the expression and sorting of onco-miRNAs within secreted extracellular vesicles. This review is focused on giving a portrait of the pros and cons of the last two decades of research aiming at the identification of inhibitors of the redox or DNA-repair functions of APE1 for the definition of novel targeted therapies for cancer. We will discuss the new perspectives in cancer therapy emerging from the unexpected finding of the APE1 role in miRNA processing for personalized therapy.

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mentioning

confidence: 99%

Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons

Malfatti,

Bellina,

Antoniali

et al. 2023

Cells

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“…From the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/ ) databases, 307 human endometrial stromal sarcoma datasets were retrieved using "Endometrial stromal sarcomas" as the keyword and "Homo sapiens" as the study subject, and the GSE85383 dataset (Last update date: August 31, 2017) was selected for analysis 8 , 9 . This dataset contained 9 LG-ESS and 4 HG-ESS samples, using Agilent GPL22303 SurePrint G3 Human GE 8 × 60 K Microarray.…”

Section: Methodsmentioning

confidence: 99%

Identification of hub genes distinguishing subtypes in endometrial stromal sarcoma through comprehensive bioinformatics analysis

Zhang,

Zhao,

Zhu

et al. 2024

Sci Rep

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Diagnosing low-grade and high-grade endometrial stromal sarcoma (LG-ESS and HG-ESS) is a challenge. This study aimed to identify biomarkers. 22 ESS cases were analyzed using Illumina microarrays. Differentially expressed genes (DEGs) were identified via Limma. DEGs were analyzed with String and Cytoscape. Core genes were enriched with GO and KEGG, their pan-cancer implications and immune aspects were studied. 413 DEGs were found by exome sequencing, 2174 by GSE85383 microarray. 36 common genes were identified by Venn analysis, and 10 core genes including RBFOX1, PCDH7, FAT1 were selected. Core gene GO enrichment included cell adhesion, T cell proliferation, and KEGG focused on related pathways. Expression was evaluated across 34 cancers, identifying immune DEGs IGF1 and AVPR1A. Identifying the DEGs not only helps improve our understanding of LG-ESS, HG-ESS but also promises to be potential biomarkers for differential diagnosis between LG-ESS and HG-ESS and new therapeutic targets.

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“…PPIs have accelerated the modeling of functional pathways to illustrate the biological process’ molecular mechanism. PPIs can modify the kinetic properties of the enzymes, construct a new building site for small effector molecules, change the specificity of a protein for its substrate through interaction with different binding partners [ 9 ], or serve a regulatory role at either the upstream or downstream level [ 10 ]. A network represents a collection of points (proteins, genes.)…”

Section: Introductionmentioning

confidence: 99%

Investigating the potential of Juglans regia phytoconstituents for the treatment of cervical cancer utilizing network biology and molecular docking approach

Dua,

Bhardwaj,

Ahmad

et al. 2024

PLoS ONE

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The fourth most frequent type of cancer in women and the leading cause of mortality for females worldwide is cervical cancer. Traditionally, medicinal plants have been utilized to treat various illnesses and ailments. The molecular docking method is used in the current study to look into the phytoconstituents of Juglans regia’s possible anticancer effects on cervical cancer target proteins. This work uses the microarray dataset analysis of GSE63678 from the NCBI Gene Expression Omnibus database to find differentially expressed genes. Furthermore, protein-protein interactions of differentially expressed genes were constructed using network biology techniques. The top five hub genes (IGF1, FGF2, ESR1, MYL9, and MYH11) are then determined by computing topological parameters with Cytohubba. In addition, molecular docking research was performed on Juglans regia phytocompounds that were extracted from the IMPPAT database versus hub genes that had been identified. Utilizing molecular dynamics, simulation confirmed that prioritized docked complexes with low binding energies were stable.

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In Silico Identification of Hub Genes as Observing Biomarkers for Gastric Cancer Metastasis

Cited by 12 publications

References 35 publications

Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons

Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons

Identification of hub genes distinguishing subtypes in endometrial stromal sarcoma through comprehensive bioinformatics analysis

Investigating the potential of Juglans regia phytoconstituents for the treatment of cervical cancer utilizing network biology and molecular docking approach

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