Unraveling the molecular landscape of non-small cell lung cancer: Integrating bioinformatics and statistical approaches to identify biomarkers and drug repurposing

Computers in Biology and Medicine, Год журнала: 2025, Номер 187, С. 109744 - 109744

Опубликована: Фев. 5, 2025

Язык: Английский

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Screening of differential gene expression patterns through survival analysis for diagnosis, prognosis and therapies of clear cell renal cell carcinoma

PLoS ONE, Год журнала: 2024, Номер 19(9), С. e0310843 - e0310843

Опубликована: Сен. 30, 2024

Clear cell renal carcinoma (ccRCC) is the most prevalent subtype of kidney cancer. Although there increasing evidence linking ccRCC to genetic alterations, exact molecular mechanism behind this relationship not yet completely known researchers. Though drug therapies are best choice after metastasis, unfortunately, majority patients progressively develop resistance against therapeutic drugs receiving it for almost 2 years. In case, multi-targeted different variants essential effective treatment ccRCC. To understand mechanisms development and progression, explore drugs, identify ccRCC-causing key genes (KGs). order obtain KGs, at first, we detected 133 common differentially expressed (cDEGs) between control samples based on nine (9) microarray gene-expression datasets with NCBI accession IDs GSE16441, GSE53757, GSE66270, GSE66272, GSE16449, GSE76351, GSE66271, GSE71963, GSE36895. Then, filtered these cDEGs through survival analysis independent TCGA GTEx database obtained 54 scDEGs having significant prognostic power. Next, used protein-protein interaction (PPI) network reduced set top-ranked eight KGs ( PLG , ENO2 ALDOB UMOD ALDH6A1 SLC12A3 SLC12A1 SERPINA5 ). The pan-cancer showed association subtypes cancers including gene regulatory (GRN) revealed some crucial transcriptional post-transcriptional regulators KGs. scDEGs-set enrichment significantly identified functions, biological processes, cellular components, pathways that linked results DNA methylation study indicated hypomethylation hyper-methylation which may lead immune infiltrating types (CD8+ T CD4+ cell, B neutrophil, dendritic macrophage) their in ccRCC, where positively correlated cells, but negatively other supported by literature review also. Then 10 repurposable molecules (Irinotecan, Imatinib, Telaglenastat, Olaparib, RG-4733, Sorafenib, Sitravatinib, Cabozantinib, Abemaciclib, Dovitinib.) docking KGs-mediated receptor proteins. Their ADME/T cross-validation receptors, also potent Therefore, outputs might be useful inputs/resources wet-lab researchers clinicians considering an strategy

Язык: Английский

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PCPE-2 (procollagen C-proteinase enhancer-2): the NON-IDENTICAL twin of PCPE-1

Matrix Biology, Год журнала: 2024, Номер 134, С. 59 - 78

Опубликована: Сен. 7, 2024

Язык: Английский

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Exploring bacterial key genes and therapeutic agents for breast cancer among the Ghanaian female population: Insights from In Silico analyses

PLoS ONE, Год журнала: 2024, Номер 19(11), С. e0312493 - e0312493

Опубликована: Ноя. 25, 2024

Breast cancer (BC) is yet a significant global health challenge across various populations including Ghana, though several studies on host-genome associated with BC have been investigated molecular mechanisms of development and progression, candidate therapeutic agents. However, little attention has given microbial genome in this regard, although alterations microbiota epigenetic modifications are recognized as substantial risk factors for BC. This study focused identifying bacterial key genes (bKGs) infections the Ghanaian population exploring potential drug molecules by targeting these bKGs through silico analyses. At first, 16S rRNA sequence data were downloaded from NCBI database comprising 520 samples patients 442 healthy controls. Analysis rRNA-Seq showed differences abundance between groups identified 26 differential genera threshold values at |log2FC|>2.0 p-value≤0.05. It was observed that two Prevotella Anaerovibria significantly upregulated others downregulated. Functional analysis based all 19 MetaCyc signaling pathways, twelve which enriched containing 165 Top-ranked 10 mdh, pykF, gapA, zwf, pgi, tpiA, pgk, pfkA, ppsA, pykA BC-causing protein-protein interaction network analysis. Subsequently, bKG-guided top ranked Digitoxin, Digoxin, Ledipasvir, Suramin, Ergotamine, Venetoclax, Nilotinib, Conivaptan, Dihydroergotamine, Elbasvir using docking The stability top-ranked three drug-target complexes (Digitoxin-pykA, Digoxin-mdh, Ledipasvir-pgi) confirmed dynamics simulation studies. Therefore, findings might be useful resources to wet-lab researchers further experimental validation therapies against

Язык: Английский

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Identification of Bacterial Key Genera Associated with Breast Cancer Using Machine Learning Techniques

The Microbe, Год журнала: 2024, Номер unknown, С. 100228 - 100228

Опубликована: Дек. 1, 2024

Язык: Английский

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