Comprehensive multi-level expression profiling of key biomarkers in breast cancer patients

OBJECTIVES

In this comprehensive breast cancer (BC) study, we aimed to identify, validate, and characterize key biomarkers with significant implications in BC diagnosis, prognosis, and as therapeutic targets.

METHODS

Our research strategy involved a multi-level methodology, combining bioinformatic analysis with experimental validation.

RESULTS

Initially, we conducted an extensive literature search to identify BC biomarkers, selecting those with reported accuracies exceeding 20% in specificity and sensitivity. This yielded nine candidate biomarkers, which we subsequently analyzed using Cytoscape to identify a few key biomarkers. Based on the degree method, we denoted four key biomarkers, including progesterone receptor (PGR), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), and Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2). Expression analysis using The Cancer Genome Atlas (TCGA) dataset revealed that PGR and EGFR exhibited significant (p-value < 0.05) down-regulation in BC samples when compared to controls, while ESR1 and ERBB2 showed up-regulation. To strengthen our findings, we collected clinical BC tissue samples from Pakistani patients and performed expression verification using real-time quantitative polymerase chain reaction (RT-qPCR). The results aligned with our initial TCGA dataset analysis, further validating the differential expression of these key biomarkers in BC. Furthermore, we utilized receiver operating characteristic (ROC) curves to demonstrate the diagnostic use of these biomarkers. Our analysis underscored their accuracy and sensitivity as diagnostic markers for BC. Survival analysis using the Kaplan-Meier Plotter tool revealed a prognostic significance of PGR, ESR1, EGFR, and ERBB2. Their expression levels were associated with poor overall survival (OS) of BC patients, shedding light on their roles as prognostic indicators in BC. Lastly, we explored DrugBank to identify drugs that may reverse the expression patterns , and estradiol, decitabine, and carbamazepine were singled out.

CONCLUSION

Our study gives valuable insight into BC biomarkers, for diagnosis and prognosis. These findings have implications for BC management using personalized and targeted therapeutic approaches for BC patients.

Effects of Structural Manipulation on the Bioactivity of some Coumarin-Based Products

Coumarin (2H-1-benzopyran-2-one) is a plant-derived natural product known for its pharmacological properties, such as anti-inflammatory, anticoagulant, antibacterial, antifungal, antiviral, anticancer, antihypertensive, antitubercular, anticonvulsant, antiadipogenic, antihyperglycemic, antioxidant, and neuroprotective. Two coumarin-based products were identified in the seeds of two apple phenotypes commonly known as Granny Smith and Red Delicious. This study aimed to evaluate the chemical manipulation of these coumarin-based products to more lipophilic semisynthetic compounds and trace the role of the phenolic hydroxyl group in the bioactivity of the parent natural products. The bioactivity evaluation included studying the potentials of the natural- and semisynthetic-coumarins as antioxidant, antineoplastic, antifungal, and antibacterial agents. At the first step, the antiradical potential of these products was evaluated versus the free radicals of hydroxyl and DPPH. The second potential was investigated utilizing an MTT-based photo assay versus several cancer-line cells,including SK-OV-3, MCF-7, KYSE-30, LC540, HeLa, AR42J, AB12, and AMN3. The third and fourth potentials were recognized by conducting a disc-diffusion method against six infective bacterial strains and three fungal strains. The test bacteria were Shigella dysenteriae, Klebsiella pneumonia, Escherichia coli, Haemophilus influenzae, Salmonella typhi, and Pseudomonas aeruginosa. On the other hand, the test fungi included Aspergillus flavus, Candida albicans, and Aspergillus niger. The results arising from these biopotentials revealed that the investigated functional group exerted a positive impact on the antiradical and antineoplastic potentials of the natural derivatives; however, they had a negative consequence on their antimicrobial potentials.