Integrated bioinformatics approach to unwind key genes and pathways involved in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is the fifth leading cause of death in India. Until now, the exact pathogenesis concerning CRC signaling pathways is largely unknown; however, the diseased condition is believed to deteriorate with lifestyle, aging, and inherited genetic disorders. Hence, the identification of hub genes and therapeutic targets is of great importance for disease monitoring.

OBJECTIVE

Identification of hub genes and targets for identification of candidate hub genes for CRC diagnosis and monitoring.

MATERIALS AND METHODS

The present study applied gene expression analysis by integrating two profile datasets (GSE20916 and GSE33113) from NCBI-GEO database to elucidate the potential key candidate genes and pathways in CRC. Differentially expressed genes (DEGs) between CRC (195 CRC tissues) and healthy control (46 normal mucosal tissue) were sorted using GEO2R tool. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed using Cluster Profiler in Rv. 3.6.1. Moreover, protein-protein interactions (PPI), module detection, and hub gene identification were accomplished and visualized through the Search Tool for the Retrieval of Interacting Genes, Molecular Complex Detection (MCODE) plug-in of Cytoscape v3.8.0. Further hub genes were imported into ToppGene webserver for pathway analysis and prognostic expression analysis was conducted using Gene Expression Profiling Interactive Analysis webserver.

RESULTS

A total of 2221 DEGs, including 1286 up-regulated and 935down-regulated genes mainly enriched in signaling pathways of NOD-like receptor, FoxO, AMPK signalling and leishmaniasis. Three key modules were detected from PPI network using MCODE. Besides, top 20 high prioritized hub genes were selected. Further, prognostic expression analysis revealed ten of the hub genes, namely IL1B, CD44, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, MMP9, CREB1, STAT1, vascular endothelial growth factor (VEGFA), CDC5 L, Ataxia-telangiectasia mutated (ATM + and CDH1 to be differently expressed in normal and cancer patients.

CONCLUSION

The present study proposed five novel therapeutic targets, i.e., ATM, GAPDH, CREB1, VEGFA, and CDH1 genes that might provide new insights into molecular oncogenesis of CRC.

Green synthesis of Piper nigrum copper-based nanoparticles: in silico study and ADMET analysis to assess their antioxidant, antibacterial, and cytotoxic effects

Nanobiotechnology is a popular branch of science that is gaining interest among scientists and researchers as it allows for the green manufacturing of nanoparticles by employing plants as reducing agents. This method is safe, cheap, reproducible, and eco-friendly. In this study, the therapeutic property of Piper nigrum fruit was mixed with the antibacterial activity of metallic copper to produce copper nanoparticles. The synthesis of copper nanoparticles was indicated by a color change from brown to blue. Physical characterization of Piper nigrum copper nanoparticles (PN-CuNPs) was performed using UV-vis spectroscopy, FT-IR, SEM, EDX, XRD, and Zeta analyzer. PN-CuNPs exhibited potential antioxidant, antibacterial, and cytotoxic activities. PN-CuNPs have shown concentration-dependent, enhanced free radical scavenging activity, reaching maximum values of 92%, 90%, and 86% with DPPH, H2O2, and PMA tests, respectively. The antibacterial zone of inhibition of PN-CuNPs was the highest against Staphylococcus aureus (23 mm) and the lowest against Escherichia coli (10 mm). PN-CuNPs showed 80% in vitro cytotoxicity against MCF-7 breast cancer cell lines. Furthermore, more than 50 components of Piper nigrum extract were selected and subjected to in silico molecular docking using the C-Docker protocol in the binding pockets of glutathione reductase, E. coli DNA gyrase topoisomerase II, and epidermal growth factor receptor (EGFR) tyrosine to discover their druggability. Pipercyclobutanamide A (26), pipernigramide F (32), and pipernigramide G (33) scored the highest Gibbs free energy at 50.489, 51.9306, and 58.615 kcal/mol, respectively. The ADMET/TOPKAT analysis confirmed the favorable pharmacokinetics, pharmacodynamics, and toxicity profiles of the three promising compounds. The present in silico analysis helps us to understand the possible mechanisms behind the antioxidant, antibacterial, and cytotoxic activities of CuNPs and recommends them as implicit inhibitors of selected proteins.

Antioxidant, Antibacterial, and Anti-diabetic Activity of Green Synthesized Copper Nanoparticles of Cocculus hirsutus (Menispermaceae)

The emergence of new technologies has led to the discovery of the biological properties of nanoparticles through green approach. In the present investigation, we report the potential antibacterial, antioxidant, and anti-diabetic properties of copper nanoparticle (CuNPs) synthesized by reducing 3 mM copper acetate solution with aqueous leaf extract of Cocculus hirsutus. A colour change from deep brown to dark greenish brown indicated the formation of copper nanoparticles. The so-formed CuNPs were characterized by employing UV spectroscopy, FTIR, SEM, and EDX analyses which described sheet-like structure morphology having typical size of 63.46 nm. Later, the synthesized CuNPs efficiency was evaluated against bacterial pathogens, and was found highly toxic to B. subtilis and S. aureus strains. The synthesized CuNPs were examined through H₂O₂ and PMA assays which demonstrated the highest free radical scavenging activity. Besides, the resulted CuNPs revealed the higher anti-diabetic efficacy in both the [Formula: see text]-amylase and [Formula: see text] -glucosidase inhibition assays (64.5% ± 0.11 and 68.5% ± 0.11, respectively). Finally, our findings report that C. hirsutus can be exploited as a source for green synthesis of CuNPs, having potent in vitro antioxidant, antibacterial, and anti-diabetic properties.

Data on GC-MS analysis, in vitro anti-oxidant and anti-microbial activity of the Catharanthus roseus and Moringa oleifera leaf extracts

The article reports data on chemical profiling by gas chromatography-mass spectrometry (GC-MS) of aqueous and methanolic leaf extracts of Madagascar periwinkle (Catharanthus roseus) and drumstick tree (Moringa oleifera) and on their antioxidant and antibacterial effects against three clinical human pathogens. In total 105 compounds were tentatively identified; in which 65 in Catharanthus roseus and 40 in Moringa oleifera compounds. A large number of peaks with good area percentage was found in methanolic extract of Catharanthus roseus with core chemical constituents such as trans-squalene, n-hexadecanoic acid, Eicosyl acetate, stearin, 1H-Benz(G)indole-3-carboxylic acid. The corresponding constituents from Moringa oleifera include 9-Octadecenoic acid (z)-, Heptadecanoic acid and phytol acetate. The highest scavenging activity (87.7% at 200 μg/mL) was shown by DPPH aqueous leaf extract of C. roseus. Moreover, the methanolic scavenging of both plant extracts was in the order of FRAP>DPPH>NO> H₂O₂ with lowest antioxidant activity (51.4% at 200 μg/mL) exposed by Catharanthus roseus in comparison of all cases. Good antibacterial action was examined against three different organisms (E.coli, B. subtilis and S. aureus) of aqueous infusion of Catharanthus roseus.