Gene Ontology Capsule GAN: an improved architecture for protein function prediction

Label-free-based quantitative proteomic analysis of the inhibition of cisplatin-resistant ovarian cancer cell proliferation by cucurbitacin B

BACKGROUND

Ovarian cancer is a serious threat to women's health, and resistance to chemotherapeutic drugs constitutes one of the principal reasons for ovarian cancer recurrence and the low overall survival rate. Therefore, it is of paramount importance to develop additional and more-effective drugs to combat resistance to chemotherapeutic drugs. Cucurbitacin B (CuB) is a natural compound found in food plants such as bitter gourd and pumpkin, and it manifests favorable antitumor effects on a variety of malignant tumors.

PURPOSE

The present study aimed to determine the mechanism effects of CuB overcomes tumor-drug resistance in ovarian cancer.

METHODS

We used CCK-8, Edu, flow cytometric assays and cisplatin-resistant ovarian cancer xenograft mouse model to evaluate the cellular proliferation, cellular apoptosis.and tumor growth. We subsequently applied a pharmacoproteomic approach to analyze the molecular mechanisms by which CuB inhibited the proliferation of cisplatin-resistant ovarian cancer cells. We also employed western blot and molecular docking experiments to verify elements of PI3K/Akt/mTOR pathway expression.

RESULTS

We found that CuB inhibited cellular proliferation and promoted apoptosis in cisplatin-resistant ovarian cancer cell lines. We discerned that CuB inhibited tumor growth of xenograft mouse tumors. We ascertained that treatment of A2780-DDP cells with CuB resulted in the differential expression of 305 proteins, with 202 proteins downregulated and 103 proteins upregulated. Of these proteins, the mTOR protein was significantly downregulated in the drug-treated group. We also found that CuB inhibited PI3K, Akt, and mTOR and that it activated cGAS expression upstream of PI3K and inhibited ATR expression. Molecular docking experiments revealed that CuB was hydrogen-bonded to mTOR proteins at Gly (2142) and Thr (2207), with a binding force of -10.2 kcal/mol.

CONCLUSION

Our study confirmed that cucurbitacin B inhibits the PI3K/Akt/mTOR signaling pathway, targets mTOR, suppresses the proliferation of cisplatin-resistant ovarian cancer cells.And we also found that cucurbitacin B induces DNA damage, activates cGASA and recruits IKBα,playing a crucial role in eliciting anti-tumor immunity. We herein uncovered a new use for CuB in inhibiting tumor-drug resistance, providing a novel approach to overcoming chemotherapeutic drug resistance in ovarian cancer.

An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

Major advances in genomic and associated technologies have demanded reliable bioinformatic tools and workflows for the annotation of genes and their products via comparative analyses using well-curated reference data sets, accessible in public repositories. However, the accurate in silico annotation of molecules (proteins) encoded in organisms (e.g., multicellular parasites) which are evolutionarily distant from those for which these extensive reference data sets are available, including invertebrate model organisms (e.g., Caenorhabditis elegans - free-living nematode, and Drosophila melanogaster - the vinegar fly) and vertebrate species (e.g., Homo sapiens and Mus musculus), remains a major challenge. Here, we constructed an informatic workflow for the enhanced annotation of biologically-important, excretory/secretory (ES) proteins ("secretome") encoded in the genome of a parasitic roundworm, called Haemonchus contortus (commonly known as the barber's pole worm). We critically evaluated the performance of five distinct methods, refined some of them, and then combined the use of all five methods to comprehensively annotate ES proteins, according to gene ontology, biological pathways and/or metabolic (enzymatic) processes. Then, using optimised parameter settings, we applied this workflow to comprehensively annotate 2591 of all 3353 proteins (77.3%) in the secretome of H. contortus. This result is a substantial improvement (10-25%) over previous annotations using individual, "off-the-shelf" algorithms and default settings, indicating the ready applicability of the present, refined workflow to gene/protein sequence data sets from a wide range of organisms in the Tree-of-Life.