AUTHOR=Lu Yuan , Bi Juan , Li Fei , Wang Gang , Zhu Junjie , Jin Jiqing , Liu Yueyun 

TITLE=Differential Gene Analysis of Trastuzumab in Breast Cancer Based on Network Pharmacology and Medical Images

JOURNAL=Frontiers in Physiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.942049

DOI=10.3389/fphys.2022.942049

ISSN=1664-042X

ABSTRACT=<p>The purpose of this study was to use network pharmacology, biomedical images and molecular docking technology in the treatment of breast cancer to investigate the feasible therapeutic targets and mechanisms of trastuzumab. In the first place, we applied pubchem swisstarget (<ext-link ext-link-type="uri" xlink:href="http://www.swisstargetprediction.ch/" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.swisstargetprediction.ch/</ext-link>), (<ext-link ext-link-type="uri" xlink:href="https://pubchem.ncbi.nlm.nih.gov/" xmlns:xlink="http://www.w3.org/1999/xlink">https://pubchem.ncbi.nlm.nih.gov/</ext-link>) pharmmapper (<ext-link ext-link-type="uri" xlink:href="http://lilab-ecust.cn/pharmmapper/" xmlns:xlink="http://www.w3.org/1999/xlink">http://lilab-ecust.cn/pharmmapper/</ext-link>), and the batman-tcm (<ext-link ext-link-type="uri" xlink:href="http://bionet.ncpsb.org.cn/batman-tcm/" xmlns:xlink="http://www.w3.org/1999/xlink">http://bionet.ncpsb.org.cn/batman-tcm/</ext-link>) database to collect the trastuzumab targets. Then, in NCBI-GEO, breast cancer target genes were chosen (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/geo/" xmlns:xlink="http://www.w3.org/1999/xlink">https://www.ncbi.nlm.nih.gov/geo/</ext-link>). The intersection regions of drug and disease target genes were used to draw a Venn diagram. Through Cytoscape 3.7.2 software, and the STRING database, we then formed a protein-protein interaction (PPI) network. Besides, we concluded KEGG pathway analysis and Geen Ontology analysis by using ClueGO in Cytospace. Finally, the top 5 target proteins in the PPI network to dock with trastuzumab were selected. After screening trastuzumab and breast cancer in databases separately, we got 521 target genes of the drug and 1,464 target genes of breast cancer. The number of overlapping genes was 54. PPI network core genes include GAPDH, MMP9, CCNA2, RRM2, CHEK1, etc. GO analysis indicated that trastuzumab treats breast cancer through abundant biological processes, especially positive regulation of phospholipase activity, linoleic acid metabolic process, and negative regulation of endothelial cell proliferation. The molecular function is NADP binding and the cellular component is tertiary granule lumen. The results of KEGG enrichment analysis exhibited four pathways related to the formation and cure of breast cancer, containing Drug metabolism, Glutathione metabolism, Pyrimidine metabolism and PPAR signaling pathway. Molecular docking showed that trastuzumab has good binding abilities with five core target proteins (GAPDH, MMP9, CCNA2, RRM2, CHEK1). This study, through network pharmacology and molecular docking, provides new pieces of evidence and ideas to understand how trastuzumab treats breast cancer at the gene level.</p>