Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network

Objective:Drug repurposing,the application of existing therapeutics to new indications,holds promise in achieving rapid clinical effects at a much lower cost than that of de novo drug development.The aim of our study was to perform a more comprehensive drug repurposing prediction of diseases,particularly cancers.Methods:Here,by targeting 4,096 human diseases,including 384 cancers,we propose a greedy computational model based on a heterogeneous multilayer network for the repurposing of 1,419 existing drugs in Drug Bank.We performed additional experimental validation for the dominant repurposed drugs in cancer.Results:The overall performance of the model was well supported by cross-validation and literature mining.Focusing on the top-ranked repurposed drugs in cancers,we verified the anticancer effects of 5 repurposed drugs widely used clinically in drug sensitivity experiments.Because of the distinctive antitumor effects of nifedipine(an antihypertensive agent)and nortriptyline(an antidepressant drug)in prostate cancer,we further explored their underlying mechanisms by using quantitative proteomics.Our analysis revealed that both nifedipine and nortriptyline affected the cancer-related pathways of DNA replication,the cell cycle,and RNA transport.Moreover,in vivo experiments demonstrated that nifedipine and nortriptyline significantly inhibited the growth of prostate tumors in a xenograft model.Conclusions:Our predicted results,which have been released in a public database named The Predictive Database for Drug Repurposing(PAD),provide an informative resource for discovering and ranking drugs that may potentially be repurposed for cancer treatment and determining new therapeutic effects of existing drugs.

Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation

AMP-activated protein kinase(AMPK)is a conserved energy sensor that plays roles in diverse biological processes via phosphorylating various substrates.Emerging studies have demonstrated the regulatory roles of AMPK in DNA repair,but the underlying mechanisms remain to be fully understood.Herein,using mass spectrometry-based proteomic technologies,we systematically investigate the regulatory network of AMPK in DNA damage response(DDR).Our system-wide phosphoproteome study uncovers a variety of newly-identified potential substrates involved in diverse biological processes,whereas our system-wide histone modification analysis reveals a link between AMPK and histone acetylation.Together with these findings,we discover that AMPK promotes apoptosis by phosphorylating apoptosis-stimulating of p53 protein 2(ASPP2)in an irradiation(IR)-dependent manner and regulates histone acetylation by phosphorylating histone deacetylase 9(HDAC9)in an IR-independent manner.Besides,we reveal that disrupting the histone acetylation by the bromodomain BRD4 inhibitor JQ-1 enhances the sensitivity of AMPKdeficient cells to IR.Therefore,our study has provided a resource to investigate the interplay between phosphorylation and histone acetylation underlying the regulatory network of AMPK,which could be beneficial to understand the exact role of AMPK in DDR.

Integrative multi-omics and drug-response characterization of patient-derived prostate cancer primary cells

Prostate cancer(PCa)is the second most prevalent malignancy in males across the world.A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa.Herein,we establish 35 Chinese PCa primary cell models to capture specific characteristics among PCa patients,including gene mutations,mRNA/protein/surface protein distributions,and pharmaceutical responses.The multi-omics analyses identify Anterior Gradient 2(AGR2)as a pre-operative prognostic biomarker in PCa.Through the drug library screening,we describe crizotinib as a selective compound for malignant PCa primary cells.We further perform the pharmacoproteome analysis and identify 14,372 significant protein-drug correlations.Surprisingly,the diminished AGR2 enhances the inhibition activity of crizotinib via ALK/c-MET-AKT axis activation which is validated by PC3 and xenograft model.Our integrated multi-omics approach yields a comprehensive understanding of PCa biomarkers and pharmacological responses,allowing for more precise diagnosis and therapies.

Comprehensive profiling of lysine acetylome in Staphylococcus aureus

The Gram-positive bacterium Staphylococcus aureus(S.aureus)is a wide spread common opportunistic pathogen that causes a wide variety of infectious diseases,from benign skin infections to life-threatening diseases such as the methicillin-resistant Staphylococcus aureus(MRSA)infection.Although emerging evidence suggests that lysine acetylation may play critical roles in bacterial physiology,the atlas of acetylome in S.aureus has not been studied.To comprehensively profile protein lysine acetylation in S.aureus,we used an integrated approach that combined immune affinity peptide enrichment using anti-lysine acetylation antibody,high-pH HPLC fractionation,and HPLC/mass spectrometry analysis.This study led to the identification of 1361 non-redundant acetylation sites on 412 proteins found in a search of S.aureus protein database extracted from the Swiss-Prot database.We further performed bioinformatic analysis to characterize this modification,including gene ontology annotation,protein-protein interaction,and domain analysis of the acetylation sites.We found that the acetylated proteins were enriched in multiple biological pathways,such as ribosomal function and energy metabolism.Our data provides a rich source for functional studies of lysine acetylation in S.aureus.

SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models

With the development of mass spectrometry(MS)-based proteomics technologies,patient-derived xenograft(PDX),which is generated from the primary tumor of a patient,is widely used for the proteome-wide analysis of cancer mechanism and biomarker identification of a drug.However,the proteomics data interpretation is still challenging due to complex data deconvolution from the PDX sample that is a cross-species mixture of human cancerous tissues and immunodeficient mouse tissues.In this study,by using the lab-assembled mixture of human and mouse cells with different mixing ratios as a benchmark,we developed and evaluated a new method,SPA(shared peptide allocation),for protein quantitation by considering the unique and shared peptides of both species.The results showed that SPA could provide more convenient and accurate protein quantitation in human–mouse mixed samples.Further validation on a pair of gastric PDX samples(one bearing FGFR2 amplification while the other one not)showed that our new method not only significantly improved the overall protein identification,but also detected the differential phosphorylation of FGFR2 and its downstream mediators(such as RAS and ERK)exclusively.The tool pdx SPA is freely available at https://github.com/LiLab-Proteomics/pdx SPA.

Detection of PRMT1 inhibitors with stopped flow fluorescence

Protein arginine methyltransferases(PRMTs)are crucial epigenetic regulators in eukaryotic organisms that serve as histone writers for chromatin remodeling.PRMTs also methylate a variety of non-histone protein substrates to modulate their function and activity.The development of potent PRMT inhibitors has become an emerging and imperative research area in the drug discovery field to provide novel therapeutic agents for treating diseases and as tools to investigate the biological functions of PRMTs.PRMT1 is the major type I enzyme that catalyzes the formation of asymmetric dimethyl arginine,and PRMT1 plays important regulatory roles in signal transduction,transcriptional activation,RNA splicing,and DNA repair.Aberrant expression of PRMT1 is found in many types of cancers,pulmonary diseases,cardiovascular disease,diabetes,and renal diseases.PRMT1 is a highly promising target for therapeutic development.We created a stopped flow fluorescence-based assay for PRMT1 inhibitor detection and characterization that has the advantages of being homogeneous,nonradioactive,and mix-and-measure in nature,allowing for continuous measurement of the methylation reaction and its inhibition.To our knowledge,this is the first continuous assay for PRMT1 reaction detection and inhibitor characterization.The approach is not only capable of quantitatively determining the potency(IC50)of PRMT1 inhibitors but can also distinguish cofactor-competitive inhibitors,substrate-competitive inhibitors,and mixed-type inhibitors.