CPDR: An R Package of Recommending Personalized Drugs for Cancer Patients by Reversing the Individual’s Disease-Related Signature

CTR-DB 2.0: an updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers

Drug resistance is a principal limiting factor in cancer treatment. CTR-DB, the Cancer Treatment Response gene signature DataBase, is the first data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. Here we proposed an upgraded version, CTR-DB 2.0 (http://ctrdb.ncpsb.org.cn). Around 190 up-to-date source datasets with primary resistance information (129% increase compared to version 1.0) and 13 acquired-resistant datasets (a new dataset type), covering 10 856 patient samples (111% increase), 39 cancer types (39% increase) and 346 therapeutic regimens (26% increase), have been collected. In terms of function, for the single dataset analysis and multiple-dataset comparison modules, CTR-DB 2.0 added new gene set enrichment, tumor microenvironment (TME) and signature connectivity analysis functions to help elucidate drug resistance mechanisms and their homogeneity/heterogeneity and discover candidate combinational therapies. Furthermore, biomarker-related functions were greatly extended. CTR-DB 2.0 newly supported the validation of cell types in the TME as predictive biomarkers of treatment response, especially the validation of a combinational biomarker panel and even the direct discovery of the optimal biomarker panel using user-customized CTR-DB patient samples. In addition, the analysis of users' own datasets, application programming interface and data crowdfunding were also added.

A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy

The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related to the heterogeneity present within the tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering to classify patients. The four subtypes obtained from the combined classification are associated with PLC's prognosis and drug response. In these subtypes, we observed mRNAsiH_ICCA subtype, the intersection between high mRNAsi and immune characteristics clustering A, had the worst prognosis. Specifically, immune characteristics clustering B (ICC_B) had high drug sensitivity in most drugs regardless of the value of mRNAsi. On the other hand, patients with low mRNAsi responded better to ten drugs including KU-55933 and NU7441, while patients with high mRNAsi might benefit from drugs like Leflunomide. By matching the specific characteristics of each combined subtype with the drug-induced cell line expression profile, we identified a group of potential therapeutic drugs that might regulate the expression of disease signature genes. We developed a feasible multiple combined typing strategy, hoping to guide therapeutic selection and promote the development of precision medicine.

Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing

BACKGROUND

There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these tools often output long lists of candidate drugs that are difficult to interpret, and individual drug candidates may suffer from unknown off-target effects. We reasoned that an approach which aggregates information from multiple drugs that share a common mechanism of action (MOA) would increase on-target signal compared to evaluating drugs on an individual basis. In this study, we present drug mechanism enrichment analysis (DMEA), an adaptation of gene set enrichment analysis (GSEA), which groups drugs with shared MOAs to improve the prioritization of drug repurposing candidates.

RESULTS

First, we tested DMEA on simulated data and showed that it can sensitively and robustly identify an enriched drug MOA. Next, we used DMEA on three types of rank-ordered drug lists: (1) perturbagen signatures based on gene expression data, (2) drug sensitivity scores based on high-throughput cancer cell line screening, and (3) molecular classification scores of intrinsic and acquired drug resistance. In each case, DMEA detected the expected MOA as well as other relevant MOAs. Furthermore, the rankings of MOAs generated by DMEA were better than the original single-drug rankings in all tested data sets. Finally, in a drug discovery experiment, we identified potential senescence-inducing and senolytic drug MOAs for primary human mammary epithelial cells and then experimentally validated the senolytic effects of EGFR inhibitors.

CONCLUSIONS

DMEA is a versatile bioinformatic tool that can improve the prioritization of candidates for drug repurposing. By grouping drugs with a shared MOA, DMEA increases on-target signal and reduces off-target effects compared to analysis of individual drugs. DMEA is publicly available as both a web application and an R package at https://belindabgarana.github.io/DMEA .