Accelerating Complex Disease Treatment through Network Medicine and GenAI: A Case Study on Drug Repurposing for Breast Cancer

TL;DR

This study presents a network medicine framework enhanced by GenAI and ChatGPT to predict drug repurposing opportunities for complex diseases like breast cancer by analyzing real-world evidence and signaling pathways.

Contribution

It introduces a novel multilayered network approach combined with ChatGPT prompt engineering to identify drug-pathway interactions for drug repurposing.

Findings

Identified 38 out of 46 breast cancer pathways covered by at least two drugs.

Found a highly covered pathway with 108 drugs, indicating potential for combination therapies.

Demonstrated ChatGPT's effectiveness in accelerating drug mention extraction from clinical trials.

Abstract

The objective of this research is to introduce a network specialized in predicting drugs that can be repurposed by investigating real-world evidence sources, such as clinical trials and biomedical literature. Specifically, it aims to generate drug combination therapies for complex diseases (e.g., cancer, Alzheimer's). We present a multilayered network medicine approach, empowered by a highly configured ChatGPT prompt engineering system, which is constructed on the fly to extract drug mentions in clinical trials. Additionally, we introduce a novel algorithm that connects real-world evidence with disease-specific signaling pathways (e.g., KEGG database). This sheds light on the repurposability of drugs if they are found to bind with one or more protein constituents of a signaling pathway. To demonstrate, we instantiated the framework for breast cancer and found that, out of 46 breast cancer signaling pathways, the framework identified 38 pathways that were covered by at least two drugs. This evidence signals the potential for combining those drugs. Specifically, the most covered signaling pathway, ID hsa:2064, was covered by 108 drugs, some of which can be combined. Conversely, the signaling pathway ID hsa:1499 was covered by only two drugs, indicating a significant gap for further research. Our network medicine framework, empowered by GenAI, shows promise in identifying drug combinations with a high degree of specificity, knowing the exact signaling pathways and proteins that serve as targets. It is noteworthy that ChatGPT successfully accelerated the process of identifying drug mentions in clinical trials, though further investigations are required to determine the relationships among the drug mentions.