PLoS Comput Biol. 2021 Feb 5;17(2):e1008631. doi: 10.1371/journal.pcbi.1008631.Online ahead of print.

Lichy Han ¹, Zahra N Sayyid ², Russ B Altman ^3 4

Author information

• ¹Biomedical Informatics Training Program, Stanford University, Stanford, California, United States of America.
• ²Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America.
• ³Department of Genetics, Stanford University, Stanford, California, United States of America.
• ⁴Department of Bioengineering, Stanford University, Stanford, California, United States of America.

Abstract

For many prevalent complex diseases, treatment regimens are frequently ineffective. For example, despite multiple available immunomodulators and immunosuppressants, inflammatory bowel disease (IBD) remains difficult to treat. Heterogeneity in the disease across patients makes it challenging to select the optimal treatment regimens, and some patients do not respond to any of the existing treatment choices. Drug repurposing strategies for IBD have had limited clinical success and have not typically offered individualized patient-level treatment recommendations. In this work, we present NetPTP, a Network-based Personalized Treatment Prediction framework which models measured drug effects from gene expression data and applies them to patient samples to generate personalized ranked treatment lists. To accomplish this, we combine publicly available network, drug target, and drug effect data to generate treatment rankings using patient data. These ranked lists can then be used to prioritize existing treatments and discover new therapies for individual patients. We demonstrate how NetPTP captures and models drug effects, and we apply our framework to individual IBD samples to provide novel insights into IBD treatment.