1. Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome.
- Author
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Dinstag G, Shulman ED, Elis E, Ben-Zvi DS, Tirosh O, Maimon E, Meilijson I, Elalouf E, Temkin B, Vitkovsky P, Schiff E, Hoang DT, Sinha S, Nair NU, Lee JS, Schäffer AA, Ronai Z, Juric D, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Gilbert MR, Aldape K, Rajagopal PS, Beker T, Ruppin E, and Aharonov R
- Subjects
- Humans, Transcriptome genetics, Precision Medicine, Interferon-gamma therapeutic use, Immunotherapy, Neoplasms genetics, Neoplasms therapy
- Abstract
Background: Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers., Methods: We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient's response to a variety of therapies in multiple cancer types without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: personalized oncology (PO), aimed at prioritizing treatments for a single patient, and clinical trial design (CTD), selecting the most likely responders in a patient cohort., Findings: Evaluating ENLIGHT's performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patient's treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable with that of supervised predictors developed for specific indications and drugs. In combination with the interferon-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy., Conclusions: ENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome., Funding: This research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority., Competing Interests: Declaration of interests G.D., E.D.S., E. Elis, D.S.B.-Z., O.T., E.M., E. Elalouf, B.T., P.V., T.B., and R.A. are employees of Pangea Biomed. I.M. is a paid consultant of Pangea Biomed. E.S. is the Chairman of the Board of Pangea Biomed. E.R. is a co-founder of MedAware, Metabomed, and Pangea Biomed (divested) and an unpaid member of Pangea Biomed’s scientific advisory board. Z.R. is a co-founder of Pangea Biomed and an unpaid member of its scientific advisory board. R.B. is a member of Pangea Biomed’s scientific advisory board., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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