High-throughput drug screening (HTDS) of patient-derived tumor organoids (PTDO) from advanced gastrointestinal malignancies: Response and identification of novel therapeutic options.
Authors: Khan Uqba , Us Ilkay , Moyer Jenna , Kasi Pashtoon Murtaza , Ocean Allyson J. , Podaza Enrique , Sarkar Sandipto , Savenkov Oleksandr , Martin M. Laura , Shah Manish A. 
Published: June 2023

e16019

Background: Most patients with advanced GI cancers lack predictive biomarkers to determine response to systemic therapies. HTDS of PDTOs allows automated screening of large numbers of compounds to identify novel therapeutic options for refractory GI cancer patients in a rapid clinically meaningful way. Our objective was to determine the feasibility of HTDS on refractory GI PDTOs and to identify the concordance of ex-vivo sensitivity with clinical response to establish a new pipeline to reveal novel therapeutic options for GI cancer patients. Methods: Tumor tissues were obtained from advanced GI cancer patients anytime during their systemic therapies from needle biopsies or surgical specimens. PDTOs were established from these tumors at Englander Institute of Precision Medicine of Weill Cornell Medicine. Successful establishment of PDTOs occurs when they can be viably expanded beyond their initial plating in Matrigel for at least 5 passages and bio-banked. Whole exome sequencing and RNA sequencing confirmed genomic similarities between PDTOs and their originating tumors. PDTOs were screened for 156 drugs by using an integrative robotic HTDS system to examine drug sensitivity and validate patients’ clinical response. To determine clinical correlation, PDTOs ex-vivo response to FOLFOX, FOLFIRI, and docetaxel/paclitaxel (taxanes) were compared with their matching patients’ clinical response. Results: 30 PDTOs were established from 25 patients (11 colorectal, 14 gastroesophageal). Dose response curves for all 156 drugs were generated and subsequently AUC and IC50s were calculated. The concordance between PDTOs and patient’s response to FOLFOX, FOLFIRI and Taxane was determined for 31 PDTO-drug treatment iterations in which the patients also received same drug. 16/31 times the tissue was collected before the patient received the corresponding therapy and 15/31 times, afterwards. 2 patients were clinically non-evaluable. The overall concordance was 59% (17/29). Concordance was 64% (9/14) for specimens collected before patient receiving the therapy and 53% (8/15) for after. Concordance for FOLFOX was 71% (10/14), FOLFIRI 86% (6/7), Paclitaxel 14% (1/7) and Docetaxel 0% (0/1). Combined concordance for FOLFOX and FOLFIRI was 76%, and for specimens collected prior to clinical drug use, 80 % (8/10). Approx. 10% of drug screens revealed potential sensitive new treatment options such as Selinexor, Crizotinib, or Osimertinib for advanced GI cancer patients. Conclusions: We successfully demonstrated feasibility of an automated, end-to-end high-throughput screening of PTDOs in patients with refractory GI malignancies. PDTOs response highly correlated with clinical response, especially for FOLFOX and FOLFIRI. The HTDS identified several novel therapeutic options for advanced GI cancer patients.