Abstract B017: An integrated workflow for multiomic characterization and functional precision medicine testing of solid tumor samples
Authors: Colin D Paul, Amber Bullock, Anthony Chatman, Km Shams Ud Doha, Harrison Leong, Sylvia Beam, Chris Yankaskas, Pradip Shahi Thakuri, Matt Dallas, David Kuninger
Journal: Cancer Research (2025)

Abstract The development of tumoroid (or cancer organoid) technology has enabled the in vitro culture of patient-derived cancer cells that retain key morphological, mutational, and transcriptomic characteristics of patient tumors. In a number of studies, the response of tumoroids to therapies has mirrored that seen in the patients from which the tumoroids were derived. As a result, there is increasing interest in the use of tumoroids in functional precision oncology, in which an individual patient’s cancer cells are used as ex vivo tumor avatars and tested for response to a range of various potential treatments to aid in therapy selection. Here, we explored a workflow to integrate genomic sequencing with functional drug sensitivity testing for precision medicine applications. Excess FFPE tissue from 6 colorectal cancer donors was processed to generate H&amp;E slides and unstained sections. Slides (2 x 10 µm sections per donor) were digested, and RNA and DNA were isolated using an automated nucleic acid purification system. The output samples were analyzed on the Genexus™ Integrated Sequencer for targeted detection of SNVs, CNVs, gene fusions, and indels for each sample using the Oncomine™ Comprehensive Assay v3. Purified RNA was also utilized for bulk RNA sequencing to generate transcriptomic profiles for each donor. In parallel, viably cryopreserved dissociated tumor cells (DTCs) were thawed and plated in Gibco™ OncoPro™ Tumoroid Culture Medium, a commercially available, serum-free, and conditioned medium-free system. OncoPro medium was developed and optimized for the culture of patient-derived tumor cells from solid cancers to provide an easy-to-use, reproducible, cGMP manufactured culture system for these samples. Where sample size allowed, RNA was isolated from DTC samples and sequenced to compare transcriptomic results generated from FFPE vs. viably cryopreserved material. Additionally, DTCs were sampled for untargeted proteomic and metabolomic profiling. DTCs were cultured for 3-7 days in OncoPro medium prior to exposure to chemotherapy drugs used in standard-of-care treatment for colorectal cancer, and cell response was quantified. Dissociated tumoroid cells formed tumoroids at high rates in culture, in line with previous studies showing that patient-derived cancer cells across colorectal, endometrial, lung, breast, and head and neck cancers form tumoroids in OncoPro medium in &amp;gt;85% of samples within 7 days of tissue receipt. We observed heterogeneous genomic, proteomic, transcriptomic, and drug response profiles across donors. Current efforts are focused on development of computational methods to tie multiomic characterization with functional response. Overall, this data presents an integrated workflow to combine genomic approaches with functional testing to inform patient care. Citation Format: Colin D Paul, Amber Bullock, Anthony Chatman, Km Shams Ud Doha, Harrison Leong, Sylvia Beam, Chris Yankaskas, Pradip Shahi Thakuri, Matt Dallas, David Kuninger. An integrated workflow for multiomic characterization and functional precision medicine testing of solid tumor samples [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals; 2025 Mar 11-13; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(5 Suppl):Abstract nr B017.