Subclonal response heterogeneity to define cancer organoid therapeutic sensitivity
Tumor heterogeneity is predicted to confer inferior clinical outcomes with precision-based strategies, however, modeling heterogeneity in a manner that still represents the tumor of origin remains a formidable challenge. Sequencing technologies are limited in their ability to identify rare subclonal populations and predict response to treatments for patients. Patient-derived organotypic cultures have significantly improved the modeling of cancer biology by faithfully representing the molecular features of primary malignant tissues. Patient-derived cancer organoid (PCO) cultures contain subclonal populations with the potential to recapitulate heterogeneity, although treatment response assessments commonly ignore diversity in the molecular profile or treatment response. Here, we demonstrate the advantage of evaluating individual PCO heterogeneity to enhance the sensitivity of these assays for predicting clinical response. Additionally, organoid subcultures identify subclonal populations with altered treatment response. Finally, dose escalation studies of PCOs to targeted anti-EGFR therapy are utilized which reveal divergent pathway expression when compared to pretreatment cultures. Overall, these studies demonstrate the importance of population-based organoid response assessments, the use of PCOs to identify molecular heterogeneity not observed with bulk tumor sequencing, and PCO heterogeneity for understanding therapeutic resistance mechanisms.
Authors
- Evie H. Carchman (ORCID: https://orcid.org/0000-0002-5536-7761)
- Noelle K. LoConte (ORCID: https://orcid.org/0000-0002-3883-4153)
- Austin Yeung
- Samantha J. Anderson
- Peter F. Favreau (ORCID: https://orcid.org/0000-0001-6900-944X)
- Eugene F. Foley
- Charles P. Heise (ORCID: https://orcid.org/0000-0001-7610-6264)
- Kayla K. Lemmon (ORCID: https://orcid.org/0009-0001-9965-5351)
- Irene M. Ong (ORCID: https://orcid.org/0000-0002-9353-6941)
- Jeremy D. Kratz (ORCID: https://orcid.org/0000-0003-1979-3955)
- Nataliya V. Uboha (ORCID: https://orcid.org/0000-0003-3449-1680)
- Sean J. McIlwain (ORCID: https://orcid.org/0000-0002-3820-8400)
- Elise H. Lawson
- Carley M. Sprackling (ORCID: https://orcid.org/0009-0005-9875-5798)
- Dustin A. Deming (ORCID: https://orcid.org/0000-0003-2394-9836)
- Amani A. Gillette (ORCID: https://orcid.org/0000-0002-1470-3300)
- Mark E. Burkard (ORCID: https://orcid.org/0000-0002-4215-7722)
- Devon Miller (ORCID: https://orcid.org/0009-0002-8898-6072)
- Aishwarya Sunil
- Linda Clipson (ORCID: https://orcid.org/0000-0002-3610-9337)
- Katherine A. Johnson (ORCID: https://orcid.org/0000-0002-6335-7782)
- Shujah Rehman (ORCID: https://orcid.org/0000-0001-9527-743X)
- Lucas C. Zarling (ORCID: https://orcid.org/0000-0003-3557-2351)
- Kristina A. Matkowskyj (ORCID: https://orcid.org/0000-0001-5223-0834)
- Randall J. Kimple (ORCID: https://orcid.org/0000-0001-8336-8000)
- M. Bassetti (ORCID: https://orcid.org/0000-0001-5012-8596)
- Sam Joseph Lubner (ORCID: https://orcid.org/0000-0002-5732-2938)
- Daniel E. Abbott (ORCID: https://orcid.org/0000-0002-5539-0734)
- Cheri A. Pasch (ORCID: https://orcid.org/0009-0005-9683-7378)
- Melissa C. Skala (ORCID: https://orcid.org/0000-0002-6320-7637)
- Daniel Mulkerin
- Jens C. Eickhoff (ORCID: https://orcid.org/0000-0003-0525-6462)
- Cristina B. Sanger
- Alyssa K Steimle
Institutions
- University of Wisconsin–Madison (US)
- Morgridge Institute for Research (US)
- University of Wisconsin Carbone Cancer Center (US)
- William S. Middleton Memorial Veterans Hospital (US)
Publication Details
- Journal
- Scientific Reports
- Published
- 2025-04-09
- DOI
- https://doi.org/10.1038/s41598-025-96204-2
- Citations
- 6
- Primary Topic
- Heat shock proteins research
- Type
- article
- Field-Weighted Citation Impact
- 4.03
Funders
- Doris Duke Charitable Foundation