Tumor Organoid-Mediated Drug Testing and Clonality Analysis in Peritoneal Surface Disease of Intestinal Origin

Project Summary The overarching goal of this project is to develop a tumor organoid-based drug screening platform that quantifies the differential drug responsiveness of tumor clonal heterogeneity to predict a patient’s therapeutic response prior to treatment selection. Our research is directed at metastatic intestinal peritoneal surface malignancies

(IPSM), with a focus on colon and appendiceal cancers. These cancers are similarly treated and present clinically with numerous spatially-distinct peritoneal metastases associated with different anatomic structures. The clinical course of these cancers typically follows a path of chemoresistance, thus, ex vivo models that can identify drug

combinations and sequencing strategies able to mitigate chemoresistance would be of significant clinical value. Innate and acquired chemoresistance results from genetic alterations that manifest within the tumor’s clonal architecture and its changing clonal composition. In IPSM, we have observed distinct clonal variants among

spatially distinct lesions within the same patient indicating the potential for differential drug responses among intrapatient lesions. Our central hypothesis is that a patient’s clinical response to chemotherapy is proportional to the magnitude of the clonal response exhibited by the patient’s predominating cancer clones, which can be

assessed by chemosensitivity testing and clonality analysis using patient-derived tumor organoids (PTOs) constructed from intra-patient lesions that reflect the patient’s metastatic clonal diversity. In Aim 1, we will construct multi-lesion PTOs from a number of IPSM patients to investigate interactions between tumor clonal

fraction and PTO chemosensitivity. We will test the hypothesis that summative measures of chemo resistant and sensitive clonal fractions will predict patient clinical treatment responses better than simple measures of organoid cell viability. Furthermore, we will seek to identify genes in IPSM that are frequently mutated in chemo sensitive

and/or resistant clonal fractions across IPSM patients, and characterize candidate gene functions in colon cancer cell line organoids and mouse xenograft models of colon cancer. In Aim 2, we will seek to extend the reach of the PTO platform to include evaluation of immune checkpoint inhibitors (ICIs) which cannot yet be faithfully

modeled in human systems, and that have emerging roles in gastro-intestinal cancers, yet remain unexplored in IPSM management. We will test the hypothesis that immune-enhanced PTOs (iPTOs) that preserve the patient- specific homeostatic relationship between cancer cells and cytotoxic T cells (CTLs) can be used to model ICI-

induced cancer cell killing by tumor-reactive CTLs as well as to gain insight into tumor clonal alterations that influence ICI responsiveness. We will use established murine immune-oncology models (CT26 and MC38) to study tumor-CTL homeostasis in iPTOs, and to confirm ICI-response parity between ex vivo iPTOs and in situ

mouse tumors. We will confirm the involvement of antigen specific CTL-mediated cancer cell killing in ICI-treated iPTOs. Finally, parallel to Aim 1, we will identify genes that are frequently mutated in ICI sensitive and/or resistant clonal fractions of IPSM, and characterize their ICI-modulatory functions in immunocompetent mouse models.