Using patient-derived tumor organoids from common epithelial cancers to analyze personalized T-cell responses to neoantigens

Adoptive cell transfer of tumor-infiltrating lymphocytes (TIL) can mediate durable complete responses in some patients with common epithelial cancers but does so infrequently. A better understanding of T-cell responses to neoantigens and tumor-related immune evasion mechanisms requires having the autologous tumor as a reagent. We investigated the ability of patient-derived tumor organoids (PDTO) to fulfill this need and evaluated their utility as a tool for selecting T-cells for adoptive cell therapy. PDTO established from metastases from patients with colorectal, breast, pancreatic, bile duct, esophageal, lung, and kidney cancers underwent whole exomic sequencing (WES), to define mutations. Organoids were then evaluated for recognition by autologous TIL or T-cells transduced with cloned T-cell receptors recognizing defined neoantigens. PDTO were also used to identify and clone TCRs from TIL targeting private neoantigens and define those tumor-specific targets. PDTO were successfully established in 38/47 attempts. 75% were available within 2 months, a timeframe compatible with screening TIL for clinical administration. These lines exhibited good genetic fidelity with their parental tumors, especially for mutations with higher clonality. Immunologic recognition assays demonstrated instances of HLA allelic loss not found by pan-HLA immunohistochemistry and in some cases WES of fresh tumor. PDTO could also be used to show differences between TCRs recognizing the same antigen and to find and clone TCRs recognizing private neoantigens. PDTO can detect tumor-specific defects blocking T-cell recognition and may have a role as a selection tool for TCRs and TIL used in adoptive cell therapy.

Abstract 365: Indotecan (LMP400), indimitecan (LMP776) and LMP744, a new class of non-camptothecin topoisomerase I inhibitors selective for schlafen11-positive and BRCA-deficient cells that synergize with olaparib

To overcome the limitations of topoisomerase inhibitors, irinotecan and topotecan (chemical instability, drug efflux substrates, short half-life, dose-limiting bone marrow and gastrointestinal toxicity), we have developed the indenoisoquinolines (LMP400, LMP776 and LMP744). To rationally select patients for phase 2 clinical trials, we have taken two approaches. First, we mined the cancer cell lines genomic databases with CellMinerCDB and found that a dominant response determinant to the indenoisoquinolines is Schlafen 11 (SLFN11), a recently identified executor of cells undergoing replication stress. We validated this finding in isogenic cell lines. Second, because the major lesions generated by the trapping of TOP1 are replication-induced DNA double-strand breaks that are repaired by homologous recombination (HR), we determined whether the indenoisoquinolines exhibit a “synthetic lethality” in cells presenting BRCA1, BRCA2 or PALB2 deficiency. In addition, we tested wether this selectivity could be enhanced when combined with the PARP inhibitor, olaparib. Survival and cell cycle alterations were tested after treatment with the indenoisoquinolines as single agents in isogenic DT40, DLD1 and OVCAR cell lines, with BRCA1, BRCA2 or PALB2 deficiencies, and organoids cultured from patient-derived xenografts with BRCA2 loss, as well as in combination with olaparib. We found that BRCA1-, BRCA2- and PALB2-deficient cells are 3 to 5 times more sensitive to the indenoisoquinolines compared to isogenic cell lines. Moreover, combination treatments showed high synergy between all three indenoisoquinolines and olaparib. We also established the synergy between LMP400 (Indotecan) and olaparib in orthotopic allograft models derived from genetically engineered mouse models for serous epithelial ovarian cancer harboring BRCA1 loss. Better efficacy was observed with the combination over single agent treatments of LMP400 or olaparib. Our results provide a rationale for Phase 2 indenoisoquinoline clinical trials with the indenoisoquinolines in HR-deficient cancers as single agents and in combination with PARP inhibitors, and for measuring Schlafen 11 (SLFN11) as a clinical response determinant.

Citation Format: Laetitia Marzi, Ludmila Szabova, Zoe Weaver Ohler, Shyam Sharan, Mike Beshiri, Junko Murai, Kathy Kelly, Yves Pommier. Indotecan (LMP400), indimitecan (LMP776) and LMP744, a new class of non-camptothecin topoisomerase I inhibitors selective for schlafen11-positive and BRCA-deficient cells that synergize with olaparib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 365.

Abstract LB-050: Interferon signaling confers resistance to androgen deprivation therapy in advanced prostate cancer

Loss of TP53 and PTEN activity are frequent genetic events in CRPC that are often associated with poorly differentiated, treatment resistant tumors. Using the Pten/Tp53-null mouse prostate cancer (PCa) model (Pb-Cre; Ptenfl/fl Tp53 fl/fl) and organoid cultures we previously have shown that a high proportion of luminal progenitors are intrinsically resistant to androgen deprivation therapy (ADT). To identify mechanisms of ADT resistance in luminal progenitors, we performed RNAseq analysis of luminal progenitor organoids derived from wild-type(WT) and Pten/Tp53-null mice. Pathway analysis identified key signaling alterations in luminal tumor organoids (AR signaling, lipid metabolism, protein secretion, inflammation etc.) that also have been described in FACS-purified human prostate luminal (CD49flo) fractions. Interestingly, we found no difference in transcriptional profiles from intact and previously castrated tumor organoids, suggesting that Pten/Tp53 null luminal progenitors are intrinsically resistance to ADT. Of note, we observed most significant enrichment of interferon(IFN) signaling in luminal progenitor tumor organoids relative to wild type luminal organoids. In other cancers and contrary to the anti-proliferative IFN signaling, expression of a subset of IFN genes contributes to genotoxic therapy resistance. This subset, referred to as IRDS (IFN-related DNA damage signature), includes a group of unphosphorylated STAT1 (U-STAT1)-driven genes that has a pro-survival function and promotes cancer cell intrinsic drug resistance. We hypothesize that the IRDS contributes to survival of PCa cells following ADT or genotoxic therapies. RT-PCR, immunofluorescence, and western blot analysis of luminal progenitor organoids showed higher U-STAT1 levels in tumor- than WT organoids, whereas pSTAT1 (Y701) was undetectable. Similarly, U-STAT1 was upregulated in Pten/Tp53-null tumor tissue relative to normal prostate. Further, for tumor organoids, ADT resulted in higher U-STAT1 levels. STAT1 depletion in tumor organoids decreased the number of progeny organoids in subsequent passages, suggesting a role in self-renewal for luminal tumor stem cells. Altogether, U-STAT1 regulated signaling has pro-survival function in Pten/Tp53-null advanced PCa. Several PDXs originating from metastatic PCa (LuCaPs 23.1, 96 and 141) express high levels of U-STAT1 dependent IFN signaling. STAT1 depletion significantly reduced self-renewing ability of these PDX derived organoids, consistent with mouse luminal tumor organoids. Interestingly, in LuCaP 141, STAT1 depletion synergized with ADT to inhibit growth ex vivo. These findings suggest that U-STAT1 dependent IFN signaling may contribute to castration resistance. We subsequently analyzed human PCa datasets to determine clinical correlates of IRDS. Analysis of the TCGA primary PCa cohort revealed IRDS as a prognostic marker for progression (n= 500, p<0.05). Further, high IRDS-expressing samples in the CRPC dataset were enriched for low AR signaling (n = 150, r= -0.33, p< 0.05). CRPC patients expressing the highest IRDS levels (n=30 of 150) showed enrichment for genes associated with stem cell features and therapy resistance. Overall, our findings suggest U-STAT1 dependent IRDS expression is correlated with poorly differentiated PCa and may contribute to intrinsic therapy resistance.

Citation Format: Supreet Agarwal, Kerry McGowen, Fathi Elloumi, Maggie Cam, Mike Beshiri, Keith Jansson, Eva Corey, Kathleen Kelly. Interferon signaling confers resistance to androgen deprivation therapy in advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-050.

Abstract 2896: STAT1 dependent interferon-related DNA damage resistance signature (IRDS) as a survival mechanism in castrate resistant prostate cancer (CRPC)

Using the organoid culture system and aggressive Pten/Tp53-null mouse model (GEMM), we have previously shown that the prostate cancer cell population harbors two classes of self-renewing luminal progenitors which are resistant to in vivo castration and to androgen receptor (AR) inhibitors (enzalutamide) ex vivo. Understanding signaling pathways governing intrinsic survival/self-renewal ability of luminal progenitors in castrate conditions can highlight pathways that play a role in acquired drug resistance. To identify mechanisms of castration resistance in luminal progenitors, we performed RNAseq analysis of luminal progenitor organoids derived from wild-type(WT) and Pten/Tp53-null mice (intact and castrated (two weeks), n=5; each). Gene enrichment analysis identified key signaling pathways altered in luminal tumor organoids (AR signaling, lipid metabolism, protein secretion, inflammation etc.) that have also been described for FACS-purified human prostate luminal (CD49flo) fraction. Interestingly, we found no difference in transcriptional profiles of intact and castrated tumor organoids, suggesting intrinsic survival ability of luminal progenitors upon castration. Of note, we observed most significant enrichment of STAT1-dependent IRDS in luminal progenitor tumor organoids relative to wild type luminal organoids. IRDS comprises of a subset of STAT1-driven genes that have been previously associated with survival of cancer cells and with breast cancer therapy resistance. Our analysis of human prostate cancer datasets revealed IRDS as a prognostic marker for progression in the TCGA primary prostate cancer cohort (p<0.05). Further, high IRDS-expressing CRPC samples (SU2C dataset) were enriched for low AR signaling (r= -0.33, p< 0.05). CRPC patients in IRDS-hi cohort showed enrichment for cancer stem cell phenotype and for genes associated with drug resistance, Consistent with the bioinformatics analysis real time PCR, immunofluorescence and western blot analysis of ex-vivo organoid cultures of castration-resistant Pten/Tp53-null tumor organoids showed higher protein expression of STAT1 and IRDS genes in luminal tumor organoids relative to luminal WT organoids. In vivo, castrated prostate tumors showed higher STAT1 levels than the intact tumors. Treatment with enzalutamide of luminal tumor organoids resulted in time dependent increase in STAT1 expression. STAT1 KD in tumor organoids decreased number of progeny organoids in subsequent generations suggesting either a direct or indirect effect upon self-renewal. Overall, our initial findings suggest STAT1 dependent signaling as a potential mechanism of androgen-independent survival in prostate cancer.

Citation Format: Supreet Agarwal, Kerry McGowen, Keith Jansson, Mike Beshiri, Fathi Elloumi, Maggie Cam, Kathy Kelly. STAT1 dependent interferon-related DNA damage resistance signature (IRDS) as a survival mechanism in castrate resistant prostate cancer (CRPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2896. doi:10.1158/1538-7445.AM2017-2896

Abstract LB-276: The identification and characterization of prostate adenocarcinoma tumor initiating cells

Primary prostate cancer is typically of luminal phenotype. However, little is known about the stem/progenitor properties of transformed luminal tumor cells as they fail to survive in culture. Using the organoid culture methodology, we show two distinct luminal progenitors in aggressive Pten/Tp53-null mouse model of prostate cancer. Not only did tumors contain previously described multipotent progenitors, but also a major population of committed luminal progenitors. The distinction between committed luminal and multipotent organoids was also evident in subcutaneous grafts as tumors of adenocarcinoma or multilineage histological phenotypes were observed, respectively. Moreover, using organoids we show that the self-renewing capacity of luminal-committed progenitors is a tumor-specific property, absent in benign luminal cells. Further, a significant fraction of luminal progenitors displayed resistance to in vivo castration as well as to androgen receptor inhibition ex vivo. Importantly, 3D organoid techniques have allowed us to relate our findings in humans as we can successfully grow similar luminal tumor populations from patient derived xenografts (PDXs) models of prostate cancer. In all, these data reveal two distinct luminal tumorigenic populations in mouse models of prostate cancer, providing insight into luminal tumor initiating cells in prostate cancer that can also influence response to therapy.

Citation Format: Supreet Agarwal, Paul Hynes, Ross Lake, Lei Fang, Heather Tillman, Mike Beshiri, Keith Jansson, Wouter Karthaus, Philip Iaquinta, Charles Sawyers, Kathleen Kelly. The identification and characterization of prostate adenocarcinoma tumor initiating cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-276.