Successful pancreatic ductal adenocarcinoma (PDAC) immunotherapy necessitates optimization and maintenance of activated effector T cells (Teff). We prospectively collected and applied multi-omic ...analyses to paired pre- and post-treatment PDAC specimens collected in a platform neoadjuvant study of granulocyte-macrophage colony-stimulating factor-secreting allogeneic PDAC vaccine (GVAX) vaccine ± nivolumab (anti-programmed cell death protein 1 PD-1) to uncover sensitivity and resistance mechanisms. We show that GVAX-induced tertiary lymphoid aggregates become immune-regulatory sites in response to GVAX + nivolumab. Higher densities of tumor-associated neutrophils (TANs) following GVAX + nivolumab portend poorer overall survival (OS). Increased T cells expressing CD137 associated with cytotoxic Teff signatures and correlated with increased OS. Bulk and single-cell RNA sequencing found that nivolumab alters CD4+ T cell chemotaxis signaling in association with CD11b+ neutrophil degranulation, and CD8+ T cell expression of CD137 was required for optimal T cell activation. These findings provide insights into PD-1-regulated immune pathways in PDAC that should inform more effective therapeutic combinations that include TAN regulators and T cell activators.
Display omitted
•Prospectively collected PDAC specimens from a neoadjuvant platform clinical trial•Identified sensitivity and resistance mechanisms to anti-PD-1 therapy in PDAC•Informed studies of additional immune-modulating agents in the ongoing platform trial•Generated hypotheses of reprogramed TME signals for combination immunotherapy strategies
Li et al. perform multi-omic analyses on pre- and post-treatment specimens from a pancreatic cancer neoadjuvant platform trial, and identify sensitivity and resistance mechanisms associated with anti-PD-1 combination therapy. Results associate tumor-associated neutrophils with poor outcomes but CD137+CD8+ T cells with better outcomes, suggesting treatment strategies for future interventions.
Full text
Available for:
GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by an immunosuppressive tumor microenvironment enriched with cancer-associated fibroblasts (CAF). This study used a ...convergence approach to identify tumor cell and CAF interactions through the integration of single-cell data from human tumors with human organoid coculture experiments. Analysis of a comprehensive atlas of PDAC single-cell RNA sequencing data indicated that CAF density is associated with increased inflammation and epithelial-mesenchymal transition (EMT) in epithelial cells. Transfer learning using transcriptional data from patient-derived organoid and CAF cocultures provided in silico validation of CAF induction of inflammatory and EMT epithelial cell states. Further experimental validation in cocultures demonstrated integrin beta 1 (ITGB1) and vascular endothelial factor A (VEGFA) interactions with neuropilin-1 mediating CAF-epithelial cell cross-talk. Together, this study introduces transfer learning from human single-cell data to organoid coculture analyses for experimental validation of discoveries of cell-cell cross-talk and identifies fibroblast-mediated regulation of EMT and inflammation.
Adaptation of transfer learning to relate human single-cell RNA sequencing data to organoid-CAF cocultures facilitates discovery of human pancreatic cancer intercellular interactions and uncovers cross-talk between CAFs and tumor cells through VEGFA and ITGB1.
Abstract Background The tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDA) is characterized by a paucity of cytotoxic tumor-infiltrating lymphocytes, an abundance of ...immune-suppressive cell populations, and a general resistance to immune checkpoint inhibitor (ICI) therapy. In preclinical models of PDA, the HDAC inhibitor entinostat modulated the transcriptional programming of myeloid cells, reducing their capacity for immunosuppression and sensitizing tumors to ICI therapy. Methods We conducted a single-center, open-label, Simon two-stage, phase II study of entinostat in combination with the PD1 inhibitor nivolumab in patients with advanced PDA. Patients received oral entinostat 5 mg once a week. After a 14-day lead-in with entinostat monotherapy, patients concurrently receive entinostat 5 mg orally once a week plus nivolumab 240 mg intravenously every 2 weeks. After 4 months, therapy was continued with entinostat 5 mg weekly plus nivolumab at a dose of 480 mg fixed dose every 4 weeks until the time of progression or unacceptable toxicities. The primary endpoint was the objective response rate by Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Peripheral immune profiles at baseline and on treatment were assessed by high-dimensional mass cytometry by time of flight (CyTOF) and by Luminex of chemokines in the plasma, and changes in the TME were performed on paired baseline and on treatment biopsies by multiplexed immunohistochemistry (mIHC), image cytometry-based quantification, and bulk RNA-seq analysis. Results From November 2017 to November 2020, 27 evaluable patients were enrolled. Three patients had a partial response (PR) by RECIST v1.1 criteria (objective response rate (ORR)) of 11%, 95% CI, 0.024-0.292), with a median duration of response of 10.2 months. Grade ≥3 treatment-related adverse events (TRAEs) were observed in 19 (63%) patients. The most common grade ≥3 TRAEs were decreased lymphocyte count, anemia hypoalbuminemia, and hyponatremia. Dendritic cell (DC) activation, maturation, migration, antigen processing, and presentation were increased in the periphery after entinostat treatment, consistent with HDAC inhibitor mediated myeloid reprogramming. Gene expression analysis of paired baseline and on treatment tumors demonstrated an enrichment in inflammatory response signaling pathways with combination treatment. Conclusions Entinostat and nivolumab demonstrated durable radiological responses in a subset of patients with PDA. Paired tissue and peripheral analysis showed immunomodulation of myeloid cell populations, consistent with the preclinical hypothesis supporting the trial. This study creates a roadmap for this strategy with future combinatorial therapeutic approaches to enhance the clinical benefit in PDA patients further. Citation Format: Marina Baretti, Ludmila Danilova, Jennifer N. Durham, Courtney B. Betts, Leslie Cope, Dimitrios N. Sidiropoulos, Joseph A. Tandurella, Soren Charmsaz, Nicole Gross, Alexei Hernandez, Won J. HO, Chris Thoburn, Rosalind Walker, James Leatherman Leatherman, Sarah Mitchell, Brian Christmas, Daria A. Gaykalova, Srinivasan Yegnasubramanian, Elana J. Fertig, Lisa M. Coussens, Mark Yarchoan, Elizabeth Jaffee, Nilofer S. Azad. Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT016.
Triple-negative breast cancer (TNBC) is an aggressive subtype associated with early metastatic recurrence and worse patient outcomes. TNBC tumors express molecular markers of the ...epithelial-mesenchymal transition (EMT), but its requirement during spontaneous TNBC metastasis in vivo remains incompletely understood. We demonstrated that spontaneous TNBC tumors from a genetically engineered mouse model (GEMM), multiple patient-derived xenografts, and archival patient samples exhibited large populations in vivo of hybrid E/M cells that lead invasion ex vivo while expressing both epithelial and mesenchymal characteristics. The mesenchymal marker vimentin promoted invasion and repressed metastatic outgrowth. We next tested the requirement for five EMT transcription factors and observed distinct patterns of utilization during invasion and colony formation. These differences suggested a sequential activation of multiple EMT molecular programs during the metastatic cascade. Consistent with this model, our longitudinal single-cell RNA analysis detected three different EMT-related molecular patterns. We observed cancer cells progressing from epithelial to hybrid E/M and strongly mesenchymal patterns during invasion and from epithelial to a hybrid E/M pattern during colony formation. We next investigated the relative epithelial versus mesenchymal state of cancer cells in both GEMM and patient metastases. In both contexts, we observed heterogeneity between and within metastases in the same individual. We observed a complex spectrum of epithelial, hybrid E/M, and mesenchymal cell states within metastases, suggesting that there are multiple successful molecular strategies for distant organ colonization. Together, our results demonstrate an important and complex role for EMT programs during TNBC metastasis.
Abstract
Introduction: Pancreatic ductal adenocarcinomas (PDACs) are immunogenically “cold” tumors that lack effector T cell infiltration associated with immune checkpoint inhibitor (ICI) ...responsiveness. Neoadjuvant immunotherapy clinical trials facilitate understanding of the complexities of combination treatment strategies on immunosuppressive mechanisms. Our recent multi-omics analysis of a neoadjuvant trial comparing the GVAX vaccine alone or with nivolumab and supporting preclinical data uncovered crosstalk between CD8+CD137+ T cells and neutrophils as an axis for therapeutic intervention. These studies have formed the foundation for the addition of the CD137 agonist, urelumab, to our combination regimen to improve T cell activation in PDACs.
Methods: Patients were enrolled on NCT02451982 and initiated treatment 2 weeks prior to surgical resection. We compared specimens from 3 treatment arms for downstream analysis: Arm A: an allogeneic whole cell vaccine, GVAX (n=7); Arm B: GVAX and nivolumab (n=4); Arm C: GVAX, nivolumab, and urelumab (n=4). Samples underwent dissociation and Percoll separation to enrich for immune cells, followed by single-cell RNA- and TCR-seq using 10X Genomics. Computational analysis was performed for cell type classification with Seurat, differential expression with DESeq2 of pseudobulk data, cell-cell communication with Domino, and TCR-seq analysis with scRepertoire.
Results: Single-cell RNA-seq analysis identified changes in immune cell proportions and immune cell states across treatment arms. Alignment of scTCR-seq to RNA data showed greater CD8+ T cell expansion following triple agent therapy. Gene set enrichment identified changes in CD8+ T cell, tumor associated macrophage (TAM), and B cell responses to cytokine signaling, locomotion, amino acid metabolism, and cell adhesion pathways in Arm C. Domino analysis demonstrated increases in the naïve T cell signal CCR7 in Arm A and integrin ligand signal ICAM1 in Arm C between the CD8+ T cells and other cell types present in PDACs. CCR7 expression was significantly downregulated in CD8+ T cells in Arm C whereas CCL5, a T cell agonist cytokine, and LCP2, a TCR signaling activator and T cell receptor which is also required for integrin signaling, were significantly upregulated in CD8+ T cells in Arm C. The increased integrin ligand signaling via ICAM1 and LCP2 in Arm C is also associated with changes in CD8+ T cell motility observed from the differential expression analysis.
Conclusions: Analysis of combination GVAX, PD-1 inhibition and CD137 agonist therapy demonstrated changes in multiple immune cell proportions and their functional pathways. These data provide new evidence that PDACs can become T cell rich and respond to combination immunotherapies.
Citation Format: Joseph A. Tandurella, Jacob T. Mitchell, Janelle M. Montagne, Eric Christenson, Qingfeng Zhu, Ludmilla V. Danilova, Alexander V. Favorov, Won J. Ho, Luciane T. Kagohara, Melanie Loth, Su Jin Lim, Rui Zheng, Jessica Gai, Sarah Mitchell, Dimitrios N. Sidiropoulos, Wenpin Hou, Yao Xu, Hao Wang, Jacquelyn W. Zimmerman, Srinivasan Yegnasubramanian, Robert Anders, Elizabeth M. Jaffee, Lei Zheng, Elana J. Fertig. Single-cell RNA and TCR sequencing of tumor infiltrating lymphocytes identifies changes in pancreatic ductal adenocarcinomas following neoadjuvant treatment with combined anti-PD-1 blocking and anti-CD137 agonist therapy abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3241.
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer-related deaths. Despite the advent of immune checkpoint inhibition (ICI) that has markedly changed the treatment ...landscape for select tumors with respect to both outcomes and tolerability, PDAC remains unresponsive to such an approach. One feature of the PDAC tumor microenvironment (TME) that remains poorly understood is the interaction between cancer-associated fibroblasts (CAFs) and immune and tumor cells. Unique subsets of CAFs have been identified, including antigen-presenting CAFs (apCAFs) which are defined by expression of MHC-II and can activate CD4 T cells in genetically engineered mouse models of PDAC. apCAFs are rarely found in human PDAC; in a human PDAC atlas consisting of six published human single cell RNA-sequencing (scRNA-seq) datasets, we identified 370 apCAFs out of 8736 total CAFs, the majority of which were found in one dataset. Here, we have orthotopically implanted cell lines derived from the autochthonous KPC murine model of PDAC which mimics the stromal components of human disease to further study the influence of apCAFs on the anti-tumor response. We have found that although the overall CAF population is equivalent between tumors, apCAFs are present primarily in tumors derived from KPC cell lines that display ICI sensitivity. apCAFs sorted from these tumors and pulsed with OVA peptides upregulated CD25 and CD69 expression on naïve OT-II CD4 T cells, confirming that apCAFs in our system can present via MHC-II. Furthermore, these apCAFs increased CD4 activation markers upon ex-vivo coculture with dissociated KPC tumors. We therefore hypothesize that apCAFs are required for the ICI-mediated anti-tumor effect and do so via modulation of CD4 T cell responses. Although a small proportion of the total compartment, the apCAF subset may be enhanced in number and function by CAF-targeted modulators to synergize with ICI to affect the antitumor response, which could provide a solution to the currently unmet need for new and more effective treatments for PDAC patients.
Citation Format: Saumya Maru, Kathryn Howe, Lalitya Andaloori, James Leatherman, Joseph Tandurella, Edward J. Pearce, Elizabeth M. Jaffee. Antigen-presenting cancer-associated fibroblasts are found in immunotherapy-sensitive murine models of pancreatic ductal adenocarcinoma abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B034.
Abstract
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a classically heterogeneous tumor for which tumor cells comprise less than 40% of the total tumor mass. To better understand ...mechanisms of intercellular interactions driving tumor response or resistance to chemotherapy, it is crucial to account for the complex tumor microenvironment (TME). Cancer associated fibroblasts (CAFs) have been implicated as key drivers supporting mechanisms that both promote and restrain tumor growth. Using our model system that investigates interactions between CAFs and cancer cells, we show a novel intercellular interaction through VEGF signaling that drives proliferation.
Methods: We interrogate intracellular crosstalk in the PDAC TME using a novel 3-dimensional (3D), patient-matched coculture system of patient-derived organoids (PDO) and CAFs, obtained from patients undergoing surgical resection. Molecular characterization is performed by profiling with a 1200 analyte multiplex ELISA screen, multiparameter flow cytometry, bulk RNA sequencing of CAF and PDO cocultures, imaging mass cytometry (IMC) on patient samples, and qPCR.
Results: Secretome profiling of 7 patient-derived CAF lines demonstrated patient-specific heterogeneity in proteins such as: FGF-12, FGF3, and CD79a. Common CAF-derived signaling proteins with the potential to regulate intercellular crosstalk that were seen across all samples include CRP, IL-6R, R-Spondin and others. To better understand how factors change with intercellular interactions, we set up direct CAF-PDO cocultures over 4 days to identify global transcriptional changes using bulk RNAseq. Phenotypically, coculture drives gene expression changes in both PDO subtype (basal vs classical) and CAF subtype (prevalence of iCAFs vs myCAFs). We used these transcriptome data to identify pathways modulated by CAF-PDO crosstalk. Profiling coculture supernatant, we identified upregulation in VEGF secretion. In tandem, when we investigate cellular surface marker changes, we see upregulation of VEGFR2 on the surface of CAFs by flow cytometry. This interaction is accompanied by an increase in PDO proliferation seen in the coculture conditions. Ongoing experiments aim to investigate the impact of this relationship spatially using matched patient tissue.
Conclusions: Interactions between cancer cells and CAFs compound the complexity of the biology of the TME and contribute to poor patient outcomes; therefore, we have put forth a model that better represents these interactions through patient matched PDO - CAF cocultures. Using this model, we demonstrate a novel interaction through VEGF that enhances tumor cell proliferation. We introduce a targeted approach to investigating the complex biology of the TME to inform the mechanisms driving cancer biology in individual patients that can also be used to develop novel therapeutic targets.
Citation Format: Samantha Guinn, Joseph Tandurella, Jignasha Patel, Richard Burkhart, Jacquelyn Zimmerman, Elizabeth Jaffee. Cancer associated fibroblast crosstalk through VEGF increases tumor cell proliferation in human pancreatic ductal adenocarcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5851.
Abstract
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a classically heterogeneous tumor for which tumor cells comprise less than 40% of the total tumor mass. To better understand ...mechanisms of intercellular interactions driving tumor response or resistance to chemotherapy, it is crucial to account for the complex tumor microenvironment (TME). Specifically, cancer associated fibroblasts (CAFs) have been implicated as both a tumor promoting and tumor restraining entity through disease progression and have therefore been a focus of our evolving model system. Methods: Our group created a 3-dimensional (3D), matched coculture system of patient-derived organoids (PDO), CAFs, and immune cells obtained from patients undergoing surgical resection. PDOs grown in 3D preserves the nascent tumor architecture and better replicates the disease in vitro than traditional 2D cell lines. The fully patient-matched coculture model of human PDAC allows for mechanistic interrogation into the PDAC TME by utilizing multiparameter flow cytometry, cellular sorting, and qPCR. Additionally, pharmacotyping experiments using a 5-drug regimen were used to assess chemotherapeutic resistance allowing for targeted questions exploring patient response to standard of care chemotherapy. Results: Using a combination of direct CAF-PDO coculture and PDO with CAF-conditioned media, we examined the direct (coculture) and indirect (conditioned media) impact of CAFs on PDOs. Using flow cytometry, we showed that CAF-conditioned human complete organoid media drives increased proliferation of PDOs when compared to PDOs grown in standard media. This effect was likely due to factors that are secreted from CAFs having a synergistic effect with compounds in the human complete organoid media, as this phenotype was not replicated in traditional serum free conditioned media. In direct coculture experiments of PDOs and CAFs, PDO numbers increased over time from day 2 to day 7 when compared to monoculture of PDOs, likely due to CAF presence. Lastly, to explore how CAFs may alter chemotherapeutic efficacy, PDOs were cocultured with CAFs and assessed for chemotherapeutic resistance. Pharmacotyping results showed that PDOs sorted from the PDO-CAF coculture exhibited a change in IC50 value in comparison to those PDOs that were not cocultured with CAFs. Conclusions: Here we put forth a model of PDO and CAF coculture and demonstrated its application for examining the impact of CAFs on PDAC proliferation and chemotherapeutic response. These data demonstrate the feasibility of establishing a patient-derived matched coculture model and provide the backbone for expanding this model to include representative immune cells.
Citation Format: Samantha Guinn, Joseph Tandurella, Jacquelyn Zimmerman, Richard Burkhart, Elizabeth M. Jaffee. Cancer associated fibroblasts are regulators of the tumor microenvironment in human pancreatic ductal adenocarcinoma abstract. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C036.
Abstract Introduction: Cancer associated fibroblasts (CAF) drive a complex tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) through incompletely understood interactions. Two ...major CAF subtypes, myofibroblastic (myCAF) and inflammatory (iCAF), dominate the tumor landscape and have been defined by gene expression profiles. There is significant plasticity between subtypes and alterations in CAF behavior likely drive changes in tumorigenicity and immune evasion. Additionally, PDAC tumor cells usually present with a predominant classical or basal phenotype that is associated with clinical outcomes. We hypothesized that CAF phenotype impacts tumor cell gene expression and alters the clinically-relevant tumor subtyping. Methods: We interrogated cellular crosstalk in the PDAC TME using a novel three-dimensional, patient-matched coculture system of patient-derived organoids (PDO) and CAFs, established from 12 patients undergoing surgical resection. Molecular characterization included bulk RNA sequencing, proteome profiling (107 factor), flow cytometry, multiplex RNA Scope, imaging mass cytometry (IMC), and RT-qPCR. Results: PDO gene expression analysis from bulk RNAseq demonstrated CAF coculture induced phenotypic shifts in the Moffitt subtype from a classical to a basal phenotype. Further, CAF coculture enhanced epithelial to mesenchymal transition (EMT) across all patients, even those with a baseline basal phenotype. We hypothesized this could be due to both cell-cell crosstalk and secreted factors. We therefore treated PDO with CAF-conditioned media (CM) and demonstrated that CM is sufficient to drive the observed classical-to-basal shift by RT-qPCR. Secretome analysis of CM derived from 3 CAF lines identified HGF, FGF19, and IL-8 as factors contributing to this transcriptional change. Next, we used spatial - omics (transcriptomics and proteomics) to examine the validity of these findings in source patient tissue. Using RNA Scope, we discovered distinct tumor neighborhoods expressing basal mRNAs KRT17 and KRT6a surrounded by CAFs compared to those expressing classical genes TFF1 and GATA6. We then used IMC to further explore CAF subtypes in patient tumors and found FAP+ myCAF regions corresponded to basal tumor regions, while CXCL12+ iCAFs were found in classical regions. Conclusions: PDAC tumor biology is likely driven by interactions between cancer cells and CAFs. Potential mediators of these interactions include both cell-cell contact and secreted factors. We introduce a novel approach combining in vitro coculture with tissue-based assays, demonstrating that modern culture techniques preserve cell type heterogeneity and plasticity. Together, these data demonstrate that a CAF-rich TME drives tumor cell plasticity not only towards EMT but also a more basal disease phenotype. Citation Format: Samantha Guinn, Brayan Perez, Jignasha Patel, Jae Lee, Daniel Zabransky, Won Ho, Elana J. Fertig, Emma Kartalia, Joseph Tandurella, Richard Burkhart, Jacquelyn W. Zimmerman, Elizabeth Jaffee. Cancer associated fibroblast - tumor cell crosstalk enhances epithelial to mesenchymal transition and promotes a classical to basal switch in human pancreatic ductal adenocarcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1577.
Abstract
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous tumor comprised of epithelial tumor, endothelial, immune, and importantly, cancer associated fibroblasts (CAFs) ...cells. CAFs drive a complex tumor microenvironment (TME) through mechanisms of intratumoral interactions that are incompletely understood. It’s crucial to account for the complex role of CAFs in modern ex-vivo tumor systems as regulators of both promoting and restraining tumor growth, providing growth factor support, reprogramming immune cells, and altering the TME. Using our patient-derived organoid (PDO) and CAF coculture, we identify novel intercellular interactions between CAF and PDO that promote tumor cell proliferation, impair response to therapy, and alter transcriptional phenotype. Methods: We interrogate mechanisms of cellular crosstalk in the PDAC TME using a novel three-dimensional, patient-matched coculture of PDO and CAFs, established from patients undergoing surgical resection. Molecular characterization included bulk RNA sequencing-based transcriptomics, comprehensive proteome profiling for 107 secreted proteins with curated validation by ELISA, cellular phenotyping by multiparameter flow cytometry, and qPCR for validation of curated gene lists. Results: Bulk RNAseq of FACS sorted CAF – PDO cocultures from 12 patients demonstrate Moffitt classification transcriptional changes in 42% of samples compared to PDO monoculture, suggesting CAFs drive basal tumor phenotype. To investigate protein level changes, we compared the secreted proteome of PDOs that transitioned to a basal phenotype after coculture to PDOs that did not undergo transition. Proteome analysis from coculture supernatant revealed that HGF, GDF15, TFF3, and VEGF-A are significantly increased in samples that undergo classical to basal transition. Pathway analysis comparing transcriptional data from classical and basal PDOs identifies significant upregulation of pathways associated with epithelial-to-mesenchymal transition (EMT), inflammation, and NF-kB in basal PDOs. Further, coculture leads to decreased expression of E-cadherin and increased expression of N-cadherin on the surface of PDOs while CAF markers remain unchanged. This interaction is accompanied by an increase in PDO proliferation in coculture, suggesting that CAF presence enhances tumorgenicity and changes epithelial tumor cell fitness. Ongoing experiments will investigate tumor cell-CAF interactions spatially using matched patient tissue to complement the in vitro coculture system. Conclusions: Interactions between cancer cells and CAFs drive overall tumor biology via a complex TME and contribute to poor PDAC patient outcomes. Using our patient matched PDO - CAF coculture, we demonstrate that a CAF competent TME drives PDO plasticity towards a more basal transcriptional phenotype and enhanced EMT. We introduce an elegant approach combining in vitro coculture experiments and high dimensional assays to investigate the complex biology of the TME and inform the mechanisms driving cancer biology in individual patients with PDAC.
Citation Format: Samantha Guinn, Joseph Tandurella, Jae W. Lee, Daniel J. Zabransky, Mili Ramani, Jignasha Patel, Elana J. Fertig, Elizabeth M. Jaffee, Richard A. Burkhart, Jacquelyn W. Zimmerman. Cancer associated fibroblasts drive transcriptional changes in tumor cells from classical to basal phenotype and promote epithelial-to-mesenchymal transition in human pancreatic ductal adenocarcinoma abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A042.
