Fibroblasts in the Aged Pancreas Drive Pancreatic Cancer Progression

Pancreatic cancer is more prevalent in older individuals and often carries a poorer prognosis for them. The relationship between the microenvironment and pancreatic cancer is multifactorial, and age-related changes in nonmalignant cells in the tumor microenvironment may play a key role in promoting cancer aggressiveness. Because fibroblasts have profound impacts on pancreatic cancer progression, we investigated whether age-related changes in pancreatic fibroblasts influence cancer growth and metastasis. Proteomics analysis revealed that aged fibroblasts secrete different factors than young fibroblasts, including increased growth/differentiation factor 15 (GDF-15). Treating young mice with GDF-15 enhanced tumor growth, whereas aged GDF-15 knockout mice showed reduced tumor growth. GDF-15 activated AKT, rendering tumors sensitive to AKT inhibition in an aged but not young microenvironment. These data provide evidence for how aging alters pancreatic fibroblasts and promotes tumor progression, providing potential therapeutic targets and avenues for studying pancreatic cancer while accounting for the effects of aging.

SIGNIFICANCE

Aged pancreatic fibroblasts secrete GDF-15 and activate AKT signaling to promote pancreatic cancer growth, highlighting the critical role of aging-mediated changes in the pancreatic cancer microenvironment in driving tumor progression. See related commentary by Isaacson et al., p. 1185.

Transfer learning reveals cancer-associated fibroblasts are associated with epithelial-mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by an immunosuppressive tumor microenvironment enriched with cancer associated fibroblasts (CAFs). This study utilized a convergence approach to identify tumor cell and CAF interactions through the integration of single-cell data from human tumors with human organoid co-culture experiments. Analysis of a comprehensive atlas of PDAC single-cell RNA sequencing (scRNA-seq) 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 co-cultures provided in silico validation of CAF induction of inflammatory and EMT epithelial cell states. Further experimental validation in co-cultures demonstrated integrin beta 1 (ITGB1) and vascular endothelial factor A (VEGF-A) interactions with neuropilin-1 (NRP1) mediating CAF-epithelial cell crosstalk. Together, this study introduces transfer learning from human single-cell data to organoid co-culture analyses for experimental validation of discoveries of cell-cell crosstalk and identifies fibroblast-mediated regulation of EMT and inflammation.

Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial

Programmed cell death protein 1 (PD-1) inhibitors have modest efficacy as a monotherapy in hepatocellular carcinoma (HCC). A personalized therapeutic cancer vaccine (PTCV) may enhance responses to PD-1 inhibitors through the induction of tumor-specific immunity. We present results from a single-arm, open-label, phase 1/2 study of a DNA plasmid PTCV (GNOS-PV02) encoding up to 40 neoantigens coadministered with plasmid-encoded interleukin-12 plus pembrolizumab in patients with advanced HCC previously treated with a multityrosine kinase inhibitor. Safety and immunogenicity were assessed as primary endpoints, and treatment efficacy and feasibility were evaluated as secondary endpoints. The most common treatment-related adverse events were injection-site reactions, observed in 15 of 36 (41.6%) patients. No dose-limiting toxicities or treatment-related grade ≥3 events were observed. The objective response rate (modified intention-to-treat) per Response Evaluation Criteria in Solid Tumors 1.1 was 30.6% (11 of 36 patients), with 8.3% (3 of 36) of patients achieving a complete response. Clinical responses were associated with the number of neoantigens encoded in the vaccine. Neoantigen-specific T cell responses were confirmed in 19 of 22 (86.4%) evaluable patients by enzyme-linked immunosorbent spot assays. Multiparametric cellular profiling revealed active, proliferative and cytolytic vaccine-specific CD4+ and CD8+ effector T cells. T cell receptor β-chain (TCRβ) bulk sequencing results demonstrated vaccination-enriched T cell clone expansion and tumor infiltration. Single-cell analysis revealed posttreatment T cell clonal expansion of cytotoxic T cell phenotypes. TCR complementarity-determining region cloning of expanded T cell clones in the tumors following vaccination confirmed reactivity against vaccine-encoded neoantigens. Our results support the PTCV's mechanism of action based on the induction of antitumor T cells and show that a PTCV plus pembrolizumab has clinical activity in advanced HCC. ClinicalTrials.gov identifier: NCT04251117 .

An orientation to the US National Cancer plan for the research community

The US National Cancer Act of 1971 designated the director of the National Cancer Institute as responsible for coordinating federal agencies and nonfederal organizations to make progress against cancer. As part of her role, the immediate past director of the National Cancer Institute (MMB) led the development of a National Cancer Plan that was formally released on April 3, 2023. The plan includes 8 aspirational goals "to achieve a society where every person with cancer lives a full and active life and to prevent most cancers so that few people need to face this diagnosis." Research findings provide a foundation for each goal, and research gaps are included in the strategies for meeting each goal. The President's Cancer Panel, also created by the National Cancer Act, conducted an initial assessment of progress toward the plan goals by hearing from 12 organizations at a virtual public meeting on September 7, 2023. The purpose of this commentary is to orient the scientific community to the plan and call attention to related knowledge gaps that could benefit from research.

Mesothelin CAR T-cells secreting anti-FAP/anti-CD3 molecules efficiently target pancreatic adenocarcinoma and its stroma

PURPOSE

Targeting solid tumors with CAR T-cells remains challenging due to heterogenous target antigen expression, antigen escape, and the immunosuppressive tumor microenvironment (TME). Pancreatic cancer is characterized by a thick stroma generated by cancer-associated fibroblasts (CAFs), which may contribute to the limited efficacy of mesothelin-directed CAR T-cells in early-phase clinical trials. To provide a more favorable TME for CAR T-cells to target pancreatic ductal adenocarcinoma (PDAC), we generated T-cells with an anti-mesothelin CAR and a secreted T-cell-engaging molecule (TEAM) that targets CAFs through fibroblast activation protein (FAP) and engages T-cells through CD3 (termed mesoFAP CAR-TEAM cells).

EXPERIMENTAL DESIGN

Using a suite of in vitro, in vivo, and ex vivo patient-derived models containing cancer cells and CAFs, we examined the ability of mesoFAP CAR-TEAM cells to target PDAC cells and CAFs within the TME. We developed and used patient-derived ex vivo models including patient-derived organoids with patient-matched CAFs and patient-derived organotypic tumor spheroids (PDOTS).

RESULTS

We demonstrated specific and significant binding of the TEAM to its respective antigens (CD3 and FAP) when released from mesothelin-targeting CAR T cells, leading to T cell activation and cytotoxicity of the target cell. MesoFAP CAR-TEAM cells were superior in eliminating PDAC and CAFs compared to T cells engineered to target either antigen alone in our ex-vivo patient-derived models and in mouse models of PDAC with primary or metastatic liver tumors.

CONCLUSIONS

CAR-TEAM cells enable modification of tumor stroma, leading to increased elimination of PDAC tumors. This approach represents a promising treatment option for pancreatic cancer.

Entinostat, nivolumab and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial

We report the results of 24 women, 50% (N = 12) with hormone receptor-positive breast cancer and 50% (N = 12) with advanced triple-negative breast cancer, treated with entinostat + nivolumab + ipilimumab from the dose escalation (N = 6) and expansion cohort (N = 18) of ETCTN-9844 ( NCT02453620 ). The primary endpoint was safety. Secondary endpoints were overall response rate, clinical benefit rate, progression-free survival and change in tumor CD8:FoxP3 ratio. There were no dose-limiting toxicities. Among evaluable participants (N = 20), the overall response rate was 25% (N = 5), with 40% (N = 4) in triple-negative breast cancer and 10% (N = 1) in hormone receptor-positive breast cancer. The clinical benefit rate was 40% (N = 8), and progression-free survival at 6 months was 50%. Exploratory analyses revealed that changes in myeloid cells may contribute to responses; however, no correlation was noted between changes in CD8:FoxP3 ratio, PD-L1 status and tumor mutational burden and response. These findings support further investigation of this treatment in a phase II trial.

Neoadjuvant radioimmunotherapy in pancreatic cancer enhances effector T cell infiltration and shortens their distances to tumor cells

Radiotherapy is hypothesized to have an immune-modulating effect on the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) to sensitize it to anti-PD-1 antibody (a-PD-1) treatment. We collected paired pre- and posttreatment specimens from a clinical trial evaluating combination treatment with GVAX vaccine, a-PD-1, and stereotactic body radiation (SBRT) following chemotherapy for locally advanced PDACs (LAPC). With resected PDACs following different neoadjuvant therapies as comparisons, effector cells in PDACs were found to skew toward a more exhausted status in LAPCs following chemotherapy. The combination of GVAX/a-PD-1/SBRT drives TME to favor antitumor immune response including increased densities of GZMB+CD8+ T cells, TH1, and TH17, which are associated with longer survival, however increases immunosuppressive M2-like tumor-associated macrophages (TAMs). Adding SBRT to GVAX/a-PD-1 shortens the distances from PD-1+CD8+ T cells to tumor cells and to PD-L1+ myeloid cells, which portends prolonged survival. These findings have guided the design of next radioimmunotherapy studies by targeting M2-like TAM in PDACs.

Mimicking the breast metastatic microenvironment: characterization of a novel syngeneic model of HER2+ breast cancer

Preclinical murine models in which primary tumors spontaneously metastasize to distant organs are valuable tools to study metastatic progression and novel cancer treatment combinations. Here, we characterize a novel syngeneic murine breast tumor cell line, NT2.5-lung metastasis (-LM), that provides a model of spontaneously metastatic neu-expressing breast cancer with quicker onset of widespread metastases after orthotopic mammary implantation in immune-competent NeuN mice. Within one week of orthotopic implantation of NT2.5-LM in NeuN mice, distant metastases can be observed in the lungs. Within four weeks, metastases are also observed in the bones, spleen, colon, and liver. Metastases are rapidly growing, proliferative, and responsive to HER2-directed therapy. We demonstrate altered expression of markers of epithelial-to-mesenchymal transition (EMT) and enrichment in EMT-regulating pathways, suggestive of their enhanced metastatic potential. The new NT2.5-LM model provides more rapid and spontaneous development of widespread metastases. Besides investigating mechanisms of metastatic progression, this new model may be used for the rationalized development of novel therapeutic interventions and assessment of therapeutic responses targeting distant visceral metastases.

Systems immunology spanning tumors, lymph nodes, and periphery

The immune system defines a complex network of tissues and cell types that orchestrate responses across the body in a dynamic manner. The local and systemic interactions between immune and cancer cells contribute to disease progression. Lymphocytes are activated in lymph nodes, traffic through the periphery, and impact cancer progression through their interactions with tumor cells. As a result, therapeutic response and resistance are mediated across tissues, and a comprehensive understanding of lymphocyte dynamics requires a systems-level approach. In this review, we highlight experimental and computational methods that can leverage the study of leukocyte trafficking through an immunomics lens and reveal how adaptive immunity shapes cancer.

CD4 T cell-activating neoantigens enhance personalized cancer vaccine efficacy

Personalized cancer vaccines aim to activate and expand cytotoxic antitumor CD8+ T cells to recognize and kill tumor cells. However, the role of CD4+ T cell activation in the clinical benefit of these vaccines is not well defined. We previously established a personalized neoantigen vaccine (PancVAX) for the pancreatic cancer cell line Panc02, which activates tumor-specific CD8+ T cells but required combinatorial checkpoint modulators to achieve therapeutic efficacy. To determine the effects of neoantigen-specific CD4+ T cell activation, we generated a vaccine (PancVAX2) targeting both major histocompatibility complex class I- (MHCI-) and MHCII-specific neoantigens. Tumor-bearing mice vaccinated with PancVAX2 had significantly improved control of tumor growth and long-term survival benefit without concurrent administration of checkpoint inhibitors. PancVAX2 significantly enhanced priming and recruitment of neoantigen-specific CD8+ T cells into the tumor with lower PD-1 expression after reactivation compared with the CD8+ vaccine alone. Vaccine-induced neoantigen-specific Th1 CD4+ T cells in the tumor were associated with decreased Tregs. Consistent with this, PancVAX2 was associated with more proimmune myeloid-derived suppressor cells and M1-like macrophages in the tumor, demonstrating a less immunosuppressive tumor microenvironment. This study demonstrates the biological importance of prioritizing and including CD4+ T cell-specific neoantigens for personalized cancer vaccine modalities.

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user's desired dataset can vary from hours to days depending on factors such as dataset size or input parameters.

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells' characteristics and regulatory programs, forecasting their evolution ultimately requires mathematical modeling. We develop a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This allows us to systematically integrate biological knowledge and multi-omics data to make them computable. We can then perform virtual "thought experiments" that challenge and extend our understanding of multicellular systems, and ultimately generate new testable hypotheses. In this paper, we motivate and describe the grammar, provide a reference implementation, and demonstrate its potential through a series of examples in tumor biology and immunotherapy. Altogether, this approach provides a bridge between biological, clinical, and systems biology researchers for mathematical modeling of biological systems at scale, allowing the community to extrapolate from single-cell characterization to emergent multicellular behavior.

Tumor- and Nerve-Derived Axon Guidance Molecule Promotes Pancreatic Ductal Adenocarcinoma Progression and Metastasis through Macrophage Reprogramming

Axon guidance molecules were found to be the gene family most frequently altered in pancreatic ductal adenocarcinoma (PDA) through mutations and copy number changes. However, the exact molecular mechanism regarding PDA development remained unclear. Using genetically engineered mouse models to examine one of the axon guidance molecules, semaphorin 3D (SEMA3D), we found a dual role for tumor-derived SEMA3D in malignant transformation of pancreatic epithelial cells and a role for nerve-derived SEMA3D in PDA development. This was demonstrated by the pancreatic-specific knockout of the SEMA3D gene from the KRAS G12D and TP53 R 172 H mutation knock-in, PDX1-Cre (KPC) mouse model which demonstrated a delayed tumor initiation and growth comparing to the original KPC mouse model. Our results showed that SEMA3D knockout skews the macrophages in the pancreas away from M2 polarization, providing a potential mechanistic role of tumor-derived SEMA3D in PDA development. The KPC mice with the SEMA3D knockout remained metastasis-free, however, died from primary tumor growth. We then tested the hypothesis that a potential compensation mechanism could result from SEMA3D which is naturally expressed by the intratumoral nerves. Our study further revealed that nerve-derived SEMA3D does not reprogram macrophages directly, but reprograms macrophages indirectly through ARF6 signaling and lactate production in PDA tumor cells. SEMA3D increases tumor-secreted lactate which is sensed by GPCR132 on macrophages and subsequently stimulates pro-tumorigenic M2 polarization in vivo. Tumor intrinsic- and extrinsic-SEMA3D induced ARF6 signaling through its receptor Plexin D1 in a mutant KRAS-dependent manner. Consistently, RNA sequencing database analysis revealed an association of higher KRAS MUT expression with an increase in SEMA3D and ARF6 expression in human PDAs. Moreover, multiplex immunohistochemistry analysis showed an increased number of M2-polarized macrophages proximal to nerves in human PDA tissue expressing SEMA3D. Thus, this study suggests altered expression of SEMA3D in tumor cells lead to acquisition of cancer-promoting functions and the axon guidance signaling originating from nerves is "hijacked" by tumor cells to support their growth. Other axon guidance and neuronal development molecules may play a similar dual role which is worth further investigation.

One sentence summary

Tumor- and nerve-derived SEMA3D promotes tumor progression and metastasis through macrophage reprogramming in the tumor microenvironment.

STATEMENT OF SIGNIFICANCE

This study established the dual role of axon guidance molecule, SEMA3D, in the malignant transformation of pancreatic epithelial cells and of nerve-derived SEMA3D in PDA progression and metastasis. It revealed macrophage reprogramming as the mechanism underlying bothroles. Together, this research elucidated how inflammatory responses promote invasive PDA progression and metastasis through an oncogenic process.

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

Neoadjuvant immunotherapy is thought to produce long-term remissions through induction of antitumor immune responses before removal of the primary tumor. Tertiary lymphoid structures (TLS), germinal center-like structures that can arise within tumors, may contribute to the establishment of immunological memory in this setting, but understanding of their role remains limited. Here, we investigated the contribution of TLS to antitumor immunity in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy. We found that neoadjuvant immunotherapy induced the formation of TLS, which were associated with superior pathologic response, improved relapse free survival, and expansion of the intratumoral T and B cell repertoire. While TLS in viable tumor displayed a highly active mature morphology, in areas of tumor regression we identified an involuted TLS morphology, which was characterized by dispersion of the B cell follicle and persistence of a T cell zone enriched for ongoing antigen presentation and T cell-mature dendritic cell interactions. Involuted TLS showed increased expression of T cell memory markers and expansion of CD8+ cytotoxic and tissue resident memory clonotypes. Collectively, these data reveal the circumstances of TLS dissolution and suggest a functional role for late-stage TLS as sites of T cell memory formation after elimination of viable tumor.

Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses

Assays linking cellular phenotypes with T cell or B cell antigen receptor sequences are crucial for characterizing adaptive immune responses. Existing methodologies are limited by low sample throughput and high cost. Here, we present INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach that combines molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility.

Molecular signature incorporating the immune microenvironment enhances thyroid cancer outcome prediction

Genomic and transcriptomic analysis has furthered our understanding of many tumors. Yet, thyroid cancer management is largely guided by staging and histology, with few molecular prognostic and treatment biomarkers. Here, we utilize a large cohort of 251 patients with 312 samples from two tertiary medical centers and perform DNA/RNA sequencing, spatial transcriptomics, and multiplex immunofluorescence to identify biomarkers of aggressive thyroid malignancy. We identify high-risk mutations and discover a unique molecular signature of aggressive disease, the Molecular Aggression and Prediction (MAP) score, which provides improved prognostication over high-risk mutations alone. The MAP score is enriched for genes involved in epithelial de-differentiation, cellular division, and the tumor microenvironment. The MAP score also identifies aggressive tumors with lymphocyte-rich stroma that may benefit from immunotherapy. Future clinical profiling of the stromal microenvironment of thyroid cancer could improve prognostication, inform immunotherapy, and support development of novel therapeutics for thyroid cancer and other stroma-rich tumors.

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

BACKGROUND

Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy.

METHODS

We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a prospective clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response at the time of resection.

RESULTS

ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer-associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell marker expression suggesting strong activity of these cells. HCC-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to the tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic responses, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by HCC-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient.

CONCLUSIONS

These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

Human clinical trials are important tools to advance novel systemic therapies improve treatment outcomes for cancer patients. The few durable treatment options have led to a critical need to advance new therapeutics in hepatocellular carcinoma (HCC). Recent human clinical trials have shown that new combination immunotherapeutic regimens provide unprecedented clinical response in a subset of patients. Computational methods that can simulate tumors from mathematical equations describing cellular and molecular interactions are emerging as promising tools to simulate the impact of therapy entirely in silico. To facilitate designing dosing regimen and identifying potential biomarkers, we developed a new computational model to track tumor progression at organ scale while reflecting the spatial heterogeneity in the tumor at tissue scale in HCC. This computational model is called a spatial quantitative systems pharmacology (spQSP) platform and it is also designed to simulate the effects of combination immunotherapy. We then validate the results from the spQSP system by leveraging real-world spatial multi-omics data from a neoadjuvant HCC clinical trial combining anti-PD-1 immunotherapy and a multitargeted tyrosine kinase inhibitor (TKI) cabozantinib. The model output is compared with spatial data from Imaging Mass Cytometry (IMC). Both IMC data and simulation results suggest closer proximity between CD8 T cell and macrophages among non-responders while the reverse trend was observed for responders. The analyses also imply wider dispersion of immune cells and less scattered cancer cells in responders' samples. We also compared the model output with Visium spatial transcriptomics analyses of samples from post-treatment tumor resections in the original clinical trial. Both spatial transcriptomic data and simulation results identify the role of spatial patterns of tumor vasculature and TGFβ in tumor and immune cell interactions. To our knowledge, this is the first spatial tumor model for virtual clinical trials at a molecular scale that is grounded in high-throughput spatial multi-omics data from a human clinical trial.

Colorectal cancer in patients of advanced age is associated with increased incidence of BRAF p.V600E mutation and mismatch repair deficiency

Introduction

The highest incidence of colorectal cancer (CRC) is in patients diagnosed at 80 years or older highlighting a need for understanding the clinical and molecular features of these tumors. Methods. In this retrospective cohort study, 544 CRCs underwent next generation sequencing and mismatch repair (MMR) evaluation. Molecular and clinical features were compared between 251 patients with traditional-onset CRC (50-69 years at diagnosis) and 60 with late-onset CRC (>80 years at diagnosis).

Results

Late-onset CRC showed a significantly higher rate of right-sided tumors (82% vs 35%), MMR deficiency (35% vs. 8%) and BRAF p.V600E mutations (35% vs. 8%) and a significantly lower rate of stage IV disease (15% vs 28%) and APC mutations (52% vs. 78%). Association of these features with advanced age was supported by stratifying patients into 6 age groups (<40, 40-49, 50-59, 60-69, 70-79 and >80 years). However, the age-related rise in MMR deficient (dMMR) CRC was only seen in the female patients with an incidence of 48% (vs. 10% in the male patient) in the >80y group. In addition, BRAF p.V600E was significantly enriched in MMR deficient CRC of advanced age (67% in late-onset CRC). Categorizing CRC by mutational profiling, late-onset CRC revealed a significantly higher rate of dMMR/BRAF ⁺ APC ^- (18% vs. 2.0%), dMMR/BRAF ^- APC ^- (8.3% vs. 1.2%) and MMR proficient (pMMR)/BRAF ⁺ APC ^- (12% vs. 4.0%) as compared to traditional-onset CRC.

Discussion

In summary, there was a higher rate of dMMR and BRAF p.V600E in late-onset CRC, independently or in combination. The higher incidence of dMMR in late-onset CRC in females is most likely predominantly driven by BRAF p.V600E induced hypermethylation. Prospective studies with treatment plans designed specifically for these older patients are warranted to improve their outcomes.

Converging on a Cure: The Roads to Predictive Immunotherapy

SUMMARY

Convergence science teams integrating clinical, biological, engineering, and computational expertise are inventing new forecast systems to monitor and predict evolutionary changes in tumor and immune interactions during early cancer progression and therapeutic response. The resulting methods should inform a new predictive medicine paradigm to select adaptive immunotherapeutic regimens personalized to patients' tumors at a given time during their cancer progression for durable patient response.

Profiling of syngeneic mouse HCC tumor models as a framework to understand anti-PD-1 sensitive tumor microenvironments

BACKGROUND AND AIMS

The treatment of hepatocellular carcinoma (HCC) has been transformed by the use of immune checkpoint inhibitors. However, most patients with HCC do not benefit from treatment with immunotherapy. There is an urgent need to understand the mechanisms that underlie response or resistance to immunotherapy for patients with HCC. The use of syngeneic mouse models that closely recapitulate the heterogeneity of human HCC will provide opportunities to examine the complex interactions between cancer cells and nonmalignant cells in the tumor microenvironment.

APPROACH AND RESULTS

We leverage a multifaceted approach that includes imaging mass cytometry and suspension cytometry by time of flight to profile the tumor microenvironments of the Hep53.4, Hepa 1-6, RIL-175, and TIBx (derivative of TIB-75) syngeneic mouse HCC models. The immune tumor microenvironments vary across these four models, and various immunosuppressive pathways exist at baseline in orthotopic liver tumors derived from these models. For instance, TIBx, which is resistant to anti-programmed cell death protein 1 therapy, contains a high proportion of "M2-like" tumor-associated macrophages with the potential to diminish antitumor immunity. Investigation of The Cancer Genome Atlas reveals that the baseline immunologic profiles of Hep53.4, RIL-175, and TIBx are broadly representative of human HCCs; however, Hepa 1-6 does not recapitulate the immune tumor microenvironment of the vast majority of human HCCs.

CONCLUSIONS

There is a wide diversity in the immune tumor microenvironments in preclinical models and in human HCC, highlighting the need to use multiple syngeneic HCC models to improve the understanding of how to treat HCC through immune modulation.

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Recent advances in spatial transcriptomics (STs) enable gene expression measurements from a tissue sample while retaining its spatial context. This technology enables unprecedented in situ resolution of the regulatory pathways that underlie the heterogeneity in the tumor as well as the tumor microenvironment (TME). The direct characterization of cellular co-localization with spatial technologies facilities quantification of the molecular changes resulting from direct cell-cell interaction, as it occurs in tumor-immune interactions. We present SpaceMarkers, a bioinformatics algorithm to infer molecular changes from cell-cell interactions from latent space analysis of ST data. We apply this approach to infer the molecular changes from tumor-immune interactions in Visium spatial transcriptomics data of metastasis, invasive and precursor lesions, and immunotherapy treatment. Further transfer learning in matched scRNA-seq data enabled further quantification of the specific cell types in which SpaceMarkers are enriched. Altogether, SpaceMarkers can identify the location and context-specific molecular interactions within the TME from ST data.

Achieving the Goals of the Cancer Moonshot Requires Progress against All Cancers

In February 2022, President Joseph R. Biden made reducing age-adjusted cancer mortality by at least 50% over the next 25 years a key goal of the Cancer Moonshot. Although recent progress puts this goal within reach, succeeding will require major commitments to progress on all fronts: basic research, clinical and translational research, health care delivery, and public health.

Strategies for Heating Up Cold Tumors to Boost Immunotherapies

Immune checkpoint inhibitors induce significant and durable treatment responses in about 20% of all cancers, but many patients have natural resistance to current immunotherapies. The past decade of technological advances has resulted in large-scale profiling of many cancers and their tumor microenvironments, rapidly expanding our understanding of the mechanisms utilized by tumors to create immune-resistant microenvironments. In this review, we discuss key factors that create immune resistance and emerging concepts that are redefining how we view immune resistance, as well as highlight novel strategies that aim to convert immune-resistant into immune-sensitive tumors.

Expected final online publication date for the Annual Review of Cancer Biology, Volume 7 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Abstract 2270: Combination of CXCR4 antagonist and anti-PD1 therapy results in significant mobilization and increased infiltration of myeloid cells into the metastatic liver microenvironment of PDAC

Pancreatic adenocarcinoma (PDAC) is extremely lethal and resistant to checkpoint immunotherapy, characterized by an immunosuppressive tumor microenvironment consisting of stromal and myeloid cells. Prior studies have demonstrated the utility of targeting the chemokine signaling axis CXCR4-CXCL12 (SDF-1), a highlighted feature in PDACs, to overcome the CXCL12-driven immobilization of T cells and thus facilitate their antitumor role within the tumor. Based on these findings, we have conducted a phase 2 trial evaluating the effects of plerixafor, a CXCR4 antagonist, and cemiplimab, a PD1 inhibitor antibody, in patients with metastatic PDAC who have progressed after one line of systemic chemotherapy (NCT04177810). To determine the immunological responses to therapy, blood samples and tissue biopsies were obtained at baseline and during treatment. Hematological assessment confirmed the activity of CXCR4 antagonist in mobilizing hematopoietic precursors (CD34+), immature myeloid cells, and lymphoid cells, as well as monocytic and granulocytic cell populations. Suspension mass cytometry analysis of peripheral blood mononuclear cells revealed that mobilized monocytic subpopulations had high expressions of chemokine receptors CCR2, CCR5, and CXCR2. Histopathologic evaluation of the serial tissue biopsies from the liver metastatic PDAC revealed increased levels of inflammation upon treatment. To further characterize the cellular constituents of the observed inflammation, multiplexed immunohistochemistry by imaging mass cytometry was performed, demonstrating strong trends toward increased infiltration of not only effector T cells but also macrophages and granulocytic cells into the tumor microenvironment. Taken together, these findings suggest that mobilization of myeloid cells by CXCR4 antagonism results in the recruitment of additional myeloid cells from circulation and that alternative chemokine signaling pathways are sufficient for doing so. This implicates a potential mode of resistance against CXCR4-targeted therapies. Furthermore, these observations reinforce the value of ongoing research efforts in the field to subvert the recruitment or immunosuppressive function of myeloid cells, which would be particularly relevant in the setting of CXCR4 antagonism.

Citation Format: Sarah M. Shin, Alexei Hernandez, Erin Coyne, Zhehao Zhang, Sarah Mitchell, Jennifer Durham, Xuan Yuan, Hongqui Yang, Elana J. Fertig, Elizabeth M. Jaffee, Katherine M. Bever, Dung T. Le, Won Jin Ho. Combination of CXCR4 antagonist and anti-PD1 therapy results in significant mobilization and increased infiltration of myeloid cells into the metastatic liver microenvironment of PDAC [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 2270.

Abstract 2768: Non-invasive detection of pancreatic adenocarcinoma using Ga-68 labelled epha2 targeting peptide

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease and early diagnosis is paramount for effective treatment. Molecular imaging techniques such as positron emission tomography (PET) could provide an early diagnosis of PDAC to potentially improve survival. EphA2, a member of Erythropoietin-producing hepatocellular (Eph) receptors, is a desirable target for PDAC detection as it is pro-oncogenic and expressed in &gt; 90% of PDACs. Here, we report the development of a peptide-based PET imaging agent, [68Ga]AJ201, evaluation of its pharmacokinetics, and its potential to non-invasively detect variable EphA2 expression in moue models of PDAC.

Methods: A bicyclic peptide, AJ201, was synthesized and its binding affinity for EphA2 was determined by surface plasmon resonance (SPR). AJ201 was labelled with Gallium-68 in high radiochemical yields and purity. In vitro uptake of the resulting [68Ga]AJ201 was carried out in different PDAC cell lines with variable EphA2 expression (Panc1, CFPAC1, Hs766T, and SU8686) and Jurkat cell line as a negative control. In vivo pharmacokinetic properties of [68Ga]AJ201 were evaluated by PET-MR imaging and ex vivo biodistribution studies in different subcutaneous PDAC xenografts and in Panc1 orthotopic model (n=4-5/tumor). [68Ga]AJ201 in vivo specificity for EphA2 was confirmed by cross-correlative immunohistochemistry of xenografts and by co-injection of a blocking dose of non-radioactive AJ201 (1 mg/kg).

Results: AJ201 binds human EphA2 with high affinity (KD ~ 0.2 nM). Flow cytometry analysis confirmed variable EphA2 expression in all the PDAC cell lines tested with Panc1 and CFPAC cell lines exhibiting highest and lowest expression, respectively. In vitro binding assays showed variable [68Ga]AJ201 uptake in all the PDAC cells and almost no uptake in the presence of 1 µM non-radioactive AJ201 and in negative control Jurkat cells. In vivo dynamic PET-MR imaging revealed high and specific uptake of [68Ga]AJ201 in Panc1 tumor xenografts within 5 min and retained for at least 90 min. In contrast, [68Ga]AJ201 exhibited fast clearance from normal tissues resulting in high contrast images at 60 minutes and a high tumor-to-muscle ratio of 25.8 ± 6.7. [68Ga]AJ201 uptake in tumors was reduced by &gt; 80 % in mice receiving blocking dose, confirming the specificity of the radiotracer. Also, [68Ga]AJ201 PET provided high contrast images of orthotopic Panc1 tumors. Furthermore, [68Ga]AJ201 PET showed variable and expression dependent uptake in all the PDAC xenografts tested that was corroborated by EphA2 expression detected by IHC.

Conclusion: [68Ga]AJ201 is an EphA2 specific high affinity peptide-based PET imaging agent that detects orthotopic PDAC in mouse models at 60 minutes and demonstrates potential to non-invasively detect PDAC in patients.

Citation Format: Ajay Kumar Sharma, Kuldeep Gupta, Akhilesh Mishra, Sophia Chen, Gabriela Lofland, Todd Armstrong, Edward Gabrielson, Lei Zheng, Elizabeth M. Jaffee, Sridhar Nimmagadda. Non-invasive detection of pancreatic adenocarcinoma using Ga-68 labelled epha2 targeting peptide [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 2768.

Abstract 5076: Combination PancVAX neo-epitope vaccine with anti-CTLA-4 and anti-PD-1 antibodies enhances infiltration of cytotoxic T cells and mitigates T cell exhaustion in a murine model of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a deadly cancer with a low tumor mutational burden and therefore few neoantigen targets that can be recognized by cytotoxic T cells. Most PDACs are thus insensitive to either single or dual immune checkpoint inhibitor (ICI) therapy. Personalized neoantigen vaccines can expand the number and repertoire of anti-tumor T cells that infiltrate the tumor and mediate cytotoxicity. To model a personalized neoantigen vaccine treatment strategy in PDAC, we previously developed PancVAX, a peptide-based vaccine targeting 12 neoantigens expressed in the murine pancreatic cell line Panc02 (Kinkead et al, JCI Insight 2018). Although we observed increased T cell infiltration present in the tumor post-vaccination, these cells expressed high levels of exhaustion markers. We therefore hypothesized that sequential administration of anti-CTLA-4 and anti-PD-1 would enhance the pool of T cells primed by the neoantigen vaccine and maintain activation of antigen-experienced T cells, respectively, to yield optimal and durable neoantigen-specific anti-tumor immunity in PDAC. To address this, mice bearing subcutaneous Panc02 tumors were vaccinated with two rounds of the PancVAX neoantigen vaccine followed by anti-CTLA-4 and anti-PD-1 3 days later. Anti-PD-1 maintenance was given twice weekly beginning at the first vaccine dose. Twelve days after the last peptide vaccine dose, tumors were harvested and dissociated into single-cell suspensions for paired single-cell RNA-sequencing and TCR-sequencing. Mice that were untreated or given ICIs without PancVAX had the highest proportions of CD8+ T cells expressing exhaustion markers. PancVAX-treated mice had more intratumoral cycling CD8 T cells and effector CD8+ T cells with high cytotoxic gene expression. Among mice treated with PancVAX, tumors from mice treated with PancVAX + anti-PD1 or PancVAX + anti-PD1 + anti-CTLA-4 had the highest proportions of effector CD8+ T cells. Ongoing analyses include differential gene expression and pathway analysis between treatment conditions in the T cell compartment in mice treated with combination ICI and PancVAX. Additionally, we will assess changes in T cell clonality and diversity within the tumors when mice are treated with single or combination therapy. These results will define a transcriptional signature associated with the generation of a productive anti-tumor immune response when neoantigen vaccines and ICI are used in combination. This work demonstrates how the addition of ICIs to personalized neo-epitope vaccines for PDAC can further enhance the quality of vaccine-induced T cell effector function in an otherwise immunologically cold tumor type and supports their inclusion in neoantigen vaccination strategies for patients with PDAC.

Citation Format: Jacob T. Mitchell, Amanda Huff, Emily Davis-Marcisak, Fangluo Chen, Todd D. Armstrong, Luciane T. Kagohara, James Leatherman, Rulin Wang, Srinivasan Yegnasubramanian, Elizabeth M. Jaffee, Elana J. Fertig, Neeha Zaidi. Combination PancVAX neo-epitope vaccine with anti-CTLA-4 and anti-PD-1 antibodies enhances infiltration of cytotoxic T cells and mitigates T cell exhaustion in a murine model of 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 5076.

Abstract 3256: Entinostat enhances the efficacy of checkpoint inhibition in breast-to-lung metastases and is associated with alterations in the phenotype and function of myeloid cell populations

Single agent immune checkpoint inhibitors (ICIs) are ineffective against metastatic breast cancer. One mechanism of intrinsic resistance is the presence of immunosuppressive myeloid cells and dysfunctional dendritic cells in the metastatic tumor microenvironment (TME) that impede the activation of anti-tumor T cells. A comparison of single-cell RNA sequencing analyses between breast-to-lung metastases and published data from breast tumors in the syngeneic NeuN mouse model of HER2+ breast cancer revealed that despite the presence of additional immune cell populations in the lungs, myeloid cells represented the predominant immune cell population in both TMEs and demonstrated similar changes in frequency and gene expression following treatment with the histone deacetylase inhibitor, entinostat. Our work highlights for the first time an increase in the frequency of conventional dendritic cells (cDC) with entinostat treatment in breast-to-lung metastases. Gene expression analyses of breast-to-lung metastases showed that entinostat-treated myeloid derived suppressor cells (MDSCs) and tumor associated macrophages (TAMs) downregulated genes associated with immunosuppression such as S100a8, Cd84, Trem2, and Mmp9. In addition, TAMs and cDCs upregulated the expression of genes associated with antigen presentation such as H2-K1, H2-Ab1, B2m, and Cd74 and pro-inflammatory markers such as Ccl3. NeuN mice were treated with the combination of entinostat and the immune checkpoint inhibitors, anti-PD-1 and anti-CTLA-4, and breast-to-lung metastases were analyzed via flow cytometry, demonstrating an increase in the frequency of cDC1s and CD8+ T cells expressing granzyme B. Furthermore, the treatment combination of entinostat + anti-PD-1 + anti-CTLA-4 significantly increased survival in an experimental model of lung metastasis using a newly characterized model derived from the original NT2.5 HER2+ cell line, NT2.5LM. These results confirm those of our breast expansion cohort from the phase I clinical trial NCI-9844 that demonstrate a 30% overall response rate in 20 heavily pretreated patients with metastatic disease treated with entinostat + Nivolumab (anti-PD-1) + Ipilimumab (anti-CTLA-4). We highlight for the first time significant alterations within multiple myeloid derived cell types, cDCs, TAMs and MDSCs, from within a native metastatic niche, that are likely driving an entinostat mediated improved response to ICI treatment.

Citation Format: Edgar Gonzalez, Adam L. MacLean, Evanthia T. Roussos Torres, Aaron Baugh, Jesse Kreger, Sofi Castanon, Valerie Narumi, Elizabeth M. Jaffee. Entinostat enhances the efficacy of checkpoint inhibition in breast-to-lung metastases and is associated with alterations in the phenotype and function of myeloid cell populations [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 3256.

Multiomics Empowers Predictive Pancreatic Cancer Immunotherapy

Advances in cancer immunotherapy, particularly immune checkpoint inhibitors, have dramatically improved the prognosis for patients with metastatic melanoma and other previously incurable cancers. However, patients with pancreatic ductal adenocarcinoma (PDAC) generally do not respond to these therapies. PDAC is exceptionally difficult to treat because of its often late stage at diagnosis, modest mutation burden, and notoriously complex and immunosuppressive tumor microenvironment. Simultaneously interrogating features of cancer, immune, and other cellular components of the PDAC tumor microenvironment is therefore crucial for identifying biomarkers of immunotherapeutic resistance and response. Notably, single-cell and multiomics technologies, along with the analytical tools for interpreting corresponding data, are facilitating discoveries of the systems-level cellular and molecular interactions contributing to the overall resistance of PDAC to immunotherapy. Thus, in this review, we will explore how multiomics and single-cell analyses provide the unprecedented opportunity to identify biomarkers of resistance and response to successfully sensitize PDAC to immunotherapy.

A phase I study of a mutant KRAS-targeted long peptide vaccine combined with ipilimumab/nivolumab in resected pancreatic cancer and MMR-proficient metastatic colorectal cancer

TPS814

Background: Novel strategies are needed to improve immune responses in “cold” tumors such as pancreatic ductal adenocarcinoma (PDAC) and mismatch repair-proficient colorectal cancer (MMRp CRC). As a frequent oncogenic driver, mutant KRAS (mKRAS) neoantigens are attractive targets to augment anti-tumor immunity in both diseases. Recently, adoptive transfer of mKRAS G12D-specific T cells has shown durable tumor regressions in patients with metastatic CRC and PDAC (Tran et. al., 2020; Leidner et. al., 2022). Furthermore, our preclinical work has demonstrated that combining a mKRAS neoantigen vaccine with immune-modulating agents prevents progression of premalignant lesions to PDAC in mice (Keenan et. al., 2014). Based on this rationale, our study pairs a pooled synthetic long peptide (SLP) mKRAS vaccine with dual checkpoint blockade to assess safety and immunogenicity in patients with resected PDAC and chemorefractory MMRp CRC. Methods: This is a first-in-human, single-arm, open-label phase I trial evaluating a pooled SLP mKRAS vaccine combined with ipilimumab/nivolumab (ipi/nivo) in patients with resected PDAC (Cohort A, n = 12) and MMRp metastatic CRC (Cohort B, n = 12) The vaccine consists of poly-ICLC adjuvant admixed with SLPs corresponding to six common mKRAS subtypes: G12D, G12R, G12V, G12A, G12C, and G13D. In priming phase, the mKRAS vaccine is given on days 1, 8, 15, and 22 along with ipi/nivo. In boost phase, the mKRAS vaccine is given on weeks 13, 21, 29, 37, and 45 along with nivo alone. Cohort A patients who remain disease-free can continue to receive boost vaccines in a 12-month extended treatment phase. Eligible patients must have molecular tumor testing that demonstrates one of the six KRAS mutations listed above. Cohort A patients must be disease-free following completion of adjuvant chemotherapy within 6 months prior to study entry. Cohort B patients must have confirmed MMRp status, exposure to ≥ 2 prior lines of standard chemotherapy, and measurable disease amenable to biopsies at baseline and week 7. The co-primary endpoints of this study are safety and T cell response. Adverse events will be graded per NCI CTCAE v5.0. T cell response will be determined by the maximal percent change in IFNγ-producing mKRAS-specific T cell density within 16 weeks post-vaccination compared to baseline. Secondary endpoints include disease control and objective response rates at 16 weeks per RECIST v1.1/iRECIST (Cohort B only) as well as disease-free/progression-free and overall survival. Correlative studies will examine treatment-associated changes in T cell receptor (TCR) repertoire diversity by next-generation TCR sequencing of peripheral blood and tumor specimens. Patient accrual began in May 2020 and is completed for Cohort A. Enrollment is currently ongoing for Cohort B. Study drug support provided by Bristol Myers Squibb. Clinical trial information: NCT04117087 .

Nivolumab and a CCR2/CCR5 dual antagonist (BMS-813160) with or without GVAX for locally advanced pancreatic ductal adenocarcinomas: Results of phase I study

730

Background: Surgical resection is the only potentially curative treatment for pancreatic adenocarcinoma (PDAC) but involvement of adjacent vital structures in locally advanced pancreatic adenocarcinoma (LAPC) precludes upfront resection. Neoadjuvant chemotherapy and/or radiation allows some LAPC patients to undergo resection but outcomes remain dismal. In this trial, we investigate the benefit of combining chemotherapy, radiation, and immunotherapy to improve outcomes in LAPC by enhancing antitumor immunity. The use of GVAX, Nivolumab, and BMS-813160 is hypothesized to promote immune responses through enhanced effector T cell infiltration and activation by GVAX and nivolumab while inhibiting immunosuppressive tumor associated macrophages via CCR2/5 inhibition with BMS-813160. Testing this combination in LAPC will facilitate assessment of the changes this combination produces in the tumor microenvironment. Methods: This open-label, single center two-arm phase I/II trial uses neoadjuvant/adjuvant nivolumab and BMS-813160 +/- GVAX following 8 to 16 doses of FOLFIRINOX and SBRT in patients with newly diagnosed LAPC. The primary endpoint of the phase I portion is safety of nivolumab, BMS-813160, and GVAX in patients with LAPC following chemotherapy and SBRT. The phase II portion randomizes patients 1:1 to nivolumab and BMS-813160 +/- GVAX with primary endpoint of immune response defined as > 80% increase in CD8+CD137+ cell infiltration. For the phase I portion a 3+3 dose escalation was used: nivolumab 480mg IV and GVAX 5x108 cells intradermal were administered at a fixed dose every 4 weeks. BMS-813160 was administered at a dose of 150mg and 300mg PO BID in levels 1 and 2 respectively. DLTs were evaluated during the 1st cycle of treatment and study-related adverse events (AE) were graded according to NCI CTCAE v5.0. Results: In the phase I portion of this trial, 13 patients were enrolled. The patient characteristics of the enrolled patients were: median age (range), 67 (44, 78), Female/Male, (4/9), Race, (Asian: 2, Black: 3, White: 8), histological grade (moderately/poor/moderately poor), (10/2/1). Nine of the 13 patients proceeded to immunotherapy after neoadjuvant chemotherapy and radiation. Three patients received treatment at dose level 1 and 6 patients at dose level 2. No DLTs were observed with the only grade 3 or higher AE being maculo-papular rash (n = 1). The RP2D for BMS-813160 was determined to be 300mg PO BID. Conclusions: We determined that nivolumab 480mg IV q4 weeks, GVAX 5x108 cells intradermal q4 weeks, and BMS-813160 300mg PO BID were the RP2D for the phase 2 portion of this investigation which is ongoing. This combination appears safe and neoadjuvant use does not lead to delay in surgery. Clinical trial information: NCT03767582 .

A phase I study of a mutant KRAS-targeted long peptide vaccine in patients at high risk of developing pancreatic cancer

TPS758

Background: KRAS mutations are identified in the majority of premalignant lesions that precede pancreatic ductal adenocarcinoma (PDAC). Arising during tumorigenesis, mutant KRAS (mKRAS) neoantigens are less susceptible to central tolerance mechanisms and serve as ideal vaccine targets. Indeed, targeting mKRAS neoantigens with vaccines has shown promising anti-tumor activity in the preclinical setting. For instance, our group previously demonstrated that a Listeria-based vaccine targeting mKRAS G12D combined with Treg-depleting agents can prevent the progression of early pancreatic intraepithelial neoplasia to overt PDAC in a mouse model (Keenan et al, 2014). Building upon this work, the current study aims to determine the safety and immunogenicity of a pooled synthetic long peptide (SLP) mKRAS vaccine in patients identified as high risk for developing PDAC based on family history and germline mutation testing. Methods: This is a single-arm, open-label phase I trial evaluating a pooled SLP mKRAS vaccine in patients at high risk of developing PDAC ( n = 20). The vaccine consists of poly-ICLC adjuvant admixed with SLPs corresponding to six common mKRAS subtypes: G12D, G12R, G12V, G12A, G12C, and G13D. A four-dose series of the mKRAS vaccine is administered on weeks 1, 3, 4, and 17. Following completion of the treatment phase, all patients have the option to continue annual follow-up visits until study closure. Eligible patients must have radiographic evidence of a premalignant pancreatic lesion and fall under at least one of the following three high-risk groups: 1) ≥ 2 familial pancreatic cancer relatives, 2) germline mutation carriers with ≥ 10% lifetime PDAC risk and 3) germline mutation carriers with ~5% lifetime PDAC risk. The co-primary endpoints of this study are safety and T cell response. Safety will be assessed by the frequency and grading of adverse events per NCI CTCAE v5.0. T cell response will be determined by the maximal percent change in IFNγ-producing mKRAS-specific T cell density within 16 weeks post-vaccination compared to baseline. Correlative studies will explore vaccine-associated changes in T cell quality (e.g., memory, exhaustion, poly-functionality, and activation) using mass cytometry analysis of peripheral blood samples. Patient accrual began in April 2022 and is currently ongoing. Clinical trial information: NCT05013216 .

Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients and recurrence can also occur. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response. ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell markers expression suggesting strong activity of these cells. Cancer-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic response, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by cancer-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.

Solid Organ Transplantation Is Associated with an Increased Rate of Mismatch Repair Deficiency and PIK3CA Mutations in Colorectal Cancer

Solid organ transplants are associated with a modestly increased risk of colorectal cancers (CRC). However, the molecular profile of these cancers has not been described. We hypothesized that transplant-related immunosuppression may promote development of more immunogenic tumors as suggested by a high tumor mutation burden or mismatch repair deficiency. We performed an electronic medical record search for patients seen in the Johns Hopkins University Health System (JHHS) between 2017 and 2022 who developed CRC following solid organ transplantation. A comparator cohort of patients treated for CRC at JHHS with molecular profiling data was also identified. In this case, 29 patients were identified that developed post-transplant CRC (renal transplant, n = 18; liver transplant, n = 8; kidney-liver transplantation, n = 3). Compared to the JHHS general population CRC cohort, patients who developed post-transplant CRC had a higher rate of mismatch repair deficiency (41% versus 12%, p-value = 0.0038), and elevated tumor mutation burden (median of 22 mut/Mb versus 3.5 mut/Mb, p-value = 0.033) (range 3.52-53.65). Post-transplant tumors were enriched for PIK3CA mutations (43% versus 24%, p-value = 0.042). Post-Transplant CRCs are associated with clinical and molecular features of immune sensitivity, supporting a potential role for impaired immune surveillance in shaping the landscape of CRCs. These results may help inform the management of patients with post-transplant CRC.

Quantitative Spatial Profiling of Immune Populations in Pancreatic Ductal Adenocarcinoma Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with poor 5-year survival rates, necessitating identification of novel therapeutic targets. Elucidating the biology of the tumor immune microenvironment (TiME) can provide vital insights into mechanisms of tumor progression. In this study, we developed a quantitative image processing platform to analyze sequential multiplexed IHC data from archival PDAC tissue resection specimens. A 27-plex marker panel was employed to simultaneously phenotype cell populations and their functional states, followed by a computational workflow to interrogate the immune contextures of the TiME in search of potential biomarkers. The PDAC TiME reflected a low-immunogenic ecosystem with both high intratumoral and intertumoral heterogeneity. Spatial analysis revealed that the relative distance between IL10+ myelomonocytes, PD-1+ CD4+ T cells, and granzyme B+ CD8+ T cells correlated significantly with survival, from which a spatial proximity signature termed imRS was derived that correlated with PDAC patient survival. Furthermore, spatial enrichment of CD8+ T cells in lymphoid aggregates was also linked to improved survival. Altogether, these findings indicate that the PDAC TiME, generally considered immuno-dormant or immunosuppressive, is a spatially nuanced ecosystem orchestrated by ordered immune hierarchies. This new understanding of spatial complexity may guide novel treatment strategies for PDAC.

SIGNIFICANCE

Quantitative image analysis of PDAC specimens reveals intertumoral and intratumoral heterogeneity of immune populations and identifies spatial immune architectures that are significantly associated with disease prognosis.

Abstract IA001: Intercepting pancreatic cancer development with oncogene targeted immunotherapy

Pancreatic adenocarcinoma (PDAC) progression is triggered by a complex interaction of genetic mutations, stromal cell interactions and tumor microenvironmental (TME) signals. Diagnosis usually occurs late in disease progression, making treatment challenging and survival rates extremely poor. PDACs are also considered non-immunogenic, therefore newly emerging immunotherapies that have been successful in other cancers have not significantly progressed PDAC treatment options. Resistance to immunotherapies progresses as normal cells undergo the earliest genetic changes that transform them into early pre-malignant lesions. The two most common premalignant lesions are pancreatic intra-epithelial neoplasms (PanINs) and intraductal papillary mucinous neoplasm (IPMN). Both types of premalignant lesions eventually accumulate additional genetic changes that lead to early-stage invasive cancer and eventually, to late stage PDAC. This transformation process is influenced by both tumor-intrinsic and extrinsic forces within the developing TME. Accumulating data suggests that immune resistance mechanisms also evolve with this progression, which has led to the hypothesis that early immune intervention may be the best time to intervene to slow or even halt disease progression and improve treatment outcomes.

We know that tumor initiation to metastases takes years to decades, providing a unique window of opportunity for the prevention of premalignant progression. KRAS mutations are an early oncogenic event present in over 90% of PanINs and 75% of IPMNs. Initial studies examining cancer vaccines targeted to early oncogenic mutations are showing promise in animal models. A listeria-based vaccine engineered to express oncogenic KrasG12D combined with and without regulatory T cell depletion by an anti-CD25 antibody (PC61) and cyclophosphamide showed increased T cell infiltration, decreased disease progression, and increased survival in Kras-driven and p53 mutated genetically engineered mice (KrasG12D/+Trp53R172H/+;Pdx-1-Cre (KPC) mice) with early PanIN lesions but not those with later stage PanINs (Keenan et. al. 2014. Gastroenterology 146: 1784). Other early oncogenic mutations in PDACs may prove to be therapeutic targets for vaccine development.

We recently initiated a pilot study to examine the feasibility and safety of targeting mKRAS in patients with resected PDAC. For this, we developed a clinical–grade pooled peptide vaccine targeting 6 common KRAS mutations. This vaccine has been tested in combination with checkpoint blockade in 10 PDAC patients who had undergone surgery plus peri–operative chemotherapy and had remained disease–free (NCT04117087). Longitudinal immune phenotyping showed a robust peripheral mKRAS–specific T cell response against the most vaccinated epitopes. Flow cytometry revealed that these CD4 and CD8 T cells were activated, polyfunctional and displayed a memory phenotype. Based on the favorable immunogenicity and safety profile of our peptide vaccine in patients with resected PDAC, we have initiated a Prevention Study testing our mKRAS vaccine in individuals at high risk for PDAC. This study is currently enrolling and early results will be described.

Citation Format: Elizabeth M. Jaffee. Intercepting pancreatic cancer development with oncogene targeted immunotherapy [abstract]. In: Proceedings of the Second Biennial NCI Meeting: Translational Advances in Cancer Prevention Agent Development (TACPAD); 2022 Sep 7-9. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_2): Abstract nr IA001.

Abstract C036: Cancer associated fibroblasts are regulators of the tumor microenvironment in human pancreatic ductal adenocarcinoma

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.

Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy

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.

Engineered bispecific antibodies targeting the interleukin-6 and -8 receptors potently inhibit cancer cell migration and tumor metastasis

Simultaneous inhibition of interleukin-6 (IL-6) and interleukin-8 (IL-8) signaling diminishes cancer cell migration, and combination therapy has recently been shown to synergistically reduce metastatic burden in a preclinical model of triple-negative breast cancer. Here, we have engineered two novel bispecific antibodies that target the IL-6 and IL-8 receptors to concurrently block the signaling activity of both ligands. We demonstrate that a first-in-class bispecific antibody design has promising therapeutic potential, with enhanced selectivity and potency compared with monoclonal antibody and small-molecule drug combinations in both cellular and animal models of metastatic triple-negative breast cancer. Mechanistic characterization revealed that our engineered bispecific antibodies have no impact on cell viability, but profoundly reduce the migratory potential of cancer cells; hence they constitute a true anti-metastatic treatment. Moreover, we demonstrate that our antibodies can be readily combined with standard-of-care anti-proliferative drugs to develop effective anti-cancer regimens. Collectively, our work establishes an innovative metastasis-focused direction for cancer drug development.

Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials

Mass cytometry, or cytometry by TOF (CyTOF), provides a robust means of determining protein-level measurements of more than 40 markers simultaneously. While the functional states of immune cells occur along continuous phenotypic transitions, cytometric studies surveying cell phenotypes often rely on static metrics, such as discrete cell-type abundances, based on canonical markers and/or restrictive gating strategies. To overcome this limitation, we applied single-cell trajectory inference and nonnegative matrix factorization methods to CyTOF data to trace the dynamics of T cell states. In the setting of cancer immunotherapy, we showed that patient-specific summaries of continuous phenotypic shifts in T cells could be inferred from peripheral blood-derived CyTOF mass cytometry data. We further illustrated that transfer learning enabled these T cell continuous metrics to be used to estimate patient-specific cell states in new sample cohorts from a reference patient data set. Our work establishes the utility of continuous metrics for CyTOF analysis as tools for translational discovery.

Precision Medicine in Pancreatic Cancer: Patient-Derived Organoid Pharmacotyping Is a Predictive Biomarker of Clinical Treatment Response

PURPOSE

Patient-derived organoids (PDO) are a promising technology to support precision medicine initiatives for patients with pancreatic ductal adenocarcinoma (PDAC). PDOs may improve clinical next-generation sequencing (NGS) and enable rapid ex vivo chemotherapeutic screening (pharmacotyping).

EXPERIMENTAL DESIGN

PDOs were derived from tissues obtained during surgical resection and endoscopic biopsies and studied with NGS and pharmacotyping. PDO-specific pharmacotype is assessed prospectively as a predictive biomarker of clinical therapeutic response by leveraging data from a randomized controlled clinical trial.

RESULTS

Clinical sequencing pipelines often fail to detect PDAC-associated somatic mutations in surgical specimens that demonstrate a good pathologic response to previously administered chemotherapy. Sequencing the PDOs derived from these surgical specimens, after biomass expansion, improves the detection of somatic mutations and enables quantification of copy number variants. The detection of clinically relevant mutations and structural variants is improved following PDO biomass expansion. On clinical trial, PDOs were derived from biopsies of treatment-naïve patients prior to treatment with FOLFIRINOX (FFX). Ex vivo PDO pharmacotyping with FFX components predicted clinical therapeutic response in these patients with borderline resectable or locally advanced PDAC treated in a neoadjuvant or induction paradigm. PDO pharmacotypes suggesting sensitivity to FFX components were associated with longitudinal declines of tumor marker, carbohydrate-antigen 19-9 (CA-19-9), and favorable RECIST imaging response.

CONCLUSIONS

PDOs established from tissues obtained from patients previously receiving cytotoxic chemotherapies can be accomplished in a clinically certified laboratory. Sequencing PDOs following biomass expansion improves clinical sequencing quality. High in vitro sensitivity to standard-of-care chemotherapeutics predicts good clinical response to systemic chemotherapy in PDAC. See related commentary by Zhang et al., p. 3176.

Pancreatic Cancer: Pathogenesis, Screening, Diagnosis, and Treatment

Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging cancer, due to both its late stage at diagnosis and its resistance to chemotherapy. However, recent advances in our understanding of the biology of PDAC have revealed new opportunities for early detection and targeted therapy of PDAC. In this review, we discuss the pathogenesis of PDAC, including molecular alterations in tumor cells, cellular alterations in the tumor microenvironment, and population-level risk factors. We review the current status of surveillance and early detection of PDAC, including populations at high risk and screening approaches. We outline the diagnostic approach to PDAC and highlight key treatment considerations, including how therapeutic approaches change with disease stage and targetable subtypes of PDAC. Recent years have seen significant improvements in our approaches to detect and treat PDAC, but large-scale, coordinated efforts will be needed to maximize the clinical impact for patients and improve overall survival.

Abstract 3638: Age-related changes in pancreatic fibroblasts promote growth and progression of pancreatic cancer

Aging is an important independent risk factor for the development of pancreatic ductal adenocarcinoma (PDAC). However, the ways in which aging alters cell populations that comprise the PDAC tumor microenvironment (TME) and impacts tumor growth are incompletely understood. PDAC tumors are highly desmoplastic, and fibroblasts are a key component of the TME that are known to alter the behavior of cancer cells and impact treatment responses. Here, we report that normal pancreatic fibroblasts acquire tumor-promoting properties during aging and alter the properties of PDAC cells both in vitro and in vivo.

To determine if PDAC tumors may be influenced by an aged microenvironment, we performed orthotopic KPC cell injections into the pancreata of aged (&gt;64-week-old) and young (6-8-week-old) syngeneic C57Bl/6J mice. Aged mice have significantly larger tumors, increased incidence of metastases, and decreased survival compared to young mice. Tumors from aged mice also have increased neovascularization as evidenced by increased CD31 and CD105 expression. We next queried whether aged pancreatic fibroblasts may contribute to this increase in tumor growth. We have generated a panel of aged (donors &gt;55 years old) and young (donors &lt;35 years old) normal human pancreatic fibroblasts to determine the effects of healthy aging fibroblasts on PDAC cell behavior. Conditioned media from aged human pancreatic fibroblasts significantly increases the proliferation of PDAC cells suggesting that secreted factors produced by aged fibroblasts enhance cancer cell growth. We confirmed this finding using the KPC mouse cell line and conditioned media from aged (&gt;68-week-old) or young (6-8-week-old) normal mouse pancreatic fibroblasts, providing evidence that aged fibroblasts may contribute to the increased tumor growth observed in our in vivo experiments. In addition, aged fibroblast conditioned media increases the migratory potential of PDAC cells in vitro.

Next, we evaluated changes in the invasiveness of PDAC cells in a 3D co-culture system with either aged or young pancreatic fibroblasts. PDAC spheroids containing cancer cells and aged fibroblasts exhibit a significant increase in invasiveness compared to those containing young fibroblasts.

In conclusion, we show that aged, non-cancer-associated pancreatic fibroblasts have the potential to promote growth, migration, and invasiveness in multiple models of pancreatic ductal adenocarcinoma.

We hypothesize that factors secreted by pancreatic fibroblast change during aging and that this aged secretome is tumor-promoting. We will present these and ongoing studies examining age-related changes in pancreatic fibroblasts in the context of PDAC tumorigenesis.

Citation Format: Daniel J. Zabransky, Yash Chhabra, Mitchell E. Fane, Daniel Delitto, Jacquelyn W. Zimmermann, Elizabeth M. Jaffee, Ashani T. Weeraratna. Age-related changes in pancreatic fibroblasts promote growth and progression of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3638.

Abstract 2728: Characterization of splicing-derived neoantigens using splicemutr shows their independence from TMB and potential as a biomarker for immunotherapy response

Alternative-splicing dysregulation has been shown to play a role in cancer oncogenesis, conferring survival benefits to tumors. Yet, similar to mutation-caused tumor immunity, alternative-splicing dysregulation in cancer has also been shown to create neoepitopes capable of causing an immune response. In this work, we develop a new bioinformatics pipeline, splicemutr, to characterize alternative splicing as a missing source of antigens in cancer from a splice-junction perspective. The splicemutr pipeline identifies antigenic, splice variants by kmerizing differentially spliced transcripts and performing mhc-binding affinity prediction using mhcnuggets. To benchmark this algorithm on established splicing alterations, we first apply our approach to HPV-positive head and neck tumors and find that splicemutr shows enrichment of immunogenic trans-splicing events and evidence for selection against immunogen-causing splice-junctions when compared to normal. Further expanding this to pan-cancer analysis in The Cancer Genome Analysis (TCGA) enables us to evaluate the extent to which alternative splicing relates to common immunogenic biomarkers, including notably tumor mutation burden. Using splicemutr, we show that within 14 cancer types, splicing antigenicity does not correlate with the tumor mutation burden, showing splicing antigenicity to be independent from a common biomarker of tumor response to treatment. To further relate splicing antigens to the efficacy of immunotherapy, we apply our pipeline to compare splicing-based antigenicity in PD1 resistant 4T1MSI implanted Balb/cJ mice sensitized to nivolumab immunotherapy through combination therapy with a BET inhibitor (BETi) and in post-treament samples from an advanced melanoma clinical trial cohort treated with combination nivolumab and ipimulimab. In the mouse experiment, the nivolumab-BETi combination arm showed marked tumor shrinkage compared to the control and nivolumab alone arms. Using splicemutr, we show that the splicing antigenicity increases from combination therapy to nivolumab alone to the untreated arm, suggesting depletion of splicing-based antigens in those samples that respond well to treatment. In the advanced melanoma clinical trial cohort treated with combination nivolumab and ipimulimab, we show that the splicing-based antigenicity is higher in the non-responders than responders. Based upon our mouse data, we hypothesize that the post-treatment human data has decreased splicing-based antigens as the tumor clones containing them may be targeted by the immune system and depleted during successful immunotherapy response. Altogether, these data suggest the potential role of splicing as candidate antigens in cancer and use of our splicemutr pipeline for biomarker discovery based upon splicing antigenicity.

Citation Format: Theron Palmer, Michael Kessler, Ludmila Danilova, Archana Balan, Mark Yarchoan, Neeha Zaidi, Tamara Lopez-Vidal, Ali Saeed, Jessica Gore, Elizabeth M. Jaffee, Alexander Favorov, Valsamo Anagnostou, Daria Gaykalova, Rachel Karchin, Elana Fertig. Characterization of splicing-derived neoantigens using splicemutr shows their independence from TMB and potential as a biomarker for immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2728.

Abstract 1970: Single cell proteomic quantification of T cell states using mass cytometry for applications in monitoring immune responses in cancer immunotherapy clinical trials

Although immunotherapies have been established as a successful treatment option for several types of cancers, additional treatment strategies are necessary to broaden the cohorts of patients who may receive clinical benefit. Common immunological profiling for immunotherapy response depends on assessment of the composition of immune cell types in tissue samples and the periphery. Still, the function and state of each of these cells further contributes to the ultimate clinical benefit of immunotherapeutic response. Additionally, our ability to comprehensively study treatment strategies depends on elucidating the temporal effects different immunotherapy regimens have on the immune system of patients. Single-cell proteomics profiling with CyTOF mass cytometry enables robust protein-level profiling of cell types and is also high-dimensional enough to characterize functional states of immune cells. To construct an immunological framework that may feasibly serve to empower functional assessment of immune cell states for clinical trial monitoring strategies using CyTOF, we are employing single cell trajectory inference methods and non-negative matrix factorization (NMF). We demonstrate this approach using peripheral blood derived CyTOF mass cytometry data to model T cell states at the proteomic level. First, we extract T helper (Th) and T cytotoxic (Tc) cell integrated metrics from CyTOF mass cytometry data obtained from diverse cell marker panel designs, immunological states, and diseases to benchmark that these computational pipelines can accurately reflect Th and Tc activation and exhaustion. Next, we develop a new pipeline that enables the use of continuous functional cell-state metrics from continuous pseudotime and NMF pattern weights as immunological profiling markers from CyTOF that can be applied to cancer immunotherapy clinical trials. For instance, we find CyTOF Tc pseudotime and memory pattern weights are higher in PDAC patients with stable disease treated with ipilimumab and a pancreatic cancer-specific vaccine. Thus, our pipeline has the ability to integrate metrics from mass cytometry data to empower translational analyses for determining patient responses in cancer immunotherapy, such as adaptive immune responses to checkpoint inhibitors and cancer vaccines. Moreover, applying this pipeline to peripheral blood samples obtained before and after treatment also enables us to map further temporal cell state transitions in Tc and Th cells resulting from that treatment. Future work will include leveraging CyTOF T cell integrated metrics in larger scale survival analyses to test the predictive potential in a clinical proof of concept.

Citation Format: Dimitrios N. Sidiropoulos, Zaw Phyo, Nicole Gross, Soren Charmsaz, Stephanie Xavier, James Leatherman, Mark Yarchoan, Elizabeth M. Jaffee, Elana J. Fertig, Won Jin Ho. Single cell proteomic quantification of T cell states using mass cytometry for applications in monitoring immune responses in cancer immunotherapy clinical trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1970.

Abstract 1480: miR-21 as a post-transcriptional regulator of pancreatic ductal adenocarcinoma (PDAC) tumorigenesis

Introduction: MicroRNAs are short non-coding RNAs that are frequently dysregulated across cancers. Specifically, microRNA-21 (miR-21) is a known oncomir overexpressed in pancreatic adenocarcinoma (PDAC) that regulates multiple gene targets downstream of KRAS, the site of the primary driver mutation in PDAC. Past efforts to target mutant KRAS have been limited by compensatory activation of other growth pathways and treatment-related toxicity. Inhibiting miR-21 expression is a novel therapeutic strategy to target KRAS effector function through post-transcriptional regulation. We previously demonstrated that systemic inhibition of miRNA-21 (miR-21) intercepts tumorigenesis in the transgenic KrasG12D/+;Trp53R172H/+;Pdx-1-Cre (KPC) mice without causing overt toxicity. Our major goal was to verify the translation of the previous findings to human models and examine the mechanistic implications of miR-21 inhibition in PDAC.

Experimental Procedures: Using publicly available data from a cohort of patients with PDAC in The Cancer Genome Atlas (TCGA), we performed differential expression analysis of miR-21 and KRAS-related gene targets as well as gene set enrichment analysis of oncogenic pathways identified by the Molecular Signatures Database (MSigDB). Concurrently, de-novo patient-derived organoid (PDO) models were generated from core biopsies and surgical resection specimens. To evaluate the effects of miR-21 inhibition on KRAS pathway activity in a human model system, we selected 6 PDO cell lines and determined miR-21 gene expression by quantitative PCR at baseline and after knockdown using a lentiviral construct.

Results: Analysis of TCGA PDAC cohort identified heterogeneous endogenous expression of miR-21, which was validated ex vivo in our PDO model system. Gene set enrichment analysis revealed enrichment of gene sets associated with KRAS dependency, MEK, AKT, and MTOR signaling in patients with higher endogenous miR-21 expression. MiR-21 knockdown in PDO cell lines was stable at multiple intervals following lentiviral transduction. Further, expression of PDCD4, a tumor suppressor gene and target of miR-21 downstream of KRAS, was enhanced in PDO lines following miR-21 inhibition.

Conclusions: We previously demonstrated that miR-21 appears to be an early and reliable molecular marker of pancreatic neoplasia and that systemic inhibition in a murine model intercepts PDAC tumorigenesis. We now demonstrate in human models that higher miR-21 expression is associated with enrichment of gene sets downstream of KRAS. Additionally, knocking down miR-21 expression enhances the expression of gene targets with tumor suppressor function, notably PDCD4. This suggests that modulating miR-21 expression subsequently modulates the expression of gene targets with critical cell regulatory functions and provides additional insight into novel therapeutic targets.

Citation Format: Jacquelyn W. Zimmerman, Daniel H. Shu, Richard A. Burkhart, Joseph Tandurella, Elana J. Fertig, Elizabeth M. Jaffee. miR-21 as a post-transcriptional regulator of pancreatic ductal adenocarcinoma (PDAC) tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1480.

Abstract 2481: Imaging pancreatic ductal adenocarcinoma using an EphA2 receptor tyrosine kinase binding 68Ga-labeled peptide radiotracer

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is difficult to diagnose and has dismal survival rates. Molecular imaging techniques such as positron emission tomography (PET) could fulfill an unmet need and enable an early diagnosis of PDAC to potentially improve survival. EphA2, a member of Erythropoietin-producing hepatocellular (Eph) receptors, plays a pivotal role in the tumorigenesis and development of an immune suppressive microenvironment in PDAC. We therefore developed a peptide-based PET imaging agent for EphA2, [68Ga]AJ201, and evaluated its pharmacokinetics and potential to non-invasively quantify variable EphA2 expression in PDAC.

Methods: A Gallium-68 labeled EphA2 binding peptide, [68Ga]AJ201, was synthesized in high radiochemical yields and purity. Surface plasmon resonance (SPR) analysis was carried out to measure binding affinity. EphA2 expression was assessed in PDAC cell lines and tissues in CCLE and TCGA. EphA2 expression in seven PDAC cell lines (Panc1, AsPC1 BxPC3, CFPAC1, Hs766T, Panc1005, and SU8686) was validated by RT-qPCR and flow cytometry. Those cell lines were then used for in vitro binding assays and the corresponding xenografts in NSG mice for PET imaging and ex vivo biodistribution studies (n=4-5/tumor). Specificity of [68Ga]AJ201 was confirmed by co-injection of a blocking dose of non-radioactive AJ201 (1 mg/kg).

Results: SPR analysis showed that AJ201 binds EphA2 with a high affinity (KD) of 0.2 nM. TCGA analysis revealed higher expression of EphA2 in PDAC vs healthy tissues. Flow cytometry analysis revealed high and variable EphA2 expression in all the PDAC cell lines tested with Panc1 exhibiting the highest levels. In vitro binding assays showed high and variable [68Ga]AJ201 uptake in all the PDAC cell lines and low uptake in the presence of 1µM non-radioactive AJ201 and in EphA2 negative Jurkat cells. Pharmacokinetics of [68Ga]AJ201 in mice with Panc1 tumors showed high contrast images of EphA2 expression at 60 minutes with a tumor/muscle ratio of 25.9±6.7. That high tumor uptake was significantly reduced in mice receiving blocking dose confirming the specificity of the radiotracer. Also, [68Ga]AJ201 PET quantified variable EphA2 expression in all the seven PDAC xenografts tested, with highest uptake observed in Panc1 tumor, followed by SU8686, and lowest in CFPAC1. Ex vivo biodistribution studies corroborated PET imaging findings.

Conclusion: [68Ga]AJ201 is a EphA2 specific high affinity peptide-based PET imaging agent that provides high contrast PET images of PDAC by 60 minutes. [68Ga]AJ201 PET has the potential to non-invasively detect PDAC in patients.

Citation Format: Kuldeep Gupta, Ajay Kumar Sharma, Akhilesh Mishra, Sophia Y. Chen, Gabi Lofland, Todd M. Armstrong, Lei Zhang, Elizabeth M. Jaffee, Sridhar Nimmagadda. Imaging pancreatic ductal adenocarcinoma using an EphA2 receptor tyrosine kinase binding 68Ga-labeled peptide radiotracer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2481.

Abstract 3820: Spatial transcriptomics of advanced hepatocellular carcinomas distinguishes intercellular interactions in responders and non-responders to cabozantinib and nivolumab neoadjuvant therapy

The recent development of genome-wide spatial transcriptomics (ST) approaches enable near single-cell gene expression profiling to infer cellular composition and intercellular interactions that drive cancer development and responses to therapy. This study applied ST on 10 surgical biospecimens from a clinical trial with neoadjuvant therapy with cabozantinib (multi-kinase inhibitor) and nivolumab (anti-PD-1 monoclonal antibody) with advanced hepatocellular carcinoma (HCC). Within our cohort, 6 of the samples were obtained from non-responders and 4 with demonstrated pathological response were previously associated with immune infiltration using spatial proteomics technologies. Our analysis with ST was performed to determine the specific pathways that drive immune infiltration in responders and to map intercellular interactions relevant for response and resistance to the combined therapy.Analysis of these data uncovered three main differences between responders and non-responders. First, to better understand the tumor mechanisms of response and resistance, we performed differential expression and pathway analysis only in the subset of tumor clusters from responders versus non-responders. In responders, we observed enrichment for pathways associated with immune response (TNF-alpha, IFN-gamma, T cell differentiation), while in non-responders the deregulated pathways are associated with cell growth, transcriptional activity and hypoxia (Myc, E2F, oxidative phosphorylation). Second, the intercellular interaction analyses indicate that CD8-HLA interactions are more abundant in responders, while interactions activating VEGFR, the main target of cabozantinib, are enriched in non-responders. The interaction profiles are evidence that in responders the tumor cells express tumor specific antigens that are recognized by the cytotoxic cells which activity is enhanced by nivolumab. In non-responders, the activation of the VEGF pathway is an indication that the tumor cells have developed mechanism of resistance to cabozantinib. Third, responding tumors have higher densities of immune and stromal cells, and the immune cells are enriched with aggregates composed of both B and T cells. The regions surrounded by these immune aggregates are transcriptionally distinct from regions enriched for stromal cells, suggesting that tumor gene expression profile drives immune infiltration.Overall, the ST analysis of neoadjuvant HCC treated samples detects tumor induced immune cell immune infiltration in responders compared to non-responders with enrichment of cytotoxic interactions to eliminate the tumor cells. It also identifies intercellular interactions suggestive of resistance to anti-VEGF blockade.

Citation Format: Luciane T. Kagohara, Shuming Zhang, Long Yuan, Qingfeng Zhu, Robert Anders, Daniel Shu, Aleksander S. Popel, Elizabeth M. Jaffee, Mark Yarchoan, Elana J. Fertig. Spatial transcriptomics of advanced hepatocellular carcinomas distinguishes intercellular interactions in responders and non-responders to cabozantinib and nivolumab neoadjuvant therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3820.

Abstract 637: Spatial transcriptomics for FFPE characterizes the molecular and cellular architecture of malignant changes in pancreatic pre-malignant lesions

We have optimized an experimental and computational pipeline to adapt spatial transcriptomics (ST) approaches based upon the Visium (10x Genomics) technology to infer cellular composition and intercellular interactions of FFPE clinical specimens. We apply this technology to deliver an approach to examine pancreatic intraepithelial neoplasia (PanIN) to identify intrinsic and extrinsic mechanisms that are associated with the progression of these pre-malignant lesions to invasive carcinoma. Currently, most pancreatic cancers are diagnosed at an advanced stage that reflects in dismal survival rates and a better understanding of PanINs biology will provide valuable insights for early therapeutic interventions. Thus, we used PanINs as our model system to implement the FFPE ST workflow. Our workflow for FFPE ST analysis facilitates sectioning of small regions (5mm in diameter) from a paraffin block that are stained and imaged with H&E and concurrently measured for genome-wide transcriptional profiling. Subsequently, the image is used for automated cell annotation using an algorithm, CODA, trained to identify normal and neoplastic pancreatic cell types. CODA identified the normal pancreatic histological regions (ducts, acini, islets of Langerhans, stroma), as well as the neoplastic cells. This automated analysis enables isolation of specific spots for differential expression analysis to pinpoint the transcriptional changes that occur within neoplastic cells along ducts in PanIn and their changes between high-grade and low-grade lesions. The spatial gene expression analysis identified clusters that mapped to the cell types annotated by CODA and the marker genes of each cluster matched known markers for the correspondent cell type. Although PanINs are very small in size (&lt; 1mm), we found specific clusters accurately mapped to these lesions in each sample. Overall, the spatial sequencing data presented enough depth and complexity to allow differential expression and pathway analysis. We observed a significant number of deregulated genes in PanINs compared to normal ducts. Some deregulated genes are known PanIN markers, but potential new markers were also identified. Moreover, the integration of CODA with gene expression changes enables us to verify that unique stromal regions annotated with CODA and associated with PanIns are in fact heterogeneous and formed by distinct cell subtypes. Altogether, our workflow combining automated cell annotation with STA from the same section provides a methodology to precisely examine the sample architecture while measuring heterogeneity at the transcriptional level. This combined approach can be applied to different FFPE tumor types to leverage the use of large bioarchives of samples not previously accessible to genome-wide spatial methods.

Citation Format: Alexander T. Bell, Kohei Fujikura, Jacob Stern, Rena Chan, James Chell, Stephen Williams, Ashley Kiemen, Elizabeth M. Jaffee, Denis Wirtz, Laura D. Wood, Elana J. Fertig, Luciane T. Kagohara. Spatial transcriptomics for FFPE characterizes the molecular and cellular architecture of malignant changes in pancreatic pre-malignant lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 637.