Subset Of Tumor Cells Research Articles

Spatial organization and stochastic fluctuations of immune cells impact clinical responsiveness to immunotherapy in melanoma patients

Abstract High-dimensional, spatial single-cell technologies such as CyTOF imaging mass cytometry (IMC) provide detailed information regarding locations of a large variety of cancer and immune cells in microscopic scales in tumor microarray (TMA) slides obtained from patients prior to immune checkpoint inhibitor (ICI) therapy. An important question is how the initial spatial organization of these cells in the tumor microenvironment (TME) change with time, regulate tumor growth and eventually outcomes as patients undergo ICI therapy. Utilizing IMC data of melanomas of patients who later underwent ICI therapy, we develop a spatially resolved interacting cell systems model that is calibrated against patient response data to address the above question. We find that the tumor fate in these patients is determined by the spatial organization of activated CD8+ T cells, macrophages, and melanoma cells and the interplay between these cells that regulate exhaustion of CD8+ T cells. We find that fencing of tumor cell boundaries by exhausted CD8+T cells is dynamically generated from the initial conditions that can play a pro-tumor role. Furthermore, we find that specific spatial features such as co-clustering of activated CD8+ T cells and macrophages in the pre-treatment samples determine the fate of the tumor progression, despite stochastic fluctuations and changes over the treatment course. Our framework enables determination of mechanisms of interplay between a key subset of tumor and immune cells in the TME that regulate clinical response to immune checkpoint inhibitors.

Abstract A040: A novel stroma-mediated positive interaction between resistant and sensitive cells in non-small cell lung cancer facilitates drug resistance

Abstract Resistance to targeted therapies, particularly those inhibiting oncogenic tyrosine kinases (TKIs), presents a significant challenge in the treatment of advanced non-small cell lung cancer (NSCLC). Despite initial robust clinical responses, tumors often relapse due to the emergence of resistant cell populations. The origins of this resistance—whether it is pre-existing in a subset of tumor cells or arises de novo during treatment—remains a critical question in understanding and combating therapeutic failure. To investigate this, we developed in silico mathematical models that integrate both pre-existing and de novo resistance mechanisms within a framework that explicitly integrates the stromal niche. Our study focused on the evolutionary dynamics of NSCLC in response to therapy, using a hybrid agent-based spatial modeling framework (HAL) to simulate tumor behavior under treatment. These models were designed to simulate the complex interactions between resistant and sensitive tumor cells, mediated by the stroma, and to predict the timing of relapse based on these interactions. Our findings suggest that stroma-mediated interactions play a crucial role in the evolutionary dynamics of therapy responses, influencing the fitness and survival of both resistant and sensitive cells. Specifically, our models predict that pre-existing resistance is unlikely to be compatible with the long remission periods observed in a substantial subset of patients treated with advanced anaplastic lymphoma kinase (ALK) inhibitors. This conclusion was supported by the observed relapse times and volumetric tumor growth data from subsequent animal models. Moreover, our analyses highlight the importance of ecological factors within the tumor microenvironment in shaping the response to therapy. The spatial models we developed reveal that the stroma can foster positive interactions between resistant and sensitive cells, thereby accelerating the emergence of resistance. These insights underscore the need to consider the stromal niche when developing new therapeutic strategies and when interpreting the dynamics of drug resistance. In conclusion, our study provides new insights into the role of stroma in mediating resistance to TKIs in NSCLC. By combining mathematical modeling with experimental data, we have elucidated how stroma-mediated interactions between tumor cells can influence the evolution of resistance, challenging the assumption that pre-existing resistance alone drives relapses in TKI-treated patients. Our findings emphasize the need for adaptive therapeutic approaches that anticipate and disrupt these microenvironmental interactions to improve patient outcomes. Citation Format: Rishi M. Shah, Sagnik Yarlagadda, Mark Robertson-Tessi, Bina Desai, Tatiana Miti, Daria Miroshnychenko, David Basanta, Andriy Marusyk, Alexander Anderson. A novel stroma-mediated positive interaction between resistant and sensitive cells in non-small cell lung cancer facilitates drug resistance [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A040.

Abstract A015: Aging limits stemness and tumor development in the lung by reprogramming iron homeostasis

Abstract Aging is the most important and well-recognized risk factor for cancer. Aging leads to systemic decline of physical fitness, significantly changing the macroenvironment from the early tumor initiation to the terminal stage of metastasis. However, the underlying mechanisms only start to emerge. Here, using physiologically aged autochthonous genetically engineered mouse models (GEMMs) and primary cells, we demonstrate that aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. Using single-cell transcriptomics, we uncover a distinct compositional landscape of cancer cell subsets in aged lung tumors, revealing a delay in the molecular progression of the lung lesions and an age-specific gene expression signature. Interestingly, key components of this gene signature were traced back to the aged cell of origin. Furthermore, the age-specific signature derived from GEMMs was predictive of patient age in human lung cancer, indicating conservation of the age-associated changes across species. Interestingly, our preliminary data suggested that tumor cells derived from aged tumor-bearing mice displayed higher metastatic potential, indicating that different mechanisms may govern tumor initiation and metastasis. Functional interrogation of the age-specific gene signature revealed that the loss of stemness and tumorigenic capacity is underpinned by aging-associated induction of the transcription factor NUPR1. We find that NUPR1 is induced in the cell of origin in aged mice and humans, which leads to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1 or iron supplementation restores stemness and promotes tumorigenic potential of aged alveolar cells. Conversely, targeting NUPR1 is detrimental to young alveolar cells by promoting ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites results in elevated NUPR1 expression, which is recapitulated in young cells by inhibition of DNA methylation. We uncover that, unlike the young, aged alveolar cells are functionally iron insufficient, which leads to loss of stemness and resistance to ferroptosis. Our results indicate that aging-associated reprogramming of the cell of origin determines tumor initiation potential, alters trajectory of tumor evolution and produces age-dependent vulnerabilities. These findings demonstrate that aging fundamentally changes the biology of lung cancer, shedding light on novel therapeutic modulation of cellular iron homeostasis or ferroptosis in regenerative medicine and in cancer prevention for the elderly population. Citation Format: Xueqian Zhuang, Qing Wang, Simon Joost, Alexander Ferrena, Melissa Blum, Klavdija Krause, Zhuxuan Li, Deyou Zheng, Emily S Wong, Tuomas Tammela. Aging limits stemness and tumor development in the lung by reprogramming iron homeostasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A015.

Abstract B013: Hallmarks of progression in early neoantigen-expressing lung adenocarcinoma

Abstract Lung adenocarcinoma (LUAD) is the leading cause of cancer-related mortality, largely due to its high prevalence rate and limited therapeutic options. Immunotherapy remains one of the most promising therapeutic avenues, yet further research is necessary to enhance therapy effectiveness for a broader range of patients. Central to the mechanism of immunotherapy is the detection of tumor neoantigens by cytotoxic T cells, which trigger the elimination of tumor cells. However, it is largely unknown how the early interaction between T cells and neoantigen-expressing tumor cells affects the acquisition of cancer hallmarks and tumor progression. To study this, our lab has developed the iNversion-INduced Joined neoAntigen (NINJA) genetically engineered mouse model in which we can initiate expression of a neoantigen in Kras-mutant, Trp53-null, tdTomato-expressing lung adenocarcinoma cells (KPT-NINJA). This system enables us to analyze tumor initiation, progression, and advanced LUAD development over 20 weeks in both neoantigen-expressing and non-expressing tumors. We defined cancer hallmark acquisition and tumor progression in our model by using a combination of multiplex immunofluorescence and computational algorithms to quantify tumor size, immune infiltration, metastasis, and expression of cancer molecular markers p-ERK and Ki67. We isolated tumor cell and immune cell subsets using neural networks to segment cells and tumor structures and used the colocalization of molecular markers to confirm the identity of various cell types. Our initial data validated that within immunogenic tumors there is an increase of T cell infiltration in tumors and have found immunogenic tumors are associated with overall smaller tumors at early time points. Interestingly, these tumors are associated with a decrease in p-ERK expression, suggesting immune infiltration is negatively correlated with p-ERK expression and tumor size. Together, these data indicate that increased immunogenic pressure may be disrupting early tumor proliferation and hallmark progression, shaping the trajectory of development at a very early stage. We are also correlating other molecular markers of tumor progression with immune infiltration, such as Ki67 expression, which we will colocalize with the other findings to construct a model of how tumors acquire hallmark capabilities from an immunogenic perspective. By isolating the mechanism of early tumor progression in immunogenic contexts, we can begin to predict disease trajectory. This will contribute to a better understanding of the mechanisms behind immune evasion and may uncover crucial insights to broaden immune therapy efficacy. Citation Format: Ishan Bansal, Jennifer Loza, Brian G. Hunt, Kelli Connolly, Srividhya Venkatesan, Nikhil Joshi. Hallmarks of progression in early neoantigen-expressing lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr B013.

Abstract A027: Acceleration of drug metabolism mediated by CYP3A4 enzyme activation provides a bona fide environmental resistance mechanism to targeted therapies

Abstract Background: Targeted therapies against oncogenic signaling addictions, including one resulting from EML4-ALK fusions, can induce strong and durable clinical responses. However, these therapies are not curative in advanced cancers, as a subset of tumor cells avoid elimination, and these persisting populations evolve resistance that drives tumor relapse. Using a drug screen, we found that the evolving ALK inhibitor (ALKi) persisters display exquisite sensitivity to the histone demethylase inhibitor, JIB04 in vitro. Paradoxically, validation studies in mice revealed that instead of enhancing tumor sensitivity, JIB04 desensitizes tumors to ALKi, alectinib and lorlatinib, suggesting that it activates an unknown environmental modifier. While JIB04 is not used in the clinics, we reasoned that deciphering the underlying mechanism could uncover environment-mediated resistance to ALKi that might be triggered by clinically relevant factors. Results: We found that the resistance-promoting effect of JIB04 in mice is mediated by reducing systemic ALKi concentrations. This reduction is attributable to accelerated pharmacokinetics, due to the hyperactivation of the P450 family member, CYP3A4. Higher CYP3A4 activity leads to faster drug clearance and reduced drug exposure to tumors. Importantly, JIB04 triggers a similar resistance to other clinically relevant CYP3A4 substrates, the frontline EGFR inhibitor, osimertinib and the recently introduced KRASG12C inhibitor, sotorasib. Finally, the resistance- promoting effects of JIB04 could be phenocopied by chemically unrelated activators of CYP3A4, indicating a wide generalizability of this macro-environmental therapy resistance mechanism. Conclusions: Our study uncovered that acceleration of drug metabolism, triggered by CYP3A4 enzyme activators is a bona fide environmental resistance mechanism. Since P450 family liver detoxifying enzymes mediate the metabolism of many drugs, this resistance mechanism is likely to be relevant to a broad range of therapeutic contexts. Significance: While the importance of pharmacokinetic considerations is widely appreciated, modulation of drug metabolism is not typically considered as a candidate mechanism when therapy resistance is encountered in research and clinical settings. Multiple dietary, pharmacological and genetic modifiers are known to modulate P450 family enzymes. Moreover, substantial variability in drug plasma concentrations was documented in patients treated with identical doses of targeted therapies, and this variability strongly correlated with variability in clinical responses. While the direct link between variability in CYP3A4 activity and clinical outcomes in human patients has yet to be established, the mechanism uncovered in our study might represent a substantial but entirely overlooked contributor to resistance. Consequently, consideration of this mechanism and monitoring of CYP3A4 activity and systemic drug levels might improve our understanding of the biology of therapy resistance and enable an actionable path to improve clinical outcomes. Citation Format: Pragya Kumar, Robert Vander Velde, Malgorzata Weh, Andriy Marusyk. Acceleration of drug metabolism mediated by CYP3A4 enzyme activation provides a bona fide environmental resistance mechanism to targeted therapies [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A027.

SMARCA4-Deficient Undifferentiated Carcinoma of the Gastroesophageal Junction: A Case Report

Abstract Introduction/Objective To report a rare case of the newly characterized variant of gastric carcinoma; undifferentiated carcinoma with intact SMARCB1 (INI1) but lost SMARCA4/SMARCA2, and approach to diagnosis. Methods/Case Report A case of gastric mass extending to the gastroesophageal junction, microscopically, showing sheets of atypical, medium to large, discohesive, polygonal cells with large eccentric and pleomorphic nuclei, variably prominent nucleoli, and eosinophilic cytoplasm with brisk mitosis, in the background of marked necrosis and granulomatous inflammation. And having focally positive staining for cytokeratin and negative for melanoma, diffuse large B-cell lymphoma, high grade neuroendocrine tumor, sarcoma, rhabdoid/myoid-specific immunohistochemistry (IHC) markers. The case was further characterized with immunophenotypic, cytogenetic, and molecular findings. Results (if a Case Study enter NA) By immunohistochemistry (IHC), the large tumor cells were positive for vimentin, FLi-1 and patchy CD71. A subset of tumor cells showed CD34 positivity. The tumor cells were mainly negative (with rare focal positivity) for all cytokeratin including (CK AE1/AE3, EMA, and CK OSCAR). Tumor cells were negative for specific markers for melanoma, GIST, sarcomatous tumors, squamous cell carcinoma, hematolymphoid malignancies, and neuroendocrine tumors. EBER-ISH and HHV-8 were negative. The Ki67 showed a proliferative index of ~60%. The tumor cells demonstrated retention of INI1 (SMARCB1) with loss of both SMARCA2 and SMARCA4 by IHC. Molecular studies detected an inactivating mutation of the retinoblastoma-1 gene (RB1 I124Rfs*6) and TP53 with altered function compared to wild-type (TP53-G245S) with no mutations or deletion of SMARCB1 gene. The status of SMARCA4 gene came as indeterminate. No microsatellite Instability detected. Conclusion Our study demonstrates the challenge of diagnosing the SMARCA4/SMARCA1-deficient undifferentiating gastric carcinoma especially with negative cytokeratin stains, showing the immunohistochemistry profile of the tumor and its molecular findings in our case.

Pan-cancer and single-cell analysis reveal dual roles of lymphocyte activation gene-3 (LAG3) in cancer immunity and prognosis

Lymphocyte activating gene-3 (LAG3) is a distinctive T cell co-receptor that is expressed on the surface of lymphocytes. It plays a special inhibitory immune checkpoint role due to its unique domain and signaling pattern. Our aim is to explore the correlation between LAG3 in cancers and physiological processes related to a range of cancers, as well as build LAG3-related immunity and prognostic models. By comprehensively using of datasets and methods from TCGA, GTE-x and GEO databases, cBioPortal, HPA, Kaplan-Meier Plotter, Spearman, CellMinerTM, we delved deeper into the potential impact of the LAG3 in cancer development. These include expression differences, Localization of tumor cell subsets, immune infiltration, matrix infiltration, gene mutations, DNA methylation, signaling pathways and prognosis. Furthermore, we explored LAG3 interactions with different drugs. LAG3 is highly expressed in ACC (p < 0.001), BRCA (p < 0.001), DLBC (p < 0.001), ESCA (p < 0.001), GBM (p < 0.001), HNSC (p < 0.001), KIRC (p < 0.001), LGG (p < 0.001), LUAD (p < 0.01), LUSC (p < 0.001), PAAD (p < 0.001), PCPG (p < 0.01), SKCM (p < 0.001), STAD (p < 0.001), TGCT (p < 0.001) and THCA (p < 0.05), while lowly expressed in COAD (p < 0.001), LIHC (p < 0.05), OV (p < 0.001), PRAD (p < 0.001), READ (p < 0.001), UCEC (p < 0.001) and UCS (p < 0.001). High expression of LAG3 correlates with longer overall survival (OS) in BLCA (HR = 0.67, p < 0.05), CESC (HR = 0.3, p < 0.001), HNSC (HR = 0.67, p < 0.01), LUSC (HR = 0.71, p < 0.05), OV (HR = 0.65, p < 0.01), STAD (HR = 0.68, p < 0.05), and UCEC (HR = 0.57, p < 0.01). Conversely, in KIRC (HR = 1.85, p < 0.001), KIRP (HR = 2.81, p < 0.001), and THYM (HR = 8.92, p < 0.001), high LAG3 expression corresponds to shorter OS. Comprehensive results for recurrence-free survival (RFS) indicate that LAG3 acts as a protective factor in BLCA, CESC, OV, and UCEC. Moreover, LAG3 is widely expressed in tumor-associated lymphocytes, positively correlating with tumor immune scores and stromal scores, and significantly present in the C2 immune subtype across various tumors. High LAG3 expression correlates with increased immune infiltration. LAG3 shows associations with MSI, TMB, and the MMR system, participating in multiple signaling pathways including the T cell receptor pathway. It also demonstrates positive correlations with sensitivity to eleven different drugs. Unlike traditional inhibitory immune checkpoints, LAG3 exhibits dual roles in clinical and immune prognostication across pan-cancers, making it a significant predictive factor. In some cancers, LAG3 serves as a risk factor, indicating adverse clinical outcomes. Conversely, in BLCA, CESC, OV, and UCEC, LAG3 acts as a protective factor associated with longer patient survival. LAG3 demonstrates strong associations within tumor immunity, participating in a range of immune and inflammatory signaling pathways. Elevated levels of LAG3 are linked not only to T cell exhaustion but also to increased immune infiltration and polarization towards M1 macrophages.

Expression of CD68 and CD163 in malignant epithelial cells of oral squamous cell carcinoma: Phenotypic shift or mere cell fusion

Background / purposeThe progression of epithelial to mesenchymal tissue (EMT) is a highly intricate process that facilitates the transformation of cancer cells, allowing them to changeover their characteristic epithelial properties to mesenchymal attributes. This notable change empowers the cells with enhanced mobility and the ability to migrate to distant locations. Furthermore, it is imperative to adopt the idea of macrophage tumor cell fusion to achieve comprehensive considerate of this phenomenon. Our primary objective was to conduct a thorough investigation of macrophage-restricted antigens expression, specifically CD68 and CD163, in malignant epithelial cells of oral cavity squamous cell carcinoma (OSCC) to elucidate aforementioned perceptions. Materials and methodsCD68 and CD163 immunohistochemical expression were assessed in oral squamous cell carcinoma (OSCC), encompassing both the neoplastic cells and the tumor-associated macrophages (TAMs). ResultsBoth CD68 and CD163 antigens were revealed in OSCC malignant epithelial cells in a granular cell pattern, localized in membrane and cytoplasm of tumor cells respectively as well as in the infiltrating TAMs. ConclusionThe macrophage antigens were not limited to the infiltrating tumor-associated macrophages (TAMs), but were also observed in a substantial proportion of OSCC malignant epithelial cells within the tumor parenchyma. This particular expression pattern may represent a subset of tumor cells that have undergone an epithelial to a mesenchymal phenotypic transition. In addition, fusion of macrophages with tumor cells cannot be excluded; both might be associated with increased metastatic activity of OSCC.

The Mechanisms of Immune Evasion in Cancer Stem Cells and Related Immunotherapy Advances

Cancer Stem Cells (CSCs), as a unique subset of tumor cells, play a crucial role in tumor initiation, progression, and recurrence due to their self-renewal and differentiation capabilities. CSCs exhibit significant immune evasion abilities, allowing them to escape host immune surveillance, leading to the failure of conventional treatments. This paper reviews the definition, characteristics, and immune evasion mechanisms of CSCs, including immune checkpoint pathways, immunosuppressive microenvironment, and changes in surface antigen expression. Additionally, it explores various immunotherapies targeting CSCs, such as immune checkpoint inhibitors, CAR-T cell therapy, tumor vaccines, and other emerging therapies, discussing their research progress and clinical application prospects. By comprehensively understanding the immune evasion mechanisms of CSCs and related immunotherapies, we aim to provide new insights and strategies for future cancer treatments.

Abstract A022: Neoadjuvant ablative radiation downstages high-risk features and alters immune response in pancreatic cancer

Abstract Purpose: Increasing evidence shows neoadjuvant (NA) therapy benefits surgical selection and survival in localized pancreatic cancer. However, the optimal NA therapy for resectable, borderline resectable (BRPC), and locally advanced pancreatic cancer (LAPC) remains unclear. We hypothesize that NA stereotactic ablative radiotherapy (SAbR) benefits patients with BRPC and LAPC who do not progress on chemotherapy (CTH), especially with arterial involvement. To evaluate this, we retrospectively reviewed outcomes and molecular features of patients treated with NA CTH and NA CTH followed by SAbR to understand the contribution of radiation. Methods: We retrospectively reviewed clinical data for 133 patients treated with NA CTH and 48 with NA CTH + SAbR. Bulk RNA sequencing was performed on fresh surgical tissue from 29 CTH-treated and 14 CTH + SABR-treated patients. We conducted gene set enrichment analysis (GSEA), CIBERSORTx cellular deconvolution, and Single-Cell Identification of Subpopulations with Bulk Sample Phenotype Correlation (Scissor) analysis to correlate clinical outcomes with transcriptomic features. Results: Molecular subtyping of PDAC transcriptomic signatures from post-treatment tissues revealed similar subtype proportions after both treatments. However, at baseline and before surgery, patients receiving SABR had more advanced clinical T staging, NCCN resectability, and arterial involvement. Despite this, the NA CTH + SAbR cohort showed similar overall survival, local-regional progression-free survival (LRPFS), and distant metastasis progression-free survival (DPFS) compared to NA CTH only. NA CTH + SABR-treated patients had significantly improved post-treatment T and N staging, tumor size, and treatment effect. These improvements correlated with better survival, LRPFS, and DPFS. RNAseq analysis indicated that patients with nodal involvement had significantly increased GSEA of MYC targets and worse DPFS. Tumor-arterial involvement at diagnosis significantly reduced local-regional control for NA CTH only. In contrast, patients with arterial involvement receiving NA CTH + SAbR had significantly improved local control. CIBERSORTx cell fraction deconvolution revealed no significant differences in tumor and immune cell subsets between treatments, but GSEA indicated substantial changes in immune-related gene sets, particularly those related to myeloid and T cell activation, suggesting functional changes correlating with treatment response and local control. Scissor identified gene signatures from activated CD8 T cells correlating with improved local control, while signatures from Treg and naïve T cells negatively impacted LRPFS. Conclusions: Molecular analysis and clinical features showed that patients treated with NA CTH + SAbR experienced downstaging and had similar outcomes, with indications of a differential immune response. Given these findings, the role of SAbR in the NA setting should be further evaluated, especially in the context of improved chemotherapy and novel combination therapies that leverage biological responses. Citation Format: Peter Q. Leung, Eslam A. Elghonaimy, Ahmed M. Elamir, Megan Wachsmann, Song Zhang, Neha Barrows, Rachel von Ebers, Cassandra Hamilton, Grace Josephson, Salwan Al Mutar, Patricio M. Polanco, Nina N. Sanford, Syed M. Ali Kazmi, Matthew R. Porembka, David Hsieh, Adam C. Yopp, Muhammad S. Beg, Herbert J. Zeh, Todd A. Aguilera. Neoadjuvant ablative radiation downstages high-risk features and alters immune response in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A022.

Abstract PR-08: Reprogramming and selective recruitment of distinct neutrophil subpopulations restrain cancer metastasis

Abstract Neutrophils are integral to the metastatic tumor microenvironment (TME), and discrete subsets of neutrophils have been associated with pro- and anti-tumor responses. However, the composition of neutrophils in the metastatic TME and strategies to harness neutrophils for the treatment of metastatic disease remain poorly understood. Here, we studied the role of neutrophils in metastatic disease using mouse models of metastatic pancreatic ductal adenocarcinoma (PDAC). By utilizing mouse PDAC cells driven by mutant KRAS and p53 with controllable expression of ovalbumin, an immunogenic antigen (“TumorAg ON” or “TumorAg OFF”), we found that TumorAg ON PDAC engendered more than 10-fold higher recruitment of neutrophils into liver metastatic lesions compared to TumorAg OFF PDAC. RNA sequencing analysis of micro-dissected metastatic lesions showed that TumorAg ON PDAC elicited transcription of genes associated with neutrophil chemotaxis, including Cxcr2 and its ligands. Multimodal immune phenotyping and imaging mass cytometry (IMC) analysis further revealed that neutrophils within metastatic lesions consisted of CXCR2high and CXCR2low subpopulations and were spatially associated with distinct subsets of tumor cells, T cells, and myeloid cells. In both mouse models of liver and lung metastasis, small molecule inhibition of CXCR2 using SX-682 led to enrichment of CXCR2low neutrophils and reduced metastatic burden in TumorAg ON PDAC. In contrast, CXCR2 inhibition had no impact on metastatic burden in TumorAg OFF PDAC. To define the subpopulations of neutrophils in further depth, we also performed single-cell spatial transcriptomics using Xenium. Notably, CXCR2 inhibition in TumorAg ON PDAC, but not in TumorAg OFF, led to enrichment of neutrophil subsets that expressed higher levels of Mpo, Nos2, and Ly6g and lower levels of Cxcr2 and Siglecf into metastatic lesions. In this setting, depletion of neutrophils using anti-Ly6G antibodies worsened metastatic burden, highlighting anti-tumor properties of these neutrophil subsets in the presence of antigenic recognition. Indeed, in a highly immune-resistant model of PDAC, 6419c5, the use of tumor-targeting listeria vaccine CRS-207 along with CXCR2 inhibition significantly reduced metastatic burden, whereas CXCR2 inhibitor or CRS-207 alone had no impact. To extend the clinical relevance of these observations, we analyzed serial tissue biopsies collected from patients with metastatic PDAC in the liver treated with immunotherapy regimen incorporating CRS-207 (NCT03190265). Consistent with our mouse model results, IMC analysis revealed increased proportion of MPOhigh NOS2high neutrophils upon treatment, suggesting that induction of tumor antigen response results in an effective remodeling of the neutrophil compartment . Taken together, our results show that neutrophils may acquire anti-tumor properties under appropriate inflammatory conditions and that distinct subpopulations of neutrophils may be leveraged for the treatment of metastatic disease. Citation Format: Jae W Lee, Diana Caroline Vargas Carvajal, Yeonju Cho, Sarah M Shin, Erin M Coyne, Alexei Hernandez, Courtney D Cannon, Xuan Yuan, Zhehao Zhang, Nicole E Gross, Soren Charmsaz, Daniel H Shu, Katherine M Bever, Dung T Le, Luciane T Kagohara, Elizabeth M Jaffee, Won Jin Ho. Reprogramming and selective recruitment of distinct neutrophil subpopulations restrain cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr PR-08.

Abstract B060: Unveiling resistance mechanisms to CAR T-cell therapy in pancreatic cancer through in vivo CRISPR/Cas9 knockout screening

Abstract Pancreatic ductal adenocarcinoma (PDAC) is projected to become the second leading cause of cancer death by 2030. PDAC lacks effective treatment options and innovative strategies for therapeutic intervention are urgently needed. Chimeric Antigen Receptor (CAR)-T cell therapy has shown remarkable success in treating hematologic malignancies, yet achieving efficacy in solid tumors remains a significant challenge. Early results from clinical trials show limited efficacy of CAR T-cell therapy in PDAC. To uncover tumor-intrinsic mechanisms of resistance to CAR T-cell therapy in vivo, we performed iterative CRISPR/Cas9-based pooled screens in a fully immunocompetent, orthotopic model of PDAC. We identified a variety of genes influencing CAR T-cell treatment efficacy. In particular, loss of genes involved in redox biology and oxidative stress sensitized PDAC tumors to CAR T-cell therapy in vivo. Additionally, single-cell RNA sequencing of PDAC tumors subjected to CAR T-cell therapy unveiled a distinct subset of tumor cells resilient to the treatment, characterized by changes in oxidative stress. Our findings indicate a potential avenue for therapeutic synergy by targeting pathways involved in oxidative stress to increase the efficacy of CAR T cell therapy in PDAC. Citation Format: Julia Fröse, Charlie Whittaker, Paul Leclerc, Adam Langenbucher, Riley Hellinger, Daniel R. Goulet, Michael T. Hemann. Unveiling resistance mechanisms to CAR T-cell therapy in pancreatic cancer through in vivo CRISPR/Cas9 knockout screening [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B060.

Abstract A055: Multiomics profiling reveals druggable tumor-stroma interactions in ATM-deficient pancreatic cancer

Abstract The complex biology of pancreatic ductal adenocarcinoma (PDAC) remains a significant challenge and limits overcoming its dismal prognosis. The tumor microenvironment (TME), shaped by dynamic interactions between cancer-associated fibroblasts (CAFs), immune and tumor cells, plays a crucial role in PDAC pathogenesis. Uncharted field lies in the impact of specific gene mutations within the tumor epithelium on orchestrating distinct oncogenic TME patterns. Our investigation into homologous recombination deficiency (HRD), caused by mutations in genes like ATM, reveals its role in promoting PDAC aggressiveness and triggering a pronounced desmoplastic reaction, suggesting a unique TME programing. Through single-cell-resolved and multiomics analyses of murine ATM and/or P53-depleted PDACs, and validation in human cases, we unveil transcriptional, translational, and secretory regulatory events, shed light on the intricate interplay between tumor genetics and PDAC microenvironment and pave the way for the elaboration of novel personalized therapies. Murine tumor analysis using single-nucleus multiomics RNA and ATAC sequencing, alongside histological validation in human tissues, revealed specific enrichment of myCAFs in ATM-deficient tumors and reduced populations of T cells and macrophages. Molecular signatures and cell-cell communication inference uncovered ATM-specific interactions within the TME, highlighting TGF-β signaling as pivotal in mediating dialog between CAFs and an aggressive EMT-like tumor cell subset prevalent in ATM-depleted tumors. Additionally, distinct communication patterns were observed between CAFs and immune cells, associated with specific epigenetic and molecular profiles. Mechanistically, transcriptomics, secretomics and proteomics investigations confirmed increased TGFβ release by ATM-deficient PDAC cells and identified a reactive oxygen species (ROS)-mediated mechanism affecting tumor cell behavior and interactions with CAFs. Consistently, a combinatorial therapy targeting TGF-β-mediated tumor-stroma dialog reversed cancer-promoting TME remodeling and exacerbated FOLFIRINOX cytotoxic effects, in vivo, exclusively in ATM-deficient HRD PDACs. Dissecting the biology of ATM-deficient HRD malignant cells, our study unveils their pivotal role in orchestrating oncogenic communication networks with CAFs and immune cells, along with specific tumor promoting stromal reprogramming. Our findings paint a comprehensive picture of how distinct tumor-stroma interactions reshape the TME, steering it towards a cancer-promoting outcome and shed light on the potential to exploit genotype-specific vulnerabilities via tailored tumor-stroma interference strategies. Citation Format: Elodie Roger, Hannah M. Mummey, Eleni Zimmer, Julia Ragg, Yuna Lee, Kyle J. Gaulton, Alica K. Beutel, Christopher J. Halbrook, Lukas Perkhofer, Johann Gout, Alexander Kleger. Multiomics profiling reveals druggable tumor-stroma interactions in ATM-deficient pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A055.

Trametinib Sensitivity is Defined by a Myeloid Differentiation Profile in Acute Myeloid Leukemia.

Acute myelogenous leukemia (AML) is a common blood cancer marked by heterogeneity in disease and diverse genetic abnormalities. Additional therapies are needed as the 5-year survival remains below 30%. Trametinib is a mitogen-activated extracellular signal-regulated kinase (MEK) inhibitor that is widely used in solid tumors and also in tumors with activating RAS mutations. A subset of patients with AML carry activating RAS mutations; however, a small-scale clinical trial with trametinib showed little efficacy. Here, we sought to identify transcriptomic determinants of trametinib sensitivity in AML. We tested the activity of trametinib against a panel of tumor cells from patients with AML ex vivo and compared this with RNA sequencing (RNA-Seq) data from untreated blasts from the same patient samples. We then used a correlation analysis between gene expression and trametinib sensitivity to identify potential biomarkers predictive of drug response. We found that a subset of AML tumor cells were sensitive to trametinib ex vivo, only a fraction of which (3/10) carried RAS mutations. On the basis of our RNA-Seq analysis we found that markers of trametinib sensitivity are associated with a myeloid differentiation profile that includes high expression of CD14 and CLEC7A (Dectin-1), similar to the gene expression profile of monocytes. Further characterization confirmed that trametinib-sensitive samples display features of monocytic differentiation with high CD14 surface expression and were enriched for the M4 subtypes of the FAB classification. Our study identifies additional molecular markers that can be used with molecular features including RAS status to identify patients with AML that may benefit from trametinib treatment.

Stimulator of Interferon Genes-Activated Biomimetic Dendritic Cell Nanovaccine as a Chemotherapeutic Booster to Enhance Systemic Fibrosarcoma Treatment.

Fibrosarcoma, a malignant mesenchymal tumor, is characterized by aggressive invasiveness and a high recurrence rate, leading to poor prognosis. Anthracycline drugs, such as doxorubicin (DOX), represent the frontline chemotherapy for fibrosarcoma, but often exhibit suboptimal efficacy. Recently, exploiting the stimulator of interferon genes (STING)-mediated innate immunity has emerged as a hopeful strategy for cancer treatment. Integrating chemotherapy with immunomodulators in chemo-immunotherapy has shown potential for enhancing treatment outcomes. Herein, we introduce an advanced dendritic cell (DC) nanovaccine, cGAMP@PLGA@CRTM (GP@CRTM), combined with low-dose DOX to enhance fibrosarcoma chemo-immunotherapy. The nanovaccine consists of poly(lactic-co-glycolic acid) (PLGA) nanoparticles encapsulating the STING agonist 2,3-cGAMP (cGAMP@PLGA, GP) as its core, and a calreticulin (CRT) high-expressing fibrosarcoma cell membrane (CRTM) as the shell. Exposing CRT on the vaccine surface aids in recruiting DCs and stimulating uptake, facilitating efficient simultaneous delivery of STING agonists and tumor antigens to DCs. This dual delivery method effectively activates the STING pathway in DCs, triggering sustained immune stimulation. Simultaneously, low-dose DOX reduces chemotherapy-related side effects, directly kills a subset of tumor cells, and increases tumor immunogenicity, thus further amplifying immune therapeutic performance. Hence, these findings demonstrate the potential of DC nanovaccine GP@CRTM as a booster for chemotherapy. Synergistically combining low-dose DOX with the DC nanovaccine emerges as a powerful chemo-immunotherapy strategy, optimizing systemic fibrosarcoma therapy.

DNA mismatch repair defect and intratumor heterogeneous deficiency differently impact immune responses in diffuse large B-cell lymphoma

ABSTRACT Deficient (d) DNA mismatch repair (MMR) is a biomarker predictive of better response to PD-1 blockade immunotherapy in solid tumors. dMMR can be caused by mutations in MMR genes or by protein inactivation, which can be detected by sequencing and immunohistochemistry, respectively. To investigate the role of dMMR in diffuse large B-cell lymphoma (DLBCL), MMR gene mutations and expression of MSH6, MSH2, MLH1, and PMS2 proteins were evaluated by targeted next-generation sequencing and immunohistochemistry in a large cohort of DLBCL patients treated with standard chemoimmunotherapy, and correlated with the tumor immune microenvironment characteristics quantified by fluorescent multiplex immunohistochemistry and gene-expression profiling. The results showed that genetic dMMR was infrequent in DLBCL and was significantly associated with increased cancer gene mutations and favorable immune microenvironment, but not prognostic impact. Phenotypic dMMR was also infrequent, and MMR proteins were commonly expressed in DLBCL. However, intratumor heterogeneity existed, and increased DLBCL cells with phenotypic dMMR correlated with significantly increased T cells and PD-1+ T cells, higher average nearest neighbor distance between T cells and PAX5+ cells, upregulated immune gene signatures, LE4 and LE7 ecotypes and their underlying Ecotyper-defined cell states, suggesting the possibility that increased T cells targeted only tumor cell subsets with dMMR. Only in patients with MYC¯ DLBCL, high MSH6/PMS2 expression showed significant adverse prognostic effects. This study shows the immunologic and prognostic effects of genetic/phenotypic dMMR in DLBCL, and raises a question on whether DLBCL-infiltrating PD-1+ T cells target only tumor subclones, relevant for the efficacy of PD-1 blockade immunotherapy in DLBCL.

Timing of whole genome duplication is associated with tumor-specific MHC-II depletion in serous ovarian cancer

Whole genome duplication is frequently observed in cancer, and its prevalence in our prior analysis of end-stage, homologous recombination deficient high grade serous ovarian cancer (almost 80% of samples) supports the notion that whole genome duplication provides a fitness advantage under the selection pressure of therapy. Here, we therefore aim to identify potential therapeutic vulnerabilities in primary high grade serous ovarian cancer with whole genome duplication by assessing differentially expressed genes and pathways in 79 samples. We observe that MHC-II expression is lowest in tumors which have acquired whole genome duplication early in tumor evolution, and further demonstrate that reduced MHC-II expression occurs in subsets of tumor cells rather than in canonical antigen-presenting cells. Early whole genome duplication is also associated with worse patient survival outcomes. Our results suggest an association between the timing of whole genome duplication, MHC-II expression and clinical outcome in high grade serous ovarian cancer that warrants further investigation for therapeutic targeting.

Tumor and cancer stem cells‐derived exosomes interplay: A secret of cancer complications

AbstractCancer stem cells (CSCs) are a small subset of tumor cells, efficient in self‐renewal within the tumor and also play a vital role in cancer resistance and metastasis. Recent cancer research has focused on exosomes, a tiny subpopulation of extracellular vesicles (EVs), known for their role in intercellular communication, and significantly contributing to tumor development and metastasis (Tumor derived exosomes‐TEXs). These exosomes complicate cancer treatment by promoting tumor and CSC formation and developing drug and therapeutic resistance. This article explores how tumor‐derived exosomes impact CSC survival, proliferation, and resistance to therapies, leading to tumor recurrence. In a tumor microenvironment (TME), exosomes facilitate tumor growth and metastasis. Targeting exosomes could disrupt CSC communication and improve cancer treatment efficacy. Current studies highlight the role of CSCs exosomes in cancer progression and therapeutic resistance. Understanding CSCs exosome‐based cell‐to‐cell communication in tumor opens a new horizon in cancer therapeutics development.

ETMR-32. SUPRATENTORIAL NEUROEPITHELIAL TUMOR WITH PLAGL1 FUSION: A CASE REPORT

Abstract BACKGROUND Supratentorial neuroepithelial tumor with PLAGL1 fusion has emerged as a novel subgroup within pediatric brain tumors. Despite its recent identification, critical aspects such as optimal clinical characteristics and management strategies remain elusive. This case report aims to contribute essential insights to the growing body of literature surrounding this enigmatic tumor entity, providing a detailed exploration of its clinical presentation and histopathological features. METHODS A retrospective chart review was conducted, and relevant data were analyzed. RESULTS An 11-year-old female presented with a two-week history of headaches, vomiting, lethargy, and decreased oral intake. Neuroimaging revealed a left frontal lesion with conspicuous mass effect and midline shift, prompting urgent craniotomy due to sudden onset altered mental status. Histopathological analysis revealed a hypercellular glial neoplasm characterized by perivascular pseudorosettes, scattered microcalcifications, microcysts, and areas of necrosis. Immunohistochemical staining revealed GFAP positivity in a substantial subset of tumor cells, rare dot-like positivity for EMA, and diffuse membranous and focal dot-like positivity for D240. Olig2 was mostly negative, indicating the absence of Oligodendrocyte lineage differentiation. The tumor exhibited an elevated Ki-67 proliferation index (approximately 20-30%). Fluorescence in situ hybridization (FISH) studies were negative for RELA, YAP1, and C19MC rearrangements. Targeted next-generation sequencing unveiled an EWSR1-PLAG1 fusion and methylation profiling classified the tumor as “Neuroepithelial tumors, PLAG1-fused” with high confidence. Given the morphological resemblance to anaplastic ependymoma, the therapeutic recommendation included focal irradiation (54 Gy) with proton therapy. The patient, now 12 months post-therapy, is showing favorable clinical outcomes. CONCLUSION This case report underscores the clinical and histopathological intricacies of supratentorial neuroepithelial tumors with PLAGL1 fusion. The identification of EWSR1-PLAG1 fusion and associated molecular alterations informs diagnostic considerations and treatment strategies for this novel entity, emphasizing the importance of continued research to enhance our understanding of its clinical behavior and optimal management approaches.

Exploring the connection between BRCA2 and thyroid cancer

Abstract Background This study investigated the multifaceted role of BRCA2 (breast cancer 2) in various cancer types, with a specific focus on thyroid carcinoma (THCA). Methods Data sets were obtained from the University of California Santa Cruz database to analyze BRCA2 expression, genetic alterations, and clinical implications. Sample filtering criteria were applied, and immunohistochemistry from the Human Protein Atlas was used to validate protein expression. Correlation analyses were used to explore associations between immune-related genes, and immunological signatures were assessed using various tools. Genetic alterations in BRCA2 were analyzed using cBioPortal, and prognostic analysis involved evaluating gene expression differences at different clinical stages of THCA. Results In patients with THCA, differences in BRCA2 expression were observed at both the mRNA and protein levels when comparing tumor and normal tissues. Correlation studies revealed associations between BRCA2 and immune-related genes, emphasizing its potential role in modulating the tumor microenvironment. Immunological signature analyses indicated distinct frequencies of tumor-infiltrating immune cell subsets in BRCA2 high versus low tumors. Moreover, genetic alterations in BRCA2, particularly the A2738S mutation in exon 18, have been identified in patients with THCA. The prognostic analysis demonstrated a significant correlation between altered BRCA2 levels and improved overall survival in patients with THCA. Additionally, BRCA2 expression was associated with prognostic factors such as stage and N. Conclusions This study provides a holistic exploration of BRCA2 in cancer and highlights its diverse roles in expression, immune modulation, genetic alterations, and clinical prognosis. These findings underscore the potential significance of BRCA2 as a diagnostic and prognostic marker and offer valuable insights for future research and potential clinical applications in cancer management.