Tumor-immune Cell Interactions Research Articles

Integrative single-cell analysis of LUAD: elucidating immune cell dynamics and prognostic modeling based on exhausted CD8+ T cells.

The tumor microenvironment (TME) plays a pivotal role in the progression and metastasis of lung adenocarcinoma (LUAD). However, the detailed characteristics of LUAD and its associated microenvironment are yet to be extensively explored. This study aims to delineate a comprehensive profile of the immune cells within the LUAD microenvironment, including CD8+ T cells, CD4+ T cells, and myeloid cells. Subsequently, based on marker genes of exhausted CD8+ T cells, we aim to establish a prognostic model for LUAD. Utilizing the Seurat and Scanpy packages, we successfully constructed an immune microenvironment atlas for LUAD. The Monocle3 and PAGA algorithms were employed for pseudotime analysis, pySCENIC for transcription factor analysis, and CellChat for analyzing intercellular communication. Following this, a prognostic model for LUAD was developed, based on the marker genes of exhausted CD8+ T cells, enabling effective risk stratification in LUAD patients. Our study included a thorough analysis to identify differences in TME, mutation landscape, and enrichment across varying risk groups. Moreover, by integrating risk scores with clinical features, we developed a new nomogram. The expression of model genes was validated via RT-PCR, and a series of cellular experiments were conducted, elucidating the potential oncogenic mechanisms of GALNT2. Our study developed a single-cell atlas for LUAD from scRNA-seq data of 19 patients, examining crucial immune cells in LUAD's microenvironment. We underscored pDCs' role in antigen processing and established a Cox regression model based on CD8_Tex-LAYN genes for risk assessment. Additionally, we contrasted prognosis and tumor environments across risk groups, constructed a new nomogram integrating clinical features, validated the expression of model genes via RT-PCR, and confirmed GALNT2's function in LUAD through cellular experiments, thereby enhancing our understanding and approach to LUAD treatment. The creation of a LUAD single-cell atlas in our study offered new insights into its tumor microenvironment and immune cell interactions, highlighting the importance of key genes associated with exhausted CD8+ T cells. These discoveries have enabled the development of an effective prognostic model for LUAD and identified GALNT2 as a potential therapeutic target, significantly contributing to the improvement of LUAD diagnosis and treatment strategies.

Abstract 6925: Integrative single-cell tracking of genome evolution and tumor cell plasticity in small cell lung cancer (SCLC)

Abstract SCLC is the deadliest type of lung cancer, which is mostly diagnosed at late stages and accounts for 15% of pulmonary tumors. Even though chemotherapy is initially effective, patients with SCLC relapse quickly and develop resistant tumors. Genome studies revealed a universal loss of TP53 and RB1; recent transcriptional studies categorized SCLC based on the expression of 4 lineage transcription factors (TFs). We aimed to dissect how genomic cues impact transcriptional phenotypes, tumor cell plasticity and the dynamics of tumor and immune cell interactions, to thus decipher molecular mechanisms of phenotypic divergence and therapy resistance in SCLC. We performed genome sequencing and single cell transcriptome profiling of 55 tumors from patients with SCLC, including primary tumors, local and distant metastases and of paired relapsing tumors acquired after chemotherapy. Single cell sequencing was performed with the 10x Genomics platform and yielded > 200.000 cells. Transcriptome profiles at single cell levels revealed co-expression of at least two of the lineage TFs ASCL1, NEUROD1 or POU2F3 in each tumor. Copy number (cn) estimation for transcriptome data pointed to genomic events impacting transcriptional heterogeneity within the tumor. Furthermore, our data pointed to a marked intra- and interpatient, as well as to inter-metastatic heterogeneity. To specifically investigate how underlying genetic alterations affect molecular phenotypes, integrative studies across all patients were performed. This revealed shared transcriptional programs in tumors with amplifications of MYC family members; trajectory inference for cases with low and high-level copy gains of MYCN pointed to distinct transcriptional states. We performed multi-regional and longitudinal studies of matched patient cases to reconstruct the genomic patterns of clonal evolution, and projected genomic subsets to transcriptional profiles at single cell level, thus analyzing the effect of genome diversity on the transcriptional landscape. Additionally, tumor intrinsic profiles of heterogeneity were mapped to single cell data of patient tumors to elucidate the effects on tumor-immune cell interactions. All together our data points to a concerted regulation of a multitude of lineage factors and transcriptional programs in each SCLC tumor and provides a first comprehensive framework for the study of underlying genetic alterations that shape the transcriptional landscape and phenotypic plasticity in SCLC. Citation Format: Marcel Schmiel, Laura Kaiser, Maria Cartolano, Martin Peifer, Roman K. Thomas, Julie George. Integrative single-cell tracking of genome evolution and tumor cell plasticity in small cell lung cancer (SCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6925.

Abstract 7228: In-vitro efficacy of Dordaviprone/GSK126 combination therapy on castration resistant and neuroendocrine prostate cancer

Abstract Neuroendocrine prostate cancer (NEPC) is an aggressive histologic subtype associated with poor prognosis that commonly arises in later stages as a mechanism of treatment resistance. Activation of oncogenic drivers, in combination with epigenetic changes (such as EZH2 overexpression and DNA methylation) further promotes tumor proliferation and expression of downstream neuroendocrine lineage pathways (in part controlled by transcription factors, including SOX2, ASCL1, and BRN2). Importantly, EZH2 inhibitors (EZH2i) can restore AR expression in CRPC (Ku et al., 2017). Imipridones, including Dordaviprone (ONC201), show promise in treating neuroendocrine tumors by interacting with DRD2 and CLpP (Anderson et al., 2022). These results warrant investigation into the potential for synergism in imipridone/EZH2i combination therapies. In the PCa cell lines LNCap, PC3, 22Rv1, and DU145 the combination of ONC201 and EZH2i GSK126 was assessed. Cell viability data after treatment with ONC201 and GSK126 reveals several dose ranges with potential synergistic activity after 72h. Preliminary western blots after 72 hours of GSK126 treatment indicate modulation of proteins relevant to the mechanism of action of imipridones, specifically DR5 and CLpP, in LNCap, PC3, and 22Rv1. Notably, the decrease in DR5 expression warrants investigation into the effects of EZH2i on TRAIL sensitivity and whether imipridones may rescue DR5 expression to maintain TRAIL sensitivity. Subsequent experiments will investigate dosing and time point-based effects on viability and protein expression, in addition to assessing the synergy of other imipridones and EZH2i’s. Further, while the cell lines PC3, 22Rv1, and DU145 are castration-resistant, the neuroendocrine prostate cell line NCI-H660 will be used as a positive control as it expresses higher neuroendocrine features, including DRD2. Additionally, the modulation in DR5 expression warrants inquiry into the effects of combination therapy on tumor-immune cell interactions. Further, we will manipulate the expression of neuroendocrine transcription factors to assess changes in therapy sensitivity. Citation Format: Connor Purcell, Praveen Srinivasan, Maximilian Pinho-Schwermann, William MacDonald, Elizabeth C. Ding, Vida Tajiknia, Wafik El-Deiry. In-vitro efficacy of Dordaviprone/GSK126 combination therapy on castration resistant and neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7228.

Abstract 7409: SpatialCells: Automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data

Abstract Cancer is a complex cellular ecosystem where malignant cells coexist and interact with immune, stromal, and other cells within the tumor microenvironment. Recent technological advancements in spatially resolved multiplexed imaging at single-cell resolution have led to the generation of large-scale and high-dimensional datasets from biological specimens. This underscores the necessity for automated methodologies that can effectively characterize the molecular, cellular, and spatial properties of tumor microenvironments for various malignancies. This study introduces SpatialCells, an open-source software package designed for region-based exploratory analysis and comprehensive characterization of tumor microenvironments using spatially resolved multiplexed single-cell data. We have provided detailed documents and tutorials at https://github.com/SemenovLab/SpatialCells. SpatialCells is featured by its capability to computationally define regions of interest based on any group of cells and subsequently conduct region-based analyses. SpatialCells incorporates several modules to facilitate its functionality, such as the spatial module and the measurements module. Our workflow starts with developing the spatial module, including functions to establish regional boundaries and check the region in which a cell is located. In particular, SpatialCells supports macro-region and micro-region analyses. In the macro-region analysis, users can employ SpatialCells to divide the whole tissue into several subregions, such as tumor, tumor border, stroma border, and stroma. In the micro-region analysis, SpatialCells identifies small regions within an area, such as within the tumor area, enabling a finer-grained understanding of the cellular landscape. The measurements module contains functions to extract the properties of tumor cells, immune cells, and tumor-immune cell interactions, such as multivariate tumor proliferation index, immune infiltration score, and tumor-immune cell distances. These properties can be assessed for the whole tissue or local regions. Importantly, SpatialCells can efficiently process datasets containing millions of cells. In summary, SpatialCells is a novel software solution for spatially analyzing the tumor microenvironment and automatically extracting quantitative features of cells using multiplexed imaging data in a streamlined fashion with the capacity to process samples containing millions of cells. Thus, SpatialCells facilitates subsequent association analyses and machine learning predictions at scale, making it an essential tool in advancing our understanding of tumor growth, invasion, and metastasis. Citation Format: Guihong Wan. SpatialCells: Automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7409.

Abstract 730: Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development

Abstract Background: Combining proteogenomics with laser capture microdissection (LCM) in cancer research offers a targeted way to explore the intricate interactions between tumor cells and the tumor microenvironment. This is especially important for immuno-oncology (IO) research where improvements in the predictability of patient response to IO-based drugs is sorely needed. An improved understanding of the spatial relationships involving tumor cells proper, stromal cells, blood supply and immune cell interactions may help to inform drug development and improve the indicators of success for IO-based drug regimens. Methods: LCM is used to isolate and obtain distinct histological cell types from fresh frozen tissue. Once cells have been captured, nucleic acids and proteins are extracted for in-depth multi-modality molecular profiling assays involving multiple genomic modalities and a customized solution-based mass spectrometry proteomics approach for samples or specimens with a limited amount of tissue. Results: Optimizing analysis of minute tissue quantities from LCM captured cells is challenging. Following the isolation of nucleic acids, RNA-seq may be performed for gene expression and DNA sequencing performed for the discovery and analysis of actionable mutations, copy number variation, and methylation profiles. Regarding genomic-based studies, commercial kits are often utilized for these steps due to their general availability, rapid innovation, and the robust performance of these products. However, this kit-based adaptive approach is not true for proteomics. There remains a need for highly sensitive proteomic methods targeting small-sized samples. A significant part of our proteogenomics approach is focused around an enhanced liquid chromatography mass spectrometry (LC-MS) analysis of micro-scale and/or nano-scale tissue sections. This is achieved with a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) approach developed for LC-MS analysis of fresh-frozen tissue specimens obtained via LCM. This includes an in-gel digestion method adjusted and specifically designed to maximize the proteome coverage from amount-limited LCM samples to better facilitate in-depth molecular profiling. Conclusions: Reported here is a proteogenomic approach that is leveraging from microdissected fresh frozen tissue. The methodology may also be applicable to other types of specimens having limited nucleic acids, protein quantity, and/or sample volume. Citation Format: Ik Jae Shin, Michael Tangrea, Michael R. Emmert-Buck, Donald J. Johann. Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 730.

Abstract 6528: Integrin ɑvβ6 upregulation as a mechanism of T-cell evasion in head and neck squamous cell carcinoma

Abstract Head and neck squamous cell carcinoma (HNSCC) encompasses malignancies of the mucosal epithelium in the oral cavity, pharynx, and larynx. The lack of effective screening strategies and the typically late stage of detection are contributors to a considerable annual death toll of HNSCC. Additionally, the anatomical proximity of the malignancy to delicate structures of the head and neck leads to tremendous treatment-related morbidity. Therefore, there is great interest in developing life-saving therapies and strategies for treatment de-escalation. The immune checkpoint inhibitor pembrolizumab (αPD-1) has been approved for recurrent or metastatic HNSCC and as a frontline therapy for unresectable disease. However, only about a quarter of patients respond to αPD-1 therapy. The immunosuppressive effect of TGFβ has been widely described as relevant to the HNSCC tumor microenvironment. However, attempts to blockade TGFβ have failed mainly due to the widespread side effects of disrupting a highly promiscuous cytokine. Integrin αvβ6 is a major activator of the inert latent TGFβ into the active, immunosuppressive form. With its high relative specificity to HNSCC tissue, inhibition of αvβ6 could offer a safer approach for disrupting TGFβ to overcome resistance to immune checkpoint blockade. After screening ɑvβ6 expression levels of HNSCC cell lines via flow cytometry, cell lines FaDu and CAL27 were selected for further investigation due to high endogenous ITGB6 expression (FaDu 35.57% cells ITGB6+, CAL27 95.69% cells ITGB6+). The cell lines were transduced with a doxycycline-inducible short hairpin RNA (shRNA) knockdown of αvβ6 using a lentiviral system. Both knockdown and control shRNA cell lines were pretreated with 1 μg/mL of doxycycline for five days to induce the shRNA and subsequently co-cultured with TALL-104 T-cells. Quantitative fluorescence microscopy of the co-culture revealed that the knockdown of αvβ6 substantially increased T-cell killing over 24hrs (FaDu CTRL shRNA 6.72%±2.49 dead vs. FaDu ITGB6 shRNA 12.80%±3.16 dead, p<0.001). However, treatment of FaDu and CAL27 cell lines with active-TGFβ showed no change in PD-L1 expression via flow cytometric analysis. To determine whether the T cell evasive effect of αvβ6 is driven by other immune checkpoints on the cancer cells or by the direct effect that TGFβ has on immune cells, we show the generation of relevant mouse αvβ6 shRNA knockdown cells. These syngeneic in vivo studies will facilitate cytokine profiling to uncover the dynamics of tumor-immune cell interactions in response to αvβ6 inhibition. Citation Format: William J. MacDonald, Praveen R. Srinivasan, Maximilian Pinho-Schwermann, Shengliang Zhang, Vida Tajiknia, Connor Purcell, Jillian Strandberg, Nolan Stubbs, Wafik S. El-Deiry. Integrin ɑvβ6 upregulation as a mechanism of T-cell evasion in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6528.

Abstract 6678: Microbial regulation of anti-tumor immunity in colorectal cancer

Abstract Colorectal cancer (CRC) is the 3rd leading site of cancers and cause of cancer cell death. Although Immunotherapies revolutionized cancer therapy, the majority of CRC patients, particularly with metastatic disease, do not respond to the treatments. This necessitates a better mechanistic understanding of the tumor-immune cell interactions in the context of CRC. Microbiome influences multiple biological aspects of the host including immune responses against cancers. Here, we show that the gut microbiome influences cancer MHC-I and -II expression levels and restricts tumor progression and metastasis, resulting in longer survival in 3 different CRC models and two different mouse strains. We found that the anti-tumor effects are dependent on T cells and B cells. Interestingly, depletion of B cell negated anti-metastatic effects of gut microbiome. Mechanistically, MHC-II expression in cancer cells mediates the anti-tumor effects of the microbiome. MHC-II upregulation on human CRC organoids enhances cancer-immune cell interactions and associated apoptosis, demonstrating an anti-tumor role and significance of MHC-II in human CRC. Thus, gut microbes that enhance MHC-II antigen presentation promotes anti-tumor immunity and may be utilized to enhance efficacy of immunotherapy in metastatic CRC. Citation Format: Charlie Chung, Elif Ozcelik, Jill Habel, Jialin Zhang, Yihan Qin, Libia Garcia, Joseph Merrill, Taemoon Chung, Scott Lyons, Zeli Shen, James G. Fox, Peter Westcott, Semir Beyaz. Microbial regulation of anti-tumor immunity in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6678.

Abstract 3379: Single-cell profiling reveals dynamic epithelial and immune cell interactions in the progression of lung adenocarcinoma

Abstract Background: Lung adenocarcinoma (LUAD) is a leading cause of cancer-related deaths. Our understanding of LUAD initiation and progression is limited, impeding early diagnosis and effective treatment. A comprehensive single-cell transcriptomic analysis, unraveling the malignant transformation from normal lung to LUAD, will provide key insights into the initiation and development of this challenging disease. However, human tissues are not amendable for such analysis. Methods: We generated two mouse models, a genetically engineered mouse model with KrasG12D activating mutation (GEMM) and a carcinogen urethane-induced mouse tumor model (CITM) in the same 129S4 background. Single-cell transcriptome sequencing was conducted on lung tissues collected at five time points after induction for each model. The LUAD and its precursors were defined by experienced lung cancer pathologists as normal lung, hyperplasia, adenoma and adenocarcinoma. This analysis aimed to characterize the dynamic interaction between epithelial and immune cells, providing insights into the initiation and progression of LUAD. Results: A comprehensive analysis identified a total of 12 major cell types, revealing a gradual increase in the proportion of epithelial cells during LUAD progression. EpiC 1, 2, 5 and 8 were consistently found in normal lung epithelium and various stages of abnormal epithelia, indicating their role as background components in lung tissues. In contrast, EpiC 4 emerged from hyperplasia and EpiC 0 and 3 emerged from early adenoma, while EpiC 6 and 7 were predominantly present in adenocarcinoma. Further investigation into the developmental trajectory of AT2 cells indicated a clear separation between normal (EpiC 1, 2, 5 and 8) and tumor cells (EpiC 0, 3, 4, 6 and 7). Cancer hallmark analysis revealed that tumor clusters exhibited higher scores in KRAS_SIGNALING_UP, HYPOXIA, APOPTOSIS, and P53_PATHWAY compared to normal epithelial clusters, suggesting the potential activation of these pathways in the tumorigenesis. Furthermore, the proportion of Macro_C1qc increased over time, accompanied by Macro_C1qc exhibiting the highest M2 signature score. This indicates a unique enrichment of M2-like macrophages in LUAD tissues. Remarkably, a notable increase in ligand-receptor pairs contributed significantly to the signaling from macrophages to tumor cells during progression. The dynamic regulatory interplay between Macro_C1qc and tumor cells was notably mediated by Thbs-Sdc1, App-Cd74, Spp1-Cd44 and other L-R pairs across various time points. Conclusion: We constructed a single-cell LUAD developmental atlas of dynamic tumor-immune cell interactions, which sheds light on the initiation and progression of LUAD. Notably, our findings underscore a potential crucial role of macrophages, particularly M2 in lung tumorigenesis. Citation Format: Hong Chen, Bo Zhu, Junya Fujimoto, Yanhua Tian, Jian-Rong Li, Chenyang Li, Pingjun Chen, Alexandre Reuben, Monique Nilsson, Xiuning Le, Alissa Poteete, Shawna M. Hubert, Don L. Gibbons, Ignacio I. Wistuba, Jia Wu, Chao Cheng, John V. Heymach, Jianjun Zhang. Single-cell profiling reveals dynamic epithelial and immune cell interactions in the progression of lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3379.

Supramolecular Heterodimer Peptides Assembly for Nanoparticles Functionalization.

Nanoparticle (NP) surface functionalization with proteins, including monoclonal antibodies (mAbs), mAb fragments, and various peptides, has emerged as a promising strategy to enhance tumor targeting specificity and immune cell interaction. However, these methods often rely on complex chemistry and suffer from batch-dependent outcomes, primarily due to limited control over the protein orientation and quantity on NP surfaces. To address these challenges, a novel approach based on the supramolecular assembly of two peptides is presented to create a heterotetramer displaying VH Hs on NP surfaces. This approach effectively targets both tumor-associated antigens (TAAs) and immune cell-associated antigens. In vitro experiments showcase its versatility, as various NP types are biofunctionalized, including liposomes, PLGA NPs, and ultrasmall silica-based NPs, and the VH Hs targeting of known TAAs (HER2 for breast cancer, CD38 for multiple myeloma), and an immune cell antigen (NKG2D for natural killer (NK) cells) is evaluated. In in vivo studies using a HER2+ breast cancer mouse model, the approach demonstrates enhanced tumor uptake, retention, and penetration compared to the behavior of nontargeted analogs, affirming its potential for diverse applications.

Spatial transcriptomic analysis of tumour-immune cell interactions in melanoma arising from congenital melanocytic nevus.

Studies on the interaction between tumour-infiltrating immune cells (TIICs) and tumour cells in melanoma arising from congenital melanocytic nevus (CMN) are lacking. The aim of this study was to determine the intratumoral immune landscape of TIICs and tumour cells during invasion and metastasis. Tissue specimens were obtained from patients with melanoma originating from CMN. Differential gene expression in melanoma cells and TIICs during invasion and metastasis was determined using spatial transcriptomics. As invasion depth increased, the expression of LGALS3, known to induce tumour-driven immunosuppression, increased in melanoma cells. In T cells, the expression of genes that inhibit T-cell activation increased with increasing invasion depth. In macrophages, the expression of genes related to the anti-inflammatory M2 phenotype was upregulated with increasing invasion depth. Compared to primary tumour cells, melanoma cells in metastatic lesions showed upregulated expression of genes associated with cancer immune evasion, including AXL and EPHA2, which impede T-cell recruitment, and BST2, associated with M2 polarization. Furthermore, T cells showed increased expression of genes related to immunosuppression, and macrophages exhibited increased expression of genes associated with the M2 phenotype. The interaction between melanomas arising from CMN and TIICs may be important for tumour progression and metastasis.

Collagen Mineralization Decreases NK Cell-Mediated Cytotoxicity of Breast Cancer Cells via Increased Glycocalyx Thickness.

Skeletal metastasis is common in patients with advanced breast cancer and often caused by immune evasion of disseminated tumor cells (DTCs). In the skeleton, tumor cells not only disseminate to the bone marrow but also to osteogenic niches in which they interact with newly mineralizing bone extracellular matrix (ECM). However, it remains unclear how mineralization of collagen type I, the primary component of bone ECM, regulates tumor-immune cell interactions. Here, a combination of synthetic bone matrix models with controlled mineral content, nanoscale optical imaging, and flow cytometry are utilized to evaluate how collagen type I mineralization affects the biochemical and biophysical properties of the tumor cell glycocalyx, a dense layer of glycosylated proteins and lipids decorating their cell surface. These results suggest that collagen mineralization upregulates mucin-type O-glycosylation and sialylation by tumor cells, which increases their glycocalyx thickness while enhancing resistance to attack by natural killer (NK) cells. These changes are functionally linked as treatment with a sialylation inhibitor decreased mineralization-dependent glycocalyx thickness and made tumor cells more susceptible to NK cell attack. Together, these results suggest that interference with glycocalyx sialylation may represent a therapeutic strategy to enhance cancer immunotherapies targeting bone-metastatic breast cancer.

Abstract A021: Evolutionary immunotherapy in NSCLC: An integrated approach

Abstract Purpose: Our study examines tumor growth dynamics and immunosuppression under the presence of immune attack to identify optimal immune pulsing treatment strategies. Motivation: Checkpoint inhibitors disrupting the PD-1/PD-L1 axis are used in multiple cancer subtypes. However, not all patients respond, and predictive biomarkers are needed to better stratify patients. Therapy for PD-L1, the most studied biomarker, has given mixed results in non-small cell lung cancer (NSCLC). The complexity of the immune response and plastic nature of PD-L1/PD-1 expression on tumor and immune cells contributes to the heterogeneity of success. IFN-γ, a cytokine released by activated immune cells, induces PD-L1 expression in some tumor cells. Chronic IFN-γ results in long-term PD-L1 expression. However, relaxation dynamics following removal of IFN-γ remains unexplored. In this study, we investigate these complex PD-L1 dynamics through a unique combination of in vitro studies and mathematical modeling. METHODS: In vitro experimental data: We have collected in vitro and temporal confocal microscopy images of PD-L1 expression on NSCLC cells, which were either untreated or treated for 48 hours with high dose IFN-γ followed by chronic low dose IFN-γ for 21 days.Agent-based model: To reinforce our in vitro experiments and findings, we developed a hybrid agent-based model (ABM) to study PD-L1 dynamics. The agents in the ABM are tumor cells having variable PD-L1 expression, and immune cells that secrete IFN-γ. Tumor cells can be randomly seeded or seeded as a cluster of cells. IFN-γ is modeled as either a binary well-mixed pulse (to simulate the in vitro experimental setup), or as a diffusible via a reaction-diffusion process (to simulate the tumor-immune cell interactions in an in-vivo spatial manner). This allows us to investigate the effects of various pulsing strategies of immunotherapy on tumor evolution where each pulse can be a variable dose of immune cells, given at regular or irregular intervals. RESULTS: Our in vitro experimental data and microscopy images confirm that PD-L1 expression continues to increase within the cells after a 48-hour IFN-γ exposure followed by low levels of IFN-γ. Our ABM has been calibrated to capture in vitro data dynamics for different conditions. Our initial results indicate that pulsing immunotherapy may lead to better overall immune efficacy than continuous immunotherapy, by preventing sustained suppression that increases immune cell exhaustion, despite the potential for tumor regrowth between pulses. We also hypothesize that pulsing immunotherapy will have different immunosuppression effects when tumors are clustered or randomly distributed. CONCLUSION: We have quantified the temporal dynamics of PD-L1 expression in NSCLC cells under different conditions of IFN-γ, and built an ABM to study tumor-immune evolution under various pulsing strategies. The results of this work could lead to improved therapy schedules in patients responsive to checkpoint inhibitors that exploit the complex dynamics of immune response and suppression. Citation Format: Sandhya Prabhakaran, Taylor M. Bursell, Kimberly Luddy, Julian Pineiro, Rafael Bravo, Jeffrey West, Megan Johnson, Mark Robertson-Tessi, Amer A. Beg, Jhanelle E. Gray, Scott Antonia, Robert A. Gatenby, Alexander R. A. Anderson. Evolutionary immunotherapy in NSCLC: An integrated approach [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A021.

Establishing mouse and human oral esophageal organoids to investigate the tumor immune response.

Organoid culture systems are very powerful models that recapitulate in vivo organ development and disease pathogenesis, offering great promise in basic research, drug screening and precision medicine. However, the application of organoids derived from patients with cancer to immunotherapeutic research is a relatively untapped area. Esophageal cancer is one of the most lethal malignancies worldwide, including two major pathological subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma. ESCC shares many biological and genomic features with oral squamous cell cancers. Herein, we provide a versatile protocol for the establishment and maintenance of oral and esophageal organoid cultures derived from both murine and human samples. We describe culture conditions for organoids derived from normal tongue, esophagus and gastroesophageal junction, esophageal cancer and Barrett's esophagus. In addition, we establish an ex vivo model by co-culturing patient tumor-derived organoids and autologous CD8+ T lymphocytes to assess CD8+ T cell-mediated tumor killing. Our protocol can also be modified for organoid establishment from other squamous epithelia and carcinomas. The co-culture model can serve as a template for studies of other tumor-immune cell interactions and the efficacy of immune checkpoint blockade therapy.

[Tumor-immune cell interaction and senescence-associated molecules in colorectal carcinoma].

Cellular senescence permanently arrests the cell cycle of premalignant cells following protumorigenic stimuli, counteracting tumor progression. Senescence induction leads to phenotypic and metabolic changes and alters the interaction with the cells' microenvironment. This mediates tumor immunosurveillance but bears promalignant potential and may contribute to disease progression. Our study aims to investigate the prognostic potential of senescence markers in colorectal carcinoma (CRC) and to understand the interaction of senescent tumor cells and immune cells. Immunohistochemical markers were studied on atissue microarray (TMA) containing tumor tissue of n = 598 CRC patients and were evaluated using digital image analysis. Results were correlated with disease-specific survival (DSS) and progression-free survival (PFS). Consecutive TMA sections were stained for senescence markers and immune cell markers to analyze the spatial relation of those cell populations. Senescence was induced in CRC cell lines in vitro and co-cultures with various immune cell lines were established to study the interactions. Expression of different senescent-associated markers is associated with increased or decreased DSS and PFS. Close proximity of p21+ senescent tumor cells and CD8+ immune cells correlates with increased DSS and PFS. In vitro, senescent cells were dose-dependently eliminated by immune cells, which is facilitated via direct cell-cell contact and induction of apoptosis. Depicting the initiation of this important anti-tumor mechanism, markers of cellular senescence are of significant prognostic relevance in CRC. Moreover, our results show the pleiotropic effect of senescence in vivo. Absence as well as exceeding expression of senescence markers are associated with anegative prognosis in CRC. The impact of cellular senescence depends on the tumor microenvironment and the immunosurveillance of senescent cells. Proximity analyses of senescent cells and tumor-infiltrating immune cells have significant prognostic relevance and reflect this.

Analysis of a delayed mathematical model for tumor-immune cell interactions with Holling type II functional response

In this study, we analyzed a three-dimensional nonlinear differential system considering Holling type II functional response that describes the dynamics of tumor cells, cytotoxic T lymphocytes, and helper T cells, with a single interaction delay. The linear stability of the internal equilibrium point and the presence of the Hopf bifurcation are examined, with the discrete time delay serving as the bifurcation parameter. To demonstrate the rich dynamic behavior of the model, we present numerical simulations with various values of the time delay τ and the attack rate of cytotoxic T lymphocytes on tumor cells (α1). These simulations exhibit the presence of periodic oscillations and tumor death with survival of the mentioned immune cells, for all α1 greater than a fixed threshold with or without delay.

Dissecting the Single Cell Landscape of Leukemic Mantle Cell Lymphoma

Introduction: Resistance to therapy remains a major challenge for Mantle Cell Lymphoma (MCL) patients, despite a diverse and expanding treatment landscape. There is thus a major need to better understand the mechanistic underpinnings of therapy resistance in order to optimize treatment selection. Given the advent of immunotherapies in recent years, there has been increasing evidence that not only tumor-intrinsic factors affect therapy resistance, but that tumor-immune cell interactions are an additional major contributor. In the context of MCL, such interactions have been poorly characterized, but hold the promise of identifying novel treatment approaches and better understanding resistance mechanisms to commonly applied therapies such as BTK inhibition. Methods: This study aimed to investigate the single-cell landscape of leukemic MCL using single-cell profiling of 26 patients and 10 healthy donors. In addition, we performed in vitro drug testing on a subset of patient samples (n=12; 6 treatments) to understand the effects of drugs on both tumor and immune cells in MCL . To comprehensively characterize the phenotypic and functional features of immune and tumor cells within a single-cell landscape, we employed high-dimensional full-spectrum cytometry. Therefore, we developed 5 high-dimensional panels covering markers to deeply interrogate T and NK cells, immune evasion and immune checkpoints, cytokines and cytotoxicity, cellular trafficking and intracellular signaling/phosphoproteome (covering >120 proteins). We combined this with single-cell RNA sequencing and a scalable and reproducible bioinformatics pipeline. To assess the disease specificity of the immune landscape, we also obtained single-cell data from other B-NHL including MZL and CLL (n=60 patients). Results: Our data indicate profound changes in the immune landscape, in particular in the T cell compartment of MCL patients. In this regard, multi-omics factor analysis (MOFA) confirmed a highly distinct T cell landscape in MCL patients, characterized by higher effector marker expression in conventional CD4+ and CD8+ T cells in addition to higher fraction of effector and effector memory T cells compared to healthy donors (Fig. 1A and B). Moreover, our analysis revealed a pronounced expansion of highly suppressive regulatory T cells (~5% of T cells) (Fig.1B). The emergence of this effector Treg (eTreg) subset in MCL patients might limit efficient anti-tumor immunity of CD8+ and conventional CD4+ T cells. Consistent with this, we observed a high fraction of several dysfunctional CD8+ T cells subsets. Notably, we found a remodeling of this eTreg subset in patients undergoing ibrutinib treatment leading to a less pronounced suppressive phenotype and concomitantly observed an increase of proteins crucial for cytotoxic function such as Granzyme B and Interferon-γ in effector T cells. We further sought to link tumor cell signatures with the healthy immune cell signatures in order to assess potential interactions and mechanisms of immune escape. As such, the tumor cell compartment (MCL cells) displayed high-expression of inhibitory immune checkpoint ligands such as PVR, HLA-G, CD70 and PD-L1 and antiphagocytic proteins such as CD47 and CD24, which may contribute to the dysfunctional T cell compartment. In line with this, our analysis revealed that high expression of the immune checkpoint ligand CD70 on malignant B cells was inversely associated with an activation module in CD4+ T cells, providing a potential axis contributing to immune escape, which may be leveraged for future therapeutic use. Finally, we identified tumor and immune cell signatures associated with in vitro drug response that may not only be useful for improving treatment selection, but also offer novel biological insights into potential mechanisms of treatment resistance. Conclusion: This study provides valuable insights into the single-cell landscape of leukemic MCL, offering crucial understanding of how tumor-immune cell interactions may contribute to disease progression and treatment resistance. The findings hold potential for therapeutic exploitation to eventually improve patient outcomes in Mantle Cell Lymphoma.

Deciphering the Dynamics of the B-NHL Single-Cell Landscape during BTK Inhibition

Introduction: The inhibition of Bruton's tyrosine kinase (BTK) as a therapeutic strategy has dramatically improved the management of patients with chronic lymphocytic leukemia (CLL) and other B-cell-Non Hodgkin lymphomas (B-NHL). However, therapy resistance and treatment toxicity persist as significant clinical challenges. It has been previously reported that BTK inhibition not only targets the overactivated BCR pathway in CLL and other B-NHL, but also coincides with profound alterations in the tumor microenvironment including immune cells. Therefore, it is vital to understand these tumor-immune cell interactions during BTK inhibition to enhance response and reduce toxicity, advancing personalized care for CLL and B-NHL patients in the future. Methods: We developed a high-parametric analysis pipeline based on full spectrum cytometry, a novel technology allowing for the simultaneous assessment of 40 markers at single-cell level. In order to comprehensively assess the phosphoproteome relevant to BTK inhibition we established a signaling panel covering >30 proteins including pBTK, pSyk, pPLCg, pS6 and pAMPKa. Additionally, we designed 3 panels with up to 40 markers characterizing T cell activation and exhaustion, cellular trafficking, inhibitory immune checkpoints and cytokine production. Using our scalable and reproducible bioinformatics pipeline, we analyzed a cohort of 160 samples, longitudinally collected from 57 patients (CLL, MCL, MZL) before BTKi treatment, directly after treatment initiation, at leukocyte peak count and during therapy up to 6 months after therapy initiation. Results: Given that T cells are a crucial arm in governing anti-lymphoma immune response, we sought to elucidate the changes associated with BTK inhibition in the T cell compartment of the patients at high resolution (figure A). We observed certain changes in the fraction of T cell subtypes, notably a decrease in central memory stem T cells and an increase in γδ T cells at leukocyte peak and during later stages of therapy. Our analysis uncovered substantial changes in the T cell marker expression over the course of BTK inhibition. This includes a reversal of exhausted phenotype marked by downregulation of PD1, CD39 and CD38 and a skewed differentiation of CD4 T cells towards Th1 phenotype illustrated by a pronounced upregulation of the transcription factor T-bet. In addition, we detected restored proliferative and cytotoxic capacity in the CD8 and CD4 T cell compartments characterized by upregulation of GRZB, CD226, CD28, CD25 and Ki67. By leveraging our platform, we successfully captured the signalosome of malignant B cells at a high resolution. As anticipated, we detected significant heterogeneity in the malignant B cell signatures across individual patients. Interestingly, even at the initial sampling timepoint following treatment start, we observed substantially altered B cell signatures encompassing both the phosphoproteome and inhibitory immune checkpoints (figure B). Our preliminary data suggest that the dynamic changes induced by BTK inhibition extend beyond the signaling nodes associated with the BCR pathway and also involve the NFkB and p53 pathways. Conclusion: In this study, we established a platform for deep and longitudinal interrogation of the tumor and immune cell compartments to capture the dynamic and patient-specific changes occurring during BTK inhibition. Our preliminary data obtained from a large patient cohort of 57 B-NHL patients reveals a profound remodeling of not only the BCR signaling pathway in tumor cells, but also of the T cell compartment. Our data will be useful for a better understanding of treatment response and toxicity in the context of BTK inhibition.

MODL-09. SCAFFOLD-BASED (MATRIGELTM) 3D CULTURE TECHNIQUE OF GLIOBLASTOMA RECOVERS A PATIENT-LIKE IMMUNOSUPPRESSIVE PHENOTYPE

Abstract 3D (organoid) models in cancer research are considered the novel gold standard for in vitro experiments. Nevertheless, a variety of different protocols exits and the models are often used uncritically in lack of further validation. In this study, we aimed to characterize a scaffold-based (MatrigelTM) 3D glioma cell culture approach. We compared the 3D technique to conventional 2D culturing in its efficacy of generating models and in respect to its exact modeling properties. Models were generated from 62 patients with CNS tumors, most of them with glioblastomas, IDH-wildtype (GBM, n = 43). Pairs of 11 GBM models (2D and 3D) together with corresponding patient material were further characterized using bulk and single-cell RNA sequencing as well as 850k methylation analyses. Functional aspects of 3D tumor organoids were analyzed using a coculture system (Incucyte® SX5 live cell imager) with tumor infiltrating lymphocytes. Compared to conventional 2D culture the MatrigelTM-based 3D protocol was not superior in terms of the successful generation of in vitro models. However, NGS-based bulk and single-cell sequencing of matched pairs of 2D and 3D models showed an altered transcription of key immune regulatory genes in the 3D models, indicating the reoccurrence of an immunosuppressive phenotype. Changes included the presentation of different HLA surface molecules as well as cellular stressors. In the coculturing approach, lymphocyte-mediated cell killing appeared less effective in clearing 3D models than their 2D counterparts. IFN-γ release as well as live cell staining and proliferation analysis pointed towards an elevated resistance of 3D models. In conclusion, we found that the Scaffold-based (MatrigelTM) 3D culture technique depicts clinically highly important aspects of tumor-immune cell interactions, with the potential to explore immunotherapeutic approaches in an easily accessible in vitro system.

Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer

Precision oncology approaches for patients with colorectal cancer (CRC) continue to lag behind other solid cancers. Functional precision oncology-a strategy that is based on perturbing primary tumor cells from cancer patients-could provide a road forward to personalize treatment. We extend this paradigm to measuring proteome activity landscapes by acquiring quantitative phosphoproteomic data from patient-derived organoids (PDOs). We show that kinase inhibitors induce inhibitor- and patient-specific off-target effects and pathway crosstalk. Reconstruction of the kinase networks revealed that the signaling rewiring is modestly affected by mutations. We show non-genetic heterogeneity of the PDOs and upregulation of stemness and differentiation genes by kinase inhibitors. Using imaging mass-cytometry-based profiling of the primary tumors, we characterize the tumor microenvironment (TME) and determine spatial heterocellular crosstalk and tumor-immune cell interactions. Collectively, we provide a framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno-) oncology in CRC.

Developing synthetic tools to decipher the tumor-immune interactome.

The ability of immune cells to directly interact with transformed cells is an essential component of immune surveillance and critical for optimal tissue function. The tumor-immune interactome (the collective cellular interactions between oncogenic cells and immune cells) is distinct and varied based on the tissue location and immunogenicity of tumor subtypes. However, comprehensive landscape and the consequences of tumor-interacting immune cells in the tumor microenvironment are not well understood. Current tools are limited in their ability to identify and record interactors in vivo or be utilized for downstream analysis. Here, we describe the development and validation of a technology leveraging synthetic Notch receptors reporting physical tumor cell-immune cell contact in vivo in order to decipher the tumor-immune interactome. We call this approach, Tumor-Immune Interactome Non-biased Discovery Retroviral Reporter or TIINDRR. Using TIINDRR, we identify the tumor-immune interactomes that define immunological refractory and sensitive tumors and how different immunotherapies alter these interactions. Thus, TIINDRR provides a flexible and versatile tool for studying in-vivo tumor-immune cell interactions, aiding in the identification of biologically relevant information needed for the rational design of immune-based therapies.