Composition Of Tumor Microenvironment Research Articles

Identification of tumor microenvironment-based gene prognostic signature with promising predictive value for chemo‐immunotherapy outcomes in lung adenocarcinoma patients

Objectives: The tumor microenvironment (TME) plays a critical role in tumor progression and therapeutic response. We aimed to establish a TME-associated gene signature for lung adenocarcinoma (LUAD) patients. Materials and Methods: We comprehensively analyzed the gene expression data of 513 LUAD patients deriving from The Cancer Genome Atlas (TCGA) database. To estimate the composition of TME, The Estimation of Stromal and Immune cells in malignant tumor tissue using the Expression data (ESTIMATE) algorithm was used. We then utilized protein-protein interaction (PPI) analysis, LASSO, and COX regression to explore the related candidate genes with survival. Eventually, a three-gene signature was constructed for risk stratification. Furthermore, we investigated its predictive value in advanced LUAD patients who received chemotherapy alone or combined with anti-PD-1 inhibitors. Results: We identified three genes, namely CCR2, CD40LG, and CCL21, to construct a TME-associated risk stratification gene signature. This gene signature was independently linked to patients' overall survival (OS) among the TCGA dataset (HR, 1.99; 95% CI 1.36-2.93, p < 0.001) and GEO dataset (HR, 1.62; 95%CI 1.19-2.20, p < 0.001). The addition of anti-PD-1 inhibitor Siltuximab to chemotherapy resulted in significantly longer progression-free survival (PFS) in low-risk patients (HR, 0.33; 95% CI: 0.20 - 0.56, p < 0.001) but not in those with high- risk (HR, 0.56; 95% CI:0.24 - 1.31, p = 0.173). Moreover, in patients who received Sintilimab combined with chemotherapy, PFS was significantly different between the high- and low-risk group (HR,1.958; 95%CI:1.079-3.555, p = 0.024), whereas no significant difference was found in chemotherapy alone treated patients (HR, 1.303; 95%CI: 0.610-2.784, p = 0.492). Conclusions: This study generated a three-gene prognostic signature based on TME-associated core genes in patients with LUAD. This gene signature has good value for prognosis prediction. In addition, this signature correlated with treatment outcomes among patients treated with chemotherapy combined with anti-PD1 therapy.

Single-cell transcriptomics analysis reveals dynamic changes and prognostic signature in tumor microenvironment of PDAC

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignant tumor characterized by a complex tumor microenvironment (TME) with significant heterogeneity, posing immense challenges for devising effective therapeutic strategies. This study aims to elucidate the dynamic changes in the TME during PDAC progression and develop a prognostic model using single-cell RNA sequencing (scRNA-seq) data. We utilized a previously published comprehensive dataset comprising 31 samples (including 8 PDAC I, 9 PDAC II, 6 PDAC III, and 8 PDAC IV) to characterize the changes in TME composition with PDAC progression through advanced scRNA-seq analysis. We found that as cancer progresses, immune cells gradually become a predominant component in late-stage PDAC. We defined a novel Treg and exhausted T cell signature gene, TNFRSF4. Additionally, we identified a prognostic gene set (RPS10, MIF, MT-ATP6, CSTB, IFI30, NPC2, BTG1, CTSD, FCGR2A, SEC61G, IER3, HSPB1, HMOX1, and ZFP36L1) and differentiated high-risk from low-risk PDAC patients based on median risk score threshold. Based on these findings, we developed a novel prognostic model that identifies poorer prognosis in high-risk groups. Furthermore, our analysis revealed significant interactions between cells at different stages of PDAC and identified three promising therapeutic agents (XR-11576, Ixabepilone, and AMONAFIDE) based on correlated genes. Finally, molecular docking studies validated their potential by confirming stable binding with key protein targets. This study not only provides insights into the evolving TME of PDAC but also offers a new prognostic model and potential therapeutic strategies, contributing to improved management and treatment of this aggressive cancer.

Beyond the Norm: The emerging interplay of complement system and extracellular matrix in the tumor microenvironment.

Ground-breaking awareness has been reached about the intricate and dynamic connection between developing tumors and the host immune system. Being a powerful arm of innate immunity and a functional bridge with adaptive immunity, the complement system (C) has also emerged as a pivotal player in the tumor microenvironment (TME). Its "double-edged sword" role in cancer can find an explanation in the controversial relationship between C capability to mediate tumor cell cytolysis or, conversely, to sustain chronic inflammation and tumor progression by enhancing cell invasion, angiogenesis, and metastasis to distant organs. However, comprehensive knowledge about the actual role of C in cancer progression is impaired by several limitations of the currently available studies. In the current review, we aim to bring a fresh eye to the controversial role of C in cancer by analyzing the interplay between C and extracellular matrix (ECM) components as potential orchestrators of the TME. The interaction of C components with specific ECM components can determine C activation or inhibition and promote specific non-canonical functions, which can, in the tumor context, favor or limit progression based on the cancer setting. An in-depth and tumor-specific characterization of TME composition in terms of C components and ECM proteins could be essential to determine their potential interactions and become a key element for improving drug development, prognosis, and therapy response prediction in solid tumors.

Predicting the tumor microenvironment composition and immunotherapy response in non-small cell lung cancer from digital histopathology images

Immune checkpoint inhibitors (ICI) have become integral to treatment of non-small cell lung cancer (NSCLC). However, reliable biomarkers predictive of immunotherapy efficacy are limited. Here, we introduce HistoTME, a novel weakly supervised deep learning approach to infer the tumor microenvironment (TME) composition directly from histopathology images of NSCLC patients. We show that HistoTME accurately predicts the expression of 30 distinct cell type-specific molecular signatures directly from whole slide images, achieving an average Pearson correlation of 0.5 with the ground truth on independent tumor cohorts. Furthermore, we find that HistoTME-predicted microenvironment signatures and their underlying interactions improve prognostication of lung cancer patients receiving immunotherapy, achieving an AUROC of 0.75 [95% CI: 0.61-0.88] for predicting treatment responses following first-line ICI treatment, utilizing an external clinical cohort of 652 patients. Collectively, HistoTME presents an effective approach for interrogating the TME and predicting ICI response, complementing PD-L1 expression, and bringing us closer to personalized immuno-oncology.

Disrupting Notch signaling related HES1 in myeloid cells reinvigorates antitumor T cell responses

BackgroundTumor-associated macrophages (TAMs) are immunosuppressive cells within the tumor microenvironment (TME) that hinder anti-tumor immunity. Notch signaling is a pathway crucial for TAM differentiation and function. Here, we investigate the role of HES1, a downstream target of Notch signaling, in TAM-mediated immunosuppression and explore its potential as a target for cancer immunotherapy.MethodsIn this work, we constructed conditional Hes1 knockout mice to selectively delete Hes1 in TAMs. We further analyzed the TME composition, T cell infiltration and activation, and anti-tumor effects in these mice, both alone and in combination with PD-1 checkpoint blockade.ResultsOur study showed that expression levels of Notch target Hes1 were increase in TAMs and mice with conditional knockout of Hes1 gene in TAMs exhibited decreased tumor growth, with increased infiltration and activation of cytotoxic T cells in tumors. Expression of tumor promoting factors was critically altered in Hes1-conditional KO TAMs, leading to the improved tumor microenvironment. Notably, arginase-1 expression was decreased in Hes1-conditional KO mice. Arg1 is known to deplete arginine and deactivate T cells in the TME. Administration of anti-PD-1 monoclonal antibody inhibited tumor growth to a greater extent in Hes1-conditional KO mice than in WT mice.ConclusionsWe identified a pivotal role for the Notch signaling pathway in shaping TAM function, suggesting that T-cell dysfunction in the TME is caused when the Notch target, HES1, in TAMs is upregulated by tumor-associated factors (TAFs), which, in turn, increases the expression of arginase-1. Targeting HES1 in TAMs appears to be a promising strategy for cancer immunotherapy.

Advances in Immunotherapy for Endometrial Cancer: Insights into MMR Status and Tumor Microenvironment.

Endometrial cancer is one of the most common gynecological malignancies, and while early-stage cases are highly treatable, recurrent or advanced EC remains challenging to manage. Immunotherapy, particularly immune checkpoint inhibitors, has revolutionized treatment approaches in oncology, and its application in EC has shown promising results. Key to immunotherapy efficacy in EC is the tumor's mismatch repair status, with MMR-deficient tumors demonstrating a higher tumor mutational burden and increased PD-L1 expression, making them more susceptible to immune checkpoint inhibitors (ICIs) such as pembrolizumab, durvalumab, and dostarlimab. However, not all mismatch repair-deficient (MMRd) tumors respond to ICIs, particularly those with a "cold" tumor microenvironment (TME) characterized by poor immune infiltration. In contrast, some MMR-proficient tumors with a "hot" TME respond well to ICIs, underscoring the complex interplay between MMR status, tumor mutational burden (TMB), and TME. To overcome resistance in cold tumors, novel therapies, including Chimeric Antigen Receptor (CAR) T cells and tumor-infiltrating lymphocytes are being explored, offering targeted immune-based strategies to enhance treatment efficacy. This review discusses the current understanding of immunotherapy in EC, emphasizing the prognostic and therapeutic implications of MMR status, TME composition, and emerging cell-based therapies.

Immunophenotypic Profile of Adult Glioblastoma IDH-Wildtype Microenvironment: A Cohort Study.

Background: Glioblastoma IDH-wildtype (GBM IDH-wt) is the most aggressive brain tumor in adults and is characterized by an immunosuppressive microenvironment. Different factors shaping its tumor microenvironment (TME) regulate tumor progression and treatment response. The aim of this study was to characterize the main immunosuppressive elements of the GBM IDH-wt TME. Methods: Immunohistochemistry for CD3, CD4, CD8, CD163, programmed death ligand 1 (PD-L1) and programmed death 1 (PD1) was performed on surgical tumor specimens from patients diagnosed with GBM IDH-wt, according to the CNS WHO 2021 criteria. The impact of categorical variables on time-dependent outcomes such as overall survival (OS) and progression-free survival (PFS) has been estimated through the Kaplan-Meier method. Results: We included 30 patients (19 males and 11 females), median age of 59.8 years (range 40.2-69.1 years). All patients underwent surgery followed by temozolomide concurrent with and adjuvant to radiotherapy. MGMT was methylated in 14 patients (47%) and unmethylated in 16 patients (53%). The overall absolute percentages of CD4+ lymphocytes, both intratumoral and perivascular, were significantly more represented than CD8+ lymphocytes in the TME (p = 0.02). A low density of CD4+ lymphocytes (≤10%) was found to be a favorable prognostic factor for GBM outcome (p = 0.02). Patients with MGMT methylated and unmethylated tumors exhibited a distinct TME composition, with a significant higher number of perivascular CD8+ lymphocytes (p = 0.002), intratumoral CD8+ lymphocytes (p = 0.0024) and perivascular CD4+ lymphocytes (p = 0.014) in MGMT unmethylated tumors. PD-L1 expression in tumor cell surface was observed in four tumors (13.3%), and PD1 expression in infiltrating T lymphocytes was observed in nine (30%) tumors, with predominantly perivascular distribution. Conclusions: MGMT methylated and unmethylated tumors exhibit different immune profiles, likely reflecting the different biology of these tumors. The expression of PD-L1 in GBM IDH-wt patients is confined to a small subpopulation. While we found a significant association between low CD4+ lymphocyte density (≤10%) and survival, given the small numbers of our cohort, the prognostic value of CD4+ lymphocyte density will need to be validated in large-scale studies.

Abstract B035: Reciprocal macrophage - T cell interactions regulate anti-tumor immunity

Abstract Cancer immunotherapy (including immune checkpoint blockade (ICB)) has shown great promise in the treatment of some solid cancers, but responses in breast cancer patients are limited. While breast cancer is generally considered poorly immunogenic, the abundance of CD8+ T cells correlates with clinical response. CD8+ T cells are critical mediators of anti-tumor immunity and the main target for ICB. However, the onset of terminal functional T cell exhaustion poses a major challenge. Although T cell exhaustion has been linked to persistent antigen exposure, it remains unclear how the immune composition of the breast tumor microenvironment (TME) contributes to this dysfunctional T cell state. Breast cancers are heavily infiltrated with tumor-associated macrophages (TAMs) and their abundance correlates with T cell exhaustion and poor prognosis. Previously, we discovered a spatiotemporal co-dependency between exhausted T cells (TEX) and TAMs in mouse models of melanoma and breast cancer. We showed that TEX actively recruit monocytes to the TME and shape their differentiation trajectory into TAMs. Reciprocally, these TAMs ‘capture’ T cells in long-lived synaptic interactions that contribute to functional T cell exhaustion. Our current work is focused on studying the TEX-derived chemokines that regulate these TAM – T cell interactions in the breast TME with the ultimate goal to alleviate immune evasion and improve responsiveness of breast cancer to immunotherapy. Citation Format: Meenakshi Sudhakaran, Sofia Lombardi, Sophie Ayma, Matthew F. Krummel, Kelly Kersten. Reciprocal macrophage - T cell interactions regulate anti-tumor immunity [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 B035.

Single-cell transcriptomics link gene expression signatures to clinicopathological features of gonadotroph and lactotroph PitNET

BackgroundPituitary neuroendocrine tumors (PitNET) are among the most common intracranial tumors. Despite a frequent benign course, aggressive behavior can occur. Tumor behavior is known to be under the influence of the tumor microenvironment (TME). However, the relationship between TME cells and aggressive tumor behavior has not been adequately explored in PitNET.MethodsWe performed differential expression analysis as well as gene expression program identification based on single-cell RNA sequencing to comparatively characterize the transcriptome of seven gonadotroph and three lactotroph PitNET and correlate it with clinical features using bulk RNA-seq data from an independent cohort of 134 PitNET. Tumor immune infiltration was quantified via immunostaining on tissue sections of gonadotroph and lactotroph PitNET.ResultsIn lactotroph PitNET, we detect a highly proliferative gene profile with significantly increased expression levels in aggressively growing tumors within bulk RNA-seq data of an independent cohort of 134 PitNET samples. We also report high intratumoral heterogeneity in gonadotroph PitNET (GoPN) and lactotroph PitNET (LaPN) and identify signatures of epithelial, endocrine, and immunological gene networks in both subtypes. A comparison of their TME composition shows enrichment of SPP1+ macrophages and CD4+ T cells in GoPN, as well as enrichment of CD4/CD8 double-negative T cells (DN) and natural killer cells (NK) in LaPN. Also notable is the presence of proliferative lymphocytes, the occurrence of which positively correlates with more aggressive tumor behavior in the bulk RNA-seq cohort. However, increased CD8+ T and NK cell abundances correlate significantly with reduced aggressiveness indicating potential anti-tumoral effects.ConclusionsOur study expands the knowledge of the differences in cellular composition of gonadotroph and lactotroph PitNET subtypes. It lays the foundation for further studies on the influence of lymphoid cells on the variable aggressive behavior of PitNET. Regarding the treatment of drug-resistant lactotroph PitNET, proliferative lymphocytes, CD8+ T, and NK cells could represent potentially valuable targets for developing new cancer immunotherapies.

TMIC-43. BIOLOGICAL AND MOLECULAR CHARACTERIZATION OF NOVEL GLIOBLASTOMA TME SUBTYPES USING TRANSCRIPTOMIC ANALYSIS AND NETWORK MODELLING TO IDENTIFY NOVEL TARGETS OF VULNERABILITY

Abstract New precision medicine therapies are urgently required for glioblastoma (GBM). Recently, we developed a novel GBM classification system, identifying three patient clusters uniquely characterized by tumor microenvironment (TME) composition: TMELow, TMEMedium, and TMEHigh1. Our objective now is to further investigate these subtypes employing transcriptomic analysis and network modelling approaches to identify novel subtype-specific targets of vulnerability. We analyzed transcriptomic data from >600 GBM samples from publicly available and in-house datasets. All samples underwent TME subtyping. Next, we performed differential gene expression (using DESeq2, edgeR) and pathway analysis (using PROGENy). The ‘TRANSFAC’ tool 2 was used to identify potential transcription factors enriched in each TME subtype. TMELow tumours manifested highly upregulated NLGN3 (P=5.777e-5) and HES5 (P=2.233e-3) expression compared to TMEHigh. Moreover, TMEHigh compared to TMELow tumours were enriched for genes associated with tissue remodelling, and showed elevated MMP7 (P=3.051e-6), CLCL13 (P= 3.843e-4), and CXCL5 expression (P= 1.592e-6). PROGENy analysis suggested that the WNT, TRAIL, and JAK/STAT pathways were significantly enriched in TMEHigh, while the PI3K pathway was significantly upregulated in TMEMedium. Additionally, VEGF pathway activity was significantly upregulated in TMELow. TRANSFAC analysis measured by regulatory score (a measure of a transcription factor effect on gene expression) revealed that in TMELow, key transcription factors includes ETS2, NANOG, and MECP2 (regulatory score: 1.97, 1.45, and 1.4, respectively). In TMEMedium, transcription factors HIF1A, PPARA, and CDX2 were identified (regulatory score: 2.52, 2.08 and 1.96, respectively). In TMEHigh, TRANSFAC indicated activiation of transcription factors SMAD3, ETS2, and NFKB1 regulatory score: 2.56, 2.41, 2.24, respectively). Overall these findings highlight distinct molecular signatures across TME subtypes, and provide a deeper understanding of associated molecular mechanisms. Ongoing work is focused on validating key subtype specific genes and associated pathways using spatial proteomics. Prioritised targets will ultimately be interrogated in vivo, as novel subtype-specific treatments. 1. White et al. Ann Oncol. 2023;34(3):300–314. 2. Matys et al. Nucleic Acids Res. 2003;31.

Genetics and biology of pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) poses a grim prognosis for patients. Recent multidisciplinary research efforts have provided critical insights into its genetics and tumor biology, creating the foundation for rational development of targeted and immune therapies. Here, we review the PDAC genomic landscape and the role of specific oncogenic events in tumor initiation and progression, as well as their contributions to shaping its tumor biology. We further summarize and synthesize breakthroughs in single-cell and metabolic profiling technologies that have illuminated the complex cellular composition and heterotypic interactions of the PDAC tumor microenvironment, with an emphasis on metabolic cross-talk across cancer and stromal cells that sustains anabolic growth and suppresses tumor immunity. These conceptual advances have generated novel immunotherapy regimens, particularly cancer vaccines, which are now in clinical testing. We also highlight the advent of KRAS targeted therapy, a milestone advance that has transformed treatment paradigms and offers a platform for combined immunotherapy and targeted strategies. This review provides a perspective summarizing current scientific and therapeutic challenges as well as practice-changing opportunities for the PDAC field at this major inflection point.

NF-ΚB Activation as a Key Driver in Chronic Lymphocytic Leukemia Evolution to Richter's Syndrome: Unraveling the Influence of Immune Microenvironment Dynamics.

Background/Objectives: Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries and it can progress to Richter's syndrome (RS), a more aggressive condition. The NF-κB pathway is pivotal in CLL pathogenesis, driven mainly by B-cell receptor (BCR) signaling. However, recent evidence indicates that BCR signaling is reduced in RS, raising questions about whether and how NF-κB activity is maintained in RS. This study aims to elucidate the triggers and dynamics of NF-κB activation and the progression from CLL to RS. Methods: Integrated single-cell RNA sequencing data from peripheral blood samples of four CLL-RS patients were analyzed. NF-κB pathway activity and gene expression profiles were assessed to determine changes in NF-κB components and their targets. Tumor microenvironment composition and cell-cell communication patterns were inferred to explore NF-κB regulatory mechanisms. Results: RS samples showed increased proportions of malignant cells expressing NF-κB components, including NFKB1, NFKB2, RELA, IKBKG, MAP3K14, CHUK, and IKBKB, with significantly higher expression levels than in CLL. Enhanced NF-κB pathway activity in RS cells was associated with targets involved in immune modulation. The tumor microenvironment in RS displayed significant compositional changes, and signaling inference revealed enhanced cell-cell communication via BAFF and APRIL pathways, involving interactions with receptors such as BAFF-R and TACI on RS cells. Conclusions: The findings from this study reveal an active state of NF-κB in RS and suggest that this state plays a critical role in the evolution of CLL to RS, which is modulated by alternative signaling pathways and the influence of the tumor microenvironment.

Clinicogenomic predictors of outcomes in patients with hepatocellular carcinoma treated with immunotherapy.

Immune checkpoint inhibitor (ICI) combinations extend overall survival (OS) while anti-PD-1/L1 monotherapy is non-inferior to sorafenib in treatment-naïve, patients with advanced hepatocellular carcinoma (HCC). Clinicogenomic features are posited to influence patient outcomes. The primary objective of this retrospective study was to define the clinical, pathologic, and genomic factors associated with outcomes to ICI therapy in patients with HCC. Patients with histologically confirmed advanced HCC treated with ICI at Memorial Sloan Kettering Cancer Center from 2012 to 2022 were included. Association between clinical, pathological, and genomic characteristics were assessed with univariable and multivariable Cox regression model for progression-free survival (PFS) and OS. Two-hundred and forty-two patients were treated with ICI-based therapy. Patients were predominantly male (82%) with virally mediated HCC (53%) and Child Pugh A score (70%). Median follow-up was 28 months (0.5-78.4). Median PFS for those treated in 1st line, 2nd line and ≥ 3rd line was 4.9 (range: 2.9-6.2), 3.1 (2.3-4.0), and 2.5 (2.1-4.0) months, respectively. Median OS for those treated in 1st line, 2nd line, and ≥ 3rd line was 16 (11-22), 7.5 (6.4-11), and 6.4 (4.6-26) months, respectively. Poor liver function and performance status associated with worse PFS and OS, while viral hepatitis C was associated with favorable outcome. Genetic alterations were not associated with outcomes. Clinicopathologic factors were the major determinates of outcomes for patients with advanced HCC treated with ICI. Molecular profiling did not aid in stratification of ICI outcomes. Future studies should explore alternative biomarkers such as the level of immune activation or the pretreatment composition of the immune tumor microenvironment.

Ovarian cancer-derived IL-4 promotes immunotherapy resistance.

Ovarian cancer is resistant to immunotherapy, and this is influenced by the immunosuppressed tumor microenvironment (TME) dominated by macrophages. Resistance is also affected by intratumoral heterogeneity, whose development is poorly understood. To identify regulators of ovarian cancer immunity, we employed a spatial functional genomics screen (Perturb-map), focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication. Perturb-map recapitulated tumor heterogeneity and revealed that interleukin-4 (IL-4) promotes resistance to anti-PD-1. We find ovarian cancer cells are the key source of IL-4, which directs the formation of an immunosuppressive TME via macrophage control. IL-4 loss was not compensated by nearby IL-4-expressing clones, revealing short-range regulation of TME composition dictating tumor evolution. Our studies show heterogeneous TMEs can emerge from localized altered expression of cancer-derived cytokines/chemokines that establish immune-rich and immune-excluded neighborhoods, which drive clone selection and immunotherapy resistance. They also demonstrate the potential of targeting IL-4 signaling to enhance ovarian cancer response to immunotherapy.

Comprehensive Analysis of a Platelet- and Coagulation-Related Prognostic Gene Signature Identifies CYP19A1 as a Key Tumorigenic Driver of Colorectal Cancer.

The intricate interplay between the platelet-coagulation system and the progression of malignant tumors has profound therapeutic implications. However, a thorough examination of platelet and coagulation markers specific to colorectal cancer (CRC) is conspicuously absent in the current literature. Consequently, there is an urgent need for further exploration into the mechanistic underpinnings of these markers and their potential clinical applications. By integrating RNA-seq data and clinicopathological information from patients with CRC in the cancer genome atlas, we identified genes related to the platelet-coagulation system using weighted gene co-expression networks and univariate Cox analysis. We established a prognostic risk model based on platelet- and coagulation-related genes using Lasso Cox regression analysis and validated the model in two independent CRC cohorts. We explored potential biological functional disparities between high-risk and low-risk groups through comprehensive bioinformatics analysis. Our findings indicate that colorectal cancer patients classified as high-risk generally exhibit poorer prognoses. Moreover, the model's risk scores were associated with the differential composition of the immune tumor microenvironment, suggesting its applicability to infer immunotherapy responsiveness. Cellular functional experiments and animal experiments indicated that CYP19A1 expression in CRC influences malignant phenotype and platelet activation. In summary, we present a novel platelet- and coagulation-related risk model for prognostic assessment of patients with CRC and confirm the important role of CYP19A1 in promoting malignant progression of CRC.

Abstract C169: Investigating the effects of ancestry in KRAS mediated lung adenocarcinoma: Exploring intratumoral heterogeneity and mitochondrial dynamics

Abstract Demonstrating a combination of high prevalence, late detection, and low survival, Lung cancer is the leading cause of cancer related deaths worldwide (Sainz de Aja J, 2021) and Lung Adenocarcinoma (LUAD) is its most prevalent pathologic subtype (Zhou, 2021). Emerging from within the distal alveolar epithelium, LUAD presents with vast heterogeneity in histology, mutational spectra, and epigenomic dysregulation (Sainz de Aja J, 2021) (Zhou, 2021). Additionally, LUAD’s considerable intratumoral heterogeneity manifests vast genomic and phenotypic diversity across tumor cells and cellular components of the tumor microenvironment (TME) within the same tumor tissue. LUAD also reveals significant racial disparities in incidence, survival and mortality rates between White and Black men in the United States. The occurrence of LUAD is approximately 68.3 per capita for Black men and 61.5 per capita for White men, reflecting an 11% higher rate in the former. Further, survival outcomes indicate that Black men generally exhibit lower 5-year relative survival rates compared to White men, highlighting greater mortality risk and conspicuously poorer prognosis (Siegel RL et al., 2023). While addressing the social determinants of health is vital for the mitigation of health disparities, understanding the genetic and molecular foundations that underly racial health inequities is essential for developing comprehensive interventions and advancing more precise therapeutic modalities for more diverse patient populations. Single Nucleotide Polymorphisms (SNPs) can influence oncogenic transformation and may be associated with distinct molecular landscapes in tumors and adjacent TME. Furthermore, ancestry may play a pivotal role in shaping individual susceptibility and risk for mitochondrial dysfunction and ensuing oncogenic transformation. To elucidate the biological underpinnings of racial health disparities in LUAD, 10 Black and 10 White male LUAD patients’ tumor and normal corresponding adjacent tissues underwent molecular profiling for KRAS mutation status, Whole Exome Sequencing (WES) to determine ancestry, and analysis of associated LUAD induced Mitochondrial Somatic Nucleotide Variants (mtSNVs). We also employed the 10X Visium HD spatial transcriptomic platform to evaluate spatially resolved molecular and cellular differences in KRAS mediated LUAD between Black and White men. Hypothesis: Thus, we propose that global ancestry is associated with variations in intratumoral heterogeneity, TME composition, and mitochondrial dynamics, indicating a potential role in the observed disparities in susceptibility, malignancy and mortality in LUAD across diverse patient populations. Citation Format: Eun Kyu Sung, Yuxin Jin, Yonatan Amzaleg, John Carpten, William Dean Wallace, Dan Raz, Aaron M. Neely. Investigating the effects of ancestry in KRAS mediated lung adenocarcinoma: Exploring intratumoral heterogeneity and mitochondrial dynamics [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C169.

Abstract A061: The impact of race and obesity on the prostate tumor microenvironment

Abstract Black Americans have the highest prostate cancer incidence and are twice as likely to die from their disease compared to Non-Hispanic White men, making this one of the largest cancer disparities between these two racial groups in the United States. While access to health care is one of the strongest contributors to this disparity, studies suggest biological distinctions exist between tumors from Black and Non-Hispanic White men. Furthermore, obesity is associated with worse prostate cancer outcomes, and research showing a stronger association between obesity and prostate cancer risk among Black men compared to Non-Hispanic White men suggests obesity and Black race may work in combination to create aggressive disease. Hence, we sought to thoroughly and precisely characterize tumors from Black men, with and without obesity, to identify tumor behavior and potential therapeutic options for this population, which to date, has not been done mostly because of the lack of racially diverse cohorts of prostate cancer. Also, we sought to determine the impact of obesity on the composition of the prostate tumor microenvironment, which to date remains unknown. Given that in the US obesity rates are over 40% and the pressing need to better address high-risk populations, it is critical to better understand how obesity and race impact disease biology. We hypothesized obesity and Black race, individually and combined, increase tumor immune infiltration, creating a distinct tumor microenvironment. Specifically, we hypothesized this microenvironment will be characterized by higher overall inflammation, but also will enable us to identify therapeutic targets that in time can lead to the creation of personalized treatments for this population. To test this hypothesis, we used a large and racially diverse patient cohort from men who underwent radical prostatectomy at the Veterans Affairs Medical Center in Durham, North Carolina. To analyze the tumor microenvironment at the single cell level and define spatial organization, we used imaging mass cytometry in tissue microarrays of tumor and normal prostate samples from patients similar in tumor stage. We created a customized marker panel to determine cell phenotype and expression of immune checkpoints. We detected 25 cell phenotypes in the prostate microenvironment and determined differential phenotypic abundance and interactions by race and obesity. Next, we will expand our study to include a larger number of samples and associate tumor microenvironment characteristics with patient recurrence, metastasis, and survival. In this study, we generated new insights into disease drivers in an understudied and disproportionately affected population and lay important groundwork for future research identifying novel therapeutic targets for high-risk populations, such as men with African descent and obesity. Citation Format: Gloria Cecilia Galvan, Simeon Mahov, Sungyong You, Simon Knott, Michael Freeman, Akil Merchant, Stephen J Freedland. The impact of race and obesity on the prostate tumor microenvironment [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr A061.

Analysis of ductal carcinoma in situ by self-reported race reveals molecular differences related to outcome

BackgroundDuctal carcinoma in situ (DCIS) is a non-obligate precursor to invasive breast cancer (IBC). Studies have indicated differences in DCIS outcome based on race or ethnicity, but molecular differences have not been investigated.MethodsWe examined the molecular profile of DCIS by self-reported race (SRR) and outcome groups in Black (n = 99) and White (n = 191) women in a large DCIS case-control cohort study with longitudinal follow up.ResultsGene expression and pathway analyses suggested that different genes and pathways are involved in diagnosis and ipsilateral breast outcome (DCIS or IBC) after DCIS treatment in White versus Black women. We identified differences in ER and HER2 expression, tumor microenvironment composition, and copy number variations by SRR and outcome groups.ConclusionsOur results suggest that different molecular mechanisms drive initiation and subsequent ipsilateral breast events in Black versus White women.

An atlas of genetic effects on cellular composition of the tumor microenvironment.

Deciphering the composition of the tumor microenvironment (TME) is critical for understanding tumorigenesis and to design immunotherapies. In the present study, we mapped genetic effects on cell-type proportions using single-cell and bulk RNA sequencing data, identifying 3,494 immunity quantitative trait loci (immunQTLs) across 23 cancer types from The Cancer Genome Atlas. Functional annotation revealed regulatory potential and we further assigned 1,668 genes that regulate TME composition. We constructed a combined immunQTL map by integrating data from European and Chinese colorectal cancer (CRC) samples. A polygenic risk score that incorporates these immunQTLs and hits on a genome-wide association study outperformed in CRC risk stratification within 447,495 multiethnic individuals. Using large-scale population cohorts, we identified that the immunQTL rs1360948 is associated with CRC risk and prognosis. Mechanistically, the rs1360948-G-allele increases CCL2 expression, recruiting regulatory T cells that can exert immunosuppressive effects on CRC progression. Blocking the CCL2-CCR2 axis enhanced anti-programmed cell death protein 1 ligand therapy. Finally, we have established a database (CancerlmmunityQTL2) to serve the research community and advance our understanding of immunogenomic interactions in cancer pathogenesis.

594. THE IMPACT OF PATIENT CHARACTERISTICS AND NEOADJUVANT TREATMENT ON THE TUMOUR MICRO-ENVIRONMENT OF ESOPHAGEAL CANCER

Abstract Background Esophageal cancer remains associated with poor prognosis, as even with the current standards of multimodal treatment and oncologic surgery many patients show no response to treatment, or suffer early recurrence after surgery. In the current era of precision medicine, a better understanding of the tumor microenvironment (TME) is needed to identify patients with unfavourable biology, but also to illustrate the physiopathology of host reaction to treatment. The aim of this monocentric translational study was to analyse the biomolecular characteristics of esophageal cancer in relation to key clinicopathologic parameters, and in particular to the response to neoadjuvant treatment. Methods A series of patients operated for esophageal cancer with curative intent between 01.2009 and 12.2021 were included in this study. Clinicopathological data were collected, and initial biopsies and surgical specimens were reassessed by a senior GI pathologist. The immune infiltrate markers CD3, CD8, CD163, CD68, PDL1and FOXP3 were recorded as cell counts/high power field. The CPS score was used for PD-L1 quantification, whereas the Mandard regression grade (TRG) assessed pathologic response to neoadjuvant treatment (NAT). Continuous variables were compared with the Mann-Whitney-U and ANOVA tests, and categorical ones with the Chi-2 test. Significance threshold was set at p<0.05. Results Overall, 68 patients (82.4% males, mean age 62.4□9.4 years, 79.4% adenocarcinoma) were included. TME in smokers had lower M2-like (CD163+, p=0.009) and total macrophages (CD68+, p=0.001), but similar CD163/68 ratio and T-cells as non-smokers. Adenocarcinoma histology compared to squamous cell, showed higher M2-like macrophages (p=0.023), mean CPS score (p=0.038) and T-cell infiltration (p=0.006). NAT increased macrophages and cytotoxic T-cells, and decreased Treg/FoxP3 cells in the TME. Chemotherapy, compared to chemoradiation, was associated with higher T-cell TME infiltration. Good responders to NAT (TRG1-2) had similar initial TME characteristics as poor responders, but they displayed lower macrophage count upon final histology (p=0.003). Conclusions In the present series, active smoking was related to attenuated, whereas adenocarcinoma histology to enhanced M2-like macrophage infiltration of esophageal cancer TME. Neoadjuvant treatment, and especially chemotherapy, recruited macrophages and T-cells in the TME. None of the biomarkers derived from the initial biopsies were associated with response to NAT, although an increased macrophage count upon final histology was related to poor response. The present study provides valuable insight to the TME composition of esophageal cancer. However, further studies are needed to assess the exact functional role of TME elements, and specifically macrophages, and their impact on clinical outcomes.