Their Tumor Microenvironment Research Articles

Immune landscape of oncohistone-mutant gliomas reveals diverse myeloid populations and tumor-promoting function

Histone H3-mutant gliomas are deadly brain tumors characterized by a dysregulated epigenome and stalled differentiation. In contrast to the extensive datasets available on tumor cells, limited information exists on their tumor microenvironment (TME), particularly the immune infiltrate. Here, we characterize the immune TME of H3.3K27M and G34R/V-mutant gliomas, and multiple H3.3K27M mouse models, using transcriptomic, proteomic and spatial single-cell approaches. Resolution of immune lineages indicates high infiltration of H3-mutant gliomas with diverse myeloid populations, high-level expression of immune checkpoint markers, and scarce lymphoid cells, findings uniformly reproduced in all H3.3K27M mouse models tested. We show these myeloid populations communicate with H3-mutant cells, mediating immunosuppression and sustaining tumor formation and maintenance. Dual inhibition of myeloid cells and immune checkpoint pathways show significant therapeutic benefits in pre-clinical syngeneic mouse models. Our findings provide a valuable characterization of the TME of oncohistone-mutant gliomas, and insight into the means for modulating the myeloid infiltrate for the benefit of patients.

Macrophage-mediated myelin recycling fuels brain cancer malignancy

Tumors growing in metabolically challenged environments, such as glioblastoma in the brain, are particularly reliant on crosstalk with their tumor microenvironment (TME) to satisfy their high energetic needs. To study the intricacies of this metabolic interplay, we interrogated the heterogeneity of the glioblastoma TME using single-cell and multi-omics analyses and identified metabolically rewired tumor-associated macrophage (TAM) subpopulations with pro-tumorigenic properties. These TAM subsets, termed lipid-laden macrophages (LLMs) to reflect their cholesterol accumulation, are epigenetically rewired, display immunosuppressive features, and are enriched in the aggressive mesenchymal glioblastoma subtype. Engulfment of cholesterol-rich myelin debris endows subsets of TAMs to acquire an LLM phenotype. Subsequently, LLMs directly transfer myelin-derived lipids to cancer cells in an LXR/Abca1-dependent manner, thereby fueling the heightened metabolic demands of mesenchymal glioblastoma. Our work provides an in-depth understanding of the immune-metabolic interplay during glioblastoma progression, thereby laying a framework to unveil targetable metabolic vulnerabilities in glioblastoma.

Atlas of metastatic gastric cancer links ferroptosis to disease progression and immunotherapy response

BACKGROUND & AIMSMetastases from gastric adenocarcinoma (GAC) lead to high morbidity and mortality. Developing innovative and effective therapies requires a comprehensive understanding of the tumor and immune biology of advanced GAC. Yet, collecting matched specimens from advanced, treatment-naïve GAC patients poses a significant challenge, limiting the scope of current research, which has predominantly focused on localized tumors. This gap hinders a deeper insight into the metastatic dynamics of GAC. METHODSWe performed in-depth single-cell transcriptome and immune profiling on 68 paired, treatment-naïve, primary-metastatic tumors to delineate alterations in cancer cells and their tumor microenvironment (TME) during metastatic progression. To validate our observations, we conducted comprehensive functional studies both in vitro and in vivo, employing cell lines, multiple PDX and novel mouse models of GAC. RESULTSLiver and peritoneal metastases exhibited distinct properties in cancer cells and dynamics of TME phenotypes, supporting the notion that cancer cells and their local TMEs co-evolve at metastatic sites. Our study also revealed differential activation of cancer meta-programs across metastases. We observed evasion of cancer cell ferroptosis via GPX4 upregulation during GAC progression. Conditional depletion of Gpx4 or pharmacological inhibition of ferroptosis resistance significantly attenuated tumor growth and metastatic progression. Additionally, ferroptosis-resensitizing treatments augmented the efficacy of CAR T-cell therapy. CONCLUSIONSThis study represents the largest single-cell dataset of metastatic GACs to date. High-resolution mapping of the molecular and cellular dynamics of GAC metastasis has revealed a rationale for targeting ferroptosis defense in combination with CAR T-cell therapy as a novel therapeutic strategy with potential immense clinical implications.

EGFR mutations induce the suppression of CD8+ T cell and anti-PD-1 resistance via ERK1/2-p90RSK-TGF-β axis in non-small cell lung cancer

BackgroundNon-small cell lung cancer (NSCLC) patients with EGFR mutations exhibit an unfavorable response to immune checkpoint inhibitor (ICI) monotherapy, and their tumor microenvironment (TME) is usually immunosuppressed. TGF-β plays an important role in immunosuppression; however, the effects of TGF-β on the TME and the efficacy of anti-PD-1 immunotherapy against EGFR-mutated tumors remain unclear.MethodsCorresponding in vitro studies used the TCGA database, clinical specimens, and self-constructed mouse cell lines with EGFR mutations. We utilized C57BL/6N and humanized M-NSG mouse models bearing EGFR-mutated NSCLC to investigate the effects of TGF-β on the TME and the combined efficacy of TGF-β blockade and anti-PD-1 therapy. The changes in immune cells were monitored by flow cytometry. The correlation between TGF-β and immunotherapy outcomes of EGFR-mutated NSCLC was verified by clinical samples.ResultsWe identified that TGF-β was upregulated in EGFR-mutated NSCLC by EGFR activation and subsequent ERK1/2-p90RSK phosphorylation. TGF-β directly inhibited CD8+ T cell infiltration, proliferation, and cytotoxicity both in vitro and in vivo, but blocking TGF-β did not suppress the growth of EGFR-mutated tumors in vivo. Anti-TGF-β antibody combined with anti-PD-1 antibody significantly inhibited the proliferation of recombinant EGFR-mutated tumors in C57BL/6N mice, which was superior to their monotherapy. Mechanistically, the combination of anti-TGF-β and anti-PD-1 antibodies significantly increased the infiltration of CD8+ T cells and enhanced the anti-tumor function of CD8+ T cells. Moreover, we found that the expression of TGF-β1 in EGFR-TKI resistant cell lines was significantly higher than that in parental cell lines. The combination of anti-TGF-β and nivolumab significantly inhibited the proliferation of EGFR-TKI resistant tumors in humanized M-NSG mice and prolonged their survival.ConclusionsOur results reveal that TGF-β expression is upregulated in NSCLC with EGFR mutations through the EGFR-ERK1/2-p90RSK signaling pathway. High TGF-β expression inhibits the infiltration and anti-tumor function of CD8+ T cells, contributing to the “cold” TME of EGFR-mutated tumors. Blocking TGF-β can reshape the TME and enhance the therapeutic efficacy of anti-PD-1 in EGFR-mutated tumors, which provides a potential combination immunotherapy strategy for advanced NSCLC patients with EGFR mutations.Graphical

Abstract PO4-28-09: Upregulation of the immune checkpoint protein B7-H3 is associated with an immune suppressive microenvironment in progression from in situ to invasive lobular breast cancer

Abstract Invasive lobular breast cancer (ILC) is an understudied subtype of breast cancer characterized by late recurrence, metastasis to serosal surfaces including the peritoneum, and poor long-term outcomes. Lobular carcinoma in situ (LCIS) is a non-obligate precursor to ILC but is associated with a 30% increased risk of developing ILC. Therefore, understanding the underlying changes that occur in the invasive lobular cells as well as their tumor microenvironment (TME) during the transition from LCIS to ILC is critical for the development of novel therapeutic targets that could be used in early disease. To address this, we used combined spatial whole genome transcriptomics and a 97-protein proteomics assay to examine the spatial molecular profiles of coexistent LCIS and ILC. PanCK-positive tumor cells and panCK-negative stromal cells were segmented and analyzed separately for both RNA and protein. Despite the close spatial proximity of LCIS and ILC, there were notable differences in gene and protein expression in the tumor cells as well as the tumor microenvironment (TME). RNA profiling revealed significant upregulation of genes encoding essential components of the extracellular matrix, including type I, 3 and 5 collagens, small leucine-rich proteoglycans byglycan (BGN) and lumican (LUM), periostin (POSTN) and secreted protein acidic and cysteine rich (SPARC). Metalloprotease genes MMP2 and MMP11 were also upregulated. Genes highly expressed in the LCIS tumor compartment were KRT5, KRT14 KRT17 and MYLK which are highly expressed in myoepithelial cells at the periphery of the LCIS. One of the most upregulated proteins in ILC cells was B7 homology 3 protein (B7-H3) or Cluster of Differentiation 276 (CD276). B7-H3 is a transmembrane immunoregulatory protein belonging to the B7 family (that also includes PD-L1 and PD-L2). This immune checkpoint protein is overexpressed in many tumors but is barely expressed in normal cells. B7-H3 has been associated with several aspects of cancer progression, such as evasion of tumor immune surveillance and metastasis, and is strongly linked to poor prognosis in cancer. Compared to the LCIS TME, B7-H3 was also the most upregulated protein in the ILC TME along with the tumor-promoting M1 macrophage marker CD68 and the regulatory T-cell marker FOXP3. The lymphocyte marker CD45 was downregulated as well as T-cell proteins CD3, CD40 and granzyme B. Moreover, CD27, a memory B-cell marker was most highly expressed in the TME surrounding LCIS compared to ILC. Overall, these molecular profiles support a transition to a toward a much more immunosuppressive environment for invasive tumor cells compared to LCIS. Based on these data, our working hypothesis is that upregulation of B7-H3 on lobular tumor cells promotes invasion allowing interaction with laminins, integrins and other ECM proteins in the basement membrane and the interstitial membrane as LCIS acquire invasive properties of ILC. Furthermore, upregulation of B7-H3 on CD3+ HLA-DR+ expressing antigen presenting cells also promotes a suppressive immune microenvironment by inhibiting T-cell proliferation and downregulating cytokine production. In sum, these strongly concurrent spatial transcriptome and protein data suggest that B7-H3 and the immune suppressive network of ILC may be a promising target for early stage lobular breast cancer. B7-H3 Inhibitors could be explored in the neoadjuvant setting to evaluate the efficacy of immunotherapy in primary ILC. Citation Format: Lynda Bennett, Sunati Sahoo, Cheryl Lewis, Indu Raman, Candace Frerich, Guanchun Chen, Min Xu, Suzanne Conzen. Upregulation of the immune checkpoint protein B7-H3 is associated with an immune suppressive microenvironment in progression from in situ to invasive lobular breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-28-09.

Abstract 6430: Gene expression signature quantifies the cellular contribution of the tumor vs. the microenvironment in determining colorectal cancer prognosis and therapeutic outcome

Abstract Accumulating evidence has suggested that cancer progression and therapeutic response may depend on not only tumor cells but also their tumor microenvironment (TME). However, their contributory roles are complex and not well understood. Here we report an analysis of 2373 human colorectal cancer (CRC) tumors representing all stages, leading to identification of a 20-gene signature capable of quantifying the cellular contribution of the tumor vs. the TME in determining colorectal cancer prognosis and therapeutic outcome. We classified these tumors into the consensus molecular subtypes (CMS1-4) with distinct, variable TME cellular features defined by CIBERSORT deconvolution analysis of bulk gene expression data. Surprisingly, all the 10 positive signature genes (portending worse survival) were strongly correlated with the TME-rich CMS1 and CMS4 tumors. By contrast, all the 10 negative signature genes (portending better survival) were highly related to the TME-poor CMS2 and CMS3 tumors. A single cell expression analysis from an independent database further revealed that strikingly, all the 10 positive genes were principally expressed by the immune/stromal TME whereas all the 10 negative genes were predominantly expressed in epithelial tumor cells. These data suggest that the TME has an equally important role as do tumor cells in determining CRC prognosis and support targeting the TME to improve survival. Moreover, distinct gene expression from tumor cells versus the TME also showed a differential impact on therapeutic outcome. Retrospective analyses on two independent clinical trial datasets show that the 20-gene signature score significantly predicted progression free survival in metastatic CRC patients treated with cetuximab, an FDA-approved EGFR inhibitor therapy. These data suggest a potential for the 20-gene signature as a predictive biomarker to identify “sensitive” versus “resistant” subpopulations of CRC patients to improve outcome of EGFR-targeted therapy. Citation Format: Mingli Yang, Timothy J. Yeatman, Michael V. Nebozhyn, Michael J. Schell, Lance Pflieger, Andrey Loboda, Warren J. Pledger, Ramani Soundararajan, Michelle Maurin, Heiman Wang, Jetsen Rodriguez Silva, Ashley Alden. Gene expression signature quantifies the cellular contribution of the tumor vs. the microenvironment in determining colorectal cancer prognosis and therapeutic outcome [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 6430.

Abstract 1749: Esophageal adenocarcinoma single-cell resolution ecotypes and subtypes mediate chemoradiation resistance

Abstract Esophageal adenocarcinoma (EAC) is an aggressive and lethal disease with a 5-year survival rate less than 20%. The current standard of care for locally advanced EAC patients is neoadjuvant chemoradiation (CRT) followed by surgery and the pathological response rate is low in clinic. An unresolved question is how the cancer cells and their tumor microenvironment (TME) mediate CRT resistance in EAC. To address this question, we performed single-cell RNA sequencing on 84 longitudinal samples from a cohort of patients (N=47) containing 20 good responders (GR) and 27 non-responders (NR). In total, we obtained 302,918 single cells which enabled us to delineate the phenotypic heterogeneity landscape in EAC at baseline, and identify reprogramming in both the immune and tumor cells during treatment that lead to CRT resistance. We identified 4 major cell type compartments in the EAC TME: lymphoid cells (T cells, NK cells, B cells, and plasma cells), myeloid cells (macrophages, neutrophils, dendritic cells, and mast cells), stromal cells (fibroblasts and endothelial cells) and epithelial cells. Our data shows that the TME enriched in lymphoid cells, including resident and effector memory CD8 T cells, follicular helper CD4 T cells, and B cells was associated with better CRT responses. Moreover, a significant myeloid cell infiltration was observed across most patients during CRT and the infiltrated macrophages from GR harbored a more pro-inflammation phenotype. In addition, we identified 4 major ecotypes of the TME cells and 4 major expression subtypes of the cancer cells. Notably, the interactions between TME ecotypes and cancer subtypes are significantly associated with CRT responsiveness. In summary, this study has provided valuable insights into the biology of EAC CRT response, and identified novel predictive biomarkers and actionable targets to enhance CRT efficacy. Citation Format: Rui Ye, Yawei Qiao, Shanshan Bai, Emi Sei, Min Hu, Jianzhong He, Nan Li, Yifan Wang, Pablo Lopez, Wei Zhang, Fei Ye, Brian Weston, Emmanuel Coronel, William Ross, Phillip Ge, Bhutani Manoop, Nicholas Navin, Steven Lin. Esophageal adenocarcinoma single-cell resolution ecotypes and subtypes mediate chemoradiation resistance [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 1749.

Abstract 5369: Mapping a T cell-cold phenotype to the colorectal cancer genome to identify POFUT1 as a driver of CD8+ T cell inhibition

Abstract CD8+ T cells are a critical anti-cancer immune subset; however, most colorectal cancer (CRC) patients have inadequate levels of CD8+ T cells in their tumor microenvironment (TME), contributing to poor survival and increased CRC aggression. While current immune checkpoint inhibitors are able to elicit anti-cancer CD8+ T cell responses in some patients, a majority of patients are still nonresponsive, and have minimal levels of tumor-infiltrating CD8+ T cells. This effect is potentially due to still-unrecognized cancer-driven mechanisms of immunosuppression. To identify candidate genes with roles in CD8+ T cell exclusion, we used a T cell gene signature (Tsig) to quantify CD8+ T cell infiltration in tumors profiled by RNA-seq. Partial Spearman correlation adjusted for tumor purity was performed for all annotated genes (N=20501) in the TCGA CRC RNA-seq data set (N=373) to identify genes most inversely correlated with Tsig. A locus at chromosome 20q was identified as the region of the genome most inversely correlated with Tsig - both by copy number analysis and by RNA expression. Interestingly, this region is the most copy number-amplified region in CRC tumors, and the genes at this locus are among the most highly expressed genes in CRC tumors. Within this region, the amplified and overexpressed gene Protein O-Fucosyltransferase 1 (POFUT1) had the strongest inverse correlation to Tsig. POFUT1 function is essential to canonical NOTCH signaling, and CRC-expressed NOTCH is implicated in increased CRC secretion of immunosuppressive factors IL-6, TGF-β and VEGF, and reduced CD8+ T cell secretion of IFN-γ and IL-2. POFUT1 overexpressing (OE) CT26 and MC38 cell lines were generated, and confirmed by Western Blot to have elevated levels of both cleaved NOTCH1 (NICD1), and NOTCH pathway transcriptional target, HES1. Murine CD8+ T cells were stimulated in vitro with CD3/CD28 microbeads and IL-2 in conditioned medium (CM) from vector or POFUT1-OE lines. CD8+ T cells cultured in CM from POFUT1-OE lines had significantly lower levels of activation markers (CD45 (p=0.0022), CD8 (p=0.0095), CD25 (p=0.0069, CD69 (p=0.0099)), reduced proliferation (CFSE, p=0.1281), and generated less ATP (Cell-Titer Glo, p=0.0003) than CD8+ T cells cultured in vector CM. In pan-cancer correlational analyses, POFUT1 is in the top 5% of genes most inversely correlated with Tsig in 12/24 solid tumor types annotated in TCGA (SKCM, THCA, COAD, READ, LUSC, CESC, KIRC, STAD, HNSC, KIRP, LIHC, UCEC p<0.0001). POFUT1 is robustly negatively correlated with T cell infiltration in many cancer types. We observed a positive association in CRC between POFUT1 and NOTCH signaling, and observed that POFUT1 expression reduced CD8+ T cell activity, potentially through upregulation of extracellular factors (in progress). Our findings fit a model where POFUT1 amplification in CRC promotes CD8+ T cell dysfunction as a mechanism of immune escape. Citation Format: Calvin J. Wagner, Eric D. Routh, Raven Rutledge, Lance D. Miller. Mapping a T cell-cold phenotype to the colorectal cancer genome to identify POFUT1 as a driver of CD8+ T cell inhibition [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 5369.

Adding New Dimensions to 3D Cancer Models.

Understanding patient-specific responses to anticancer therapies and how individual tumors interact with their tumor microenvironment (TME) is a challenging task. To measure the impact of the TME on diverse and clinically relevant treatments, Ramos Zapatero and colleagues coupled patient-derived organoid (PDO) and cancer-associated fibroblast (CAF) cocultures with high-throughput mass cytometry-based assessment of cell state. Using a newly developed "Trellis" algorithm enabled integration and analysis of highly complex, multidimensional treatment response data. This work showed that tumor cell response to chemotherapy was associated with both intrinsic and nonintrinsic signaling states, whereby proliferative rate, growth factor signaling, and CAFs interaction influenced chemoprotection. Furthermore, the work suggests a potential role for the TME in promoting lineage plasticity associated with drug resistance. In all, the pipeline described provides a blueprint for exploring the intricate interplay of factors influencing cancer treatment response.

It Takes Two to Tango: The Interplay between Prostate Cancer and Its Microenvironment from an Epigenetic Perspective.

Prostate cancer is the second most common cancer in men worldwide and is associated with high morbidity and mortality. Consequently, there is an urgent unmet need for novel treatment avenues. In addition to somatic genetic alterations, deviations in the epigenetic landscape of cancer cells and their tumor microenvironment (TME) are critical drivers of prostate cancer initiation and progression. Unlike genomic mutations, epigenetic modifications are potentially reversible. Therefore, the inhibition of aberrant epigenetic modifications represents an attractive and exciting novel treatment strategy for castration-resistant prostate cancer patients. Moreover, drugs targeting the epigenome also exhibit synergistic interactions with conventional therapeutics by directly enhancing their anti-tumorigenic properties by "priming" the tumor and tumor microenvironment to increase drug sensitivity. This review summarizes the major epigenetic alterations in prostate cancer and its TME, and their involvement in prostate tumorigenesis, and discusses the impact of epigenome-targeted therapies.

Identification and validation of a dysregulated TME-related gene signature for predicting prognosis, and immunological properties in bladder cancer.

During tumor growth, tumor cells interact with their tumor microenvironment (TME) resulting in the development of heterogeneous tumors that promote tumor occurrence and progression. Recently, there has been extensive attention on TME as a possible therapeutic target for cancers. However, an accurate TME-related prediction model is urgently needed to aid in the assessment of patients' prognoses and therapeutic value, and to assist in clinical decision-making. As such, this study aimed to develop and validate a new prognostic model based on TME-associated genes for BC patients. Transcriptome data and clinical information for BC patients were extracted from The Cancer Genome Atlas (TCGA) database. Gene Expression Omnibus (GEO) and IMvigor210 databases, along with the MSigDB, were utilized to identify genes associated with TMEs (TMRGs). A consensus clustering approach was used to identify molecular clusters associated with TMEs. LASSO Cox regression analysis was conducted to establish a prognostic TMRG-related signature, with verifications being successfully conducted internally and externally. Gene ontology (GO), KEGG, and single-sample gene set enrichment analyses (ssGSEA) were performed to investigate the underlying mechanisms. The potential response to ICB therapy was estimated using the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and Immunophenoscore (IPS). Additionally, it was found that the expression level of certain genes in the model was significantly correlated with objective responses to anti-PD-1 or anti-PD-L1 treatment in the IMvigor210, GSE111636, GSE176307, or Truce01 (registration number NCT04730219) cohorts. Finally, real-time PCR validation was performed on 10 paired tissue samples, and in vitro cytological experiments were also conducted on BC cell lines. In BC patients, 133 genes differentially expressed that were associated with prognosis in TME. Consensus clustering analysis revealed three distinct clinicopathological characteristics and survival outcomes. A novel prognostic model based on nine TMRGs (including C3orf62, DPYSL2, GZMA, SERPINB3, RHCG, PTPRR, STMN3, TMPRSS4, COMP) was identified, and a TMEscore for OS prediction was constructed, with its reliable predictive performance in BC patients being validated. MultiCox analysis showed that the risk score was an independent prognostic factor. A nomogram was developed to facilitate the clinical viability of TMEscore. Based on GO and KEGG enrichment analyses, biological processes related to ECM and collagen binding were significantly enriched among high-risk individuals. In addition, the low-risk group, characterized by a higher number of infiltrating CD8+ T cells and a lower burden of tumor mutations, demonstrated a longer survival time. Our study also found that TMEscore correlated with drug susceptibility, immune cell infiltration, and the prediction of immunotherapy efficacy. Lastly, we identified SERPINB3 as significantly promoting BC cells migration and invasion through differential expression validation and in vitro phenotypic experiments. Our study developed a prognostic model based on nine TMRGs that accurately and stably predicted survival, guiding individual treatment for patients with BC, and providing new therapeutic strategies for the disease.

ADP-Ribosylation Factor 6 Pathway Acts as a Key Executor of Mesenchymal Tumor Plasticity.

Despite the "big data" on cancer from recent breakthroughs in high-throughput technology and the development of new therapeutic modalities, it remains unclear as to how intra-tumor heterogeneity and phenotypic plasticity created by various somatic abnormalities and epigenetic and metabolic adaptations orchestrate therapy resistance, immune evasiveness, and metastatic ability. Tumors are formed by various cells, including immune cells, cancer-associated fibroblasts, and endothelial cells, and their tumor microenvironment (TME) plays a crucial role in malignant tumor progression and responses to therapy. ADP-ribosylation factor 6 (ARF6) and AMAP1 are often overexpressed in cancers, which statistically correlates with poor outcomes. The ARF6-AMAP1 pathway promotes the intracellular dynamics and cell-surface expression of various proteins. This pathway is also a major target for KRAS/TP53 mutations to cooperatively promote malignancy in pancreatic ductal adenocarcinoma (PDAC), and is closely associated with immune evasion. Additionally, this pathway is important in angiogenesis, acidosis, and fibrosis associated with tumor malignancy in the TME, and its inhibition in PDAC cells results in therapeutic synergy with an anti-PD-1 antibody in vivo. Thus, the ARF6-based pathway affects the TME and the intrinsic function of tumors, leading to malignancy. Here, we discuss the potential mechanisms of this ARF6-based pathway in tumorigenesis, and novel therapeutic strategies.

Heterogeneity of the Tumor Microenvironment Across Molecular Subtypes of Breast Cancer.

Breast cancer is a heterogenous disease at the molecular level thus, it can be hypothesized that different molecular subtypes differ in their tumor microenvironment (TME) also. Understanding the TME heterogeneity may provide new prognostic biomarkers and new targets for cancer therapy. For deciphering heterogeneity in the TME, immunohistochemistry for immune markers (CD3, CD4, CD8, CD68, CD163, and programmed death-ligand 1), Cancer-associated fibroblast markers [anti-fibroblast activating protein α (FAP-α), platelet-derived growth factor receptor α (PDGFR-α), S100A4, Neuron-glial antigen 2, and Caveolin-1], and angiogenesis (CD31) was performed on tissue microarrays of different molecular subtypes of breast cancer. High CD3 + T cells were noted in the Luminal B subtype ( P =0.002) of which the majority were CD8 + cytotoxic T cells. Programmed death-ligand 1 expression in immune cells was highest in the human epidermal growth factor receptor 2 (Her-2)-positive and Luminal B subtypes compared with the triple-negative breast cancer (TNBC) subtype ( P =0.003). Her-2 subtype is rich in M2 tumor-associated macrophages ( P =0.000) compared with TNBC and Luminal B subtypes. M2 immune microenvironment correlated with high tumor grade and high Ki-67. Her-2 and TNBC subtypes are rich in extracellular matrix remodeling (FAP-α, P =0.003), angiogenesis-promoting (PDGFR-α; P =0.000) and invasion markers (Neuron-glial antigen 2, P =0.000; S100A4, P =0.07) compared with Luminal subtypes. Mean Microvessel density showed an increasing trend: Luminal A>Luminal B>Her-2 positive>TNBC; however, this difference was not statistically significant. The cancer-associated fibroblasts (FAP-α, PDGFR-α, and Neuron-glial antigen 2) showed a positive correlation with lymph node metastasis in specific subtypes. Immune cells, tumor-associated macrophage, and cancer-associated fibroblast-related s tromal markers showed higher expression in Luminal B, Her-2 positive, and TNBC respectively. This differential expression of different components of TME indicates heterogeneity of the TME across molecular subtypes of breast cancer.

Omics-Based Investigations of Breast Cancer.

Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.

The Novel-Natural-Killer-Cell-Related Gene Signature Predicts the Prognosis and Immune Status of Patients with Hepatocellular Carcinoma.

The current understanding of the prognostic significance of natural killer (NK) cells and their tumor microenvironment (TME) in hepatocellular carcinoma (HCC) is limited. Thus, we screened for NK-cell-related genes by single-cell transcriptome data analysis and developed an NK-cell-related gene signature (NKRGS) using multi-regression analyses. Patients in the Cancer Genome Atlas cohort were stratified into high- and low-risk groups according to their median NKRGS risk scores. Overall survival between the risk groups was estimated using the Kaplan-Meier method, and a NKRGS-based nomogram was constructed. Immune infiltration profiles were compared between the risk groups. The NKRGS risk model suggests significantly worse prognoses in patients with high NKRGS risk (p < 0.05). The NKRGS-based nomogram showed good prognostic performance. The immune infiltration analysis revealed that the high-NKRGS-risk patients had significantly lower immune cell infiltration levels (p < 0.05) and were more likely to be in an immunosuppressive state. The enrichment analysis revealed that immune-related and tumor metabolism pathways highly correlated with the prognostic gene signature. In this study, a novel NKRGS was developed to stratify the prognosis of HCC patients. An immunosuppressive TME coincided with the high NKRGS risk among the HCC patients. The higher KLRB1 and DUSP10 expression levels correlated with the patients' favorable survival.

Abstract 6765: Spatial insights into tumor immune evasion illuminated with 1000-plex RNA profiling with CosMx Spatial Molecular Imager

Abstract Patient response to immunotherapy has been revolutionary but remains limited due to the inability to convert excluded or cold tumors into ones which would be permissive to therapeutic intervention. To treat patients that evade immune therapy, comprehensive understanding of their tumor microenvironment (TME) is needed. To date, most profiling efforts have lacked the ability to capture high-plex ‘omics data while retaining the spatial architecture of the TME. We developed the CosMx™ Spatial Molecular Imager (SMI) for analyzing formalin-fixed paraffin-embedded (FFPE) or fresh-frozen (FF) tissue and capturing the expression of over 1000 RNA targets simultaneously with subcellular resolution from a single histopathology slide. We profiled a cohort of 16 slides with CosMx using the Human Universal Cell Characterization (UCC) Panel across a range of solid tumors. This cohort represents a diverse array of patients which include both infiltrated and excluded tumors. We included technical replicates for 5 of the samples to better understand reproducibility of the assay. We were able to characterize over 4.5 million cells and detected on average over 80% of the panel per patient and assigning more than 95% of the transcripts profiled to unique cells across these samples. We were able to robustly identify more than 20 cell types by integrating our data with previous single-cell sequencing projects from the human cell atlas. We demonstrate robust delineation of critical immune cell populations from across lymphoid and myeloid lineages, as well as stromal cell populations inclusive of cell types frequently missed using dissociated cell sequencing, such as vascular endothelium associated with immune cell migration into the tumor bed. We leveraged 450+ genes from our panel dedicated to cell lineage, cell-cell interaction, and ligand-receptor signaling to identify unique interactions occurring at different scales between the tumor and the TME. We find that diverse mechanisms of immune evasion can be captured, and a clear role for cell types such as SPP1+ Macrophages emerges in multiple cancer types. Utilizing the CosMx platform to profile tissues allows for robust resolution of critical immunogenic signaling cascades and cellular interactions that are necessary to truly understand the tumor architecture. By maintaining the tissue structure, we can directly measure cellular interactions and capture cells commonly missed during dissociative studies. With this new platform, we are better poised than ever to truly understand the molecular mechanisms that drive tumor response to intervention. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures Citation Format: Claire Williams, Jason W. Reeves, Patrick Danaher, Shanshan He, Sean Kim, Michael Patrick, Julian Preciado, Mark Gregory, Zach Reitz, Justin Jenkins, Rachel Liu, Sarah Murphy, Christine Kang, Byron Hartman, Vikram Devgan, Michael Rhodes, Joseph Beechem. Spatial insights into tumor immune evasion illuminated with 1000-plex RNA profiling with CosMx Spatial Molecular Imager [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6765.

New insights into the role of adipocytes in pancreatic cancer progression: paving the way towards novel therapeutic targets.

Pancreatic cancer (PC) remains one of the most lethal malignancies across the world, which is due to delayed diagnosis and resistance to current therapies. The interactions between pancreatic tumor cells and their tumor microenvironment (TME) allow cancer cells to escape from anti-cancer therapies, leading to difficulties in treating PC. With endocrine function and lipid storage capacity, adipose tissue can maintain energy homeostasis. Direct or indirect interaction between adipocytes and PC cells leads to adipocyte dysfunction characterized by morphological change, fat loss, abnormal adipokine secretion, and fibroblast-like transformation. Various adipokines released from dysfunctional adipocytes have been reported to promote proliferation, invasion, metastasis, stemness, and chemoresistance of PC cells via different mechanisms. Additional lipid outflow from adipocytes can be taken into the TME and thus alter the metabolism in PC cells and surrounding stromal cells. Besides, the trans-differentiation potential enables adipocytes to turn into various cell types, which may give rise to an inflammatory response as well as extracellular matrix reorganization to modulate tumor burden. Understanding the molecular basis behind the protumor functions of adipocytes in PC may offer new therapeutic targets.

Abstract A080: The immunological signatures of African American prostate cancer as biological determinants of disease disparity

Abstract Background: Prostate cancer (PCa) is currently the second leading cause of cancer-related deaths among men in the United States. African American men suffer the highest incidence of disease morbidity and mortality compared to other racial groups. Although socio-economic, cultural, epidemiological, and genomic factors have been described to contribute to cancer health disparities in African American men, there is a knowledge gap regarding how the tumor immune landscape shapes aggressive disease patterns in this patient population, and whether their tumor microenvironment (TME) is amenable to immune modulation. This study aims to identify distinct and targetable immunosuppressive phenotypes and immunological signatures in prostate tumors of AA patients. Methodology: Peripheral blood from consented African American (AA) and Caucasian American (CA) patients undergoing prostatectomy at Moffitt Cancer Center were analyzed by Luminex multiplex cytokine/chemokine assay and comprehensive immune profiling via multi-parameter flow cytometry. Also, multiparameter immune profiling of freshly resected PCa specimens obtained from these same patients after prostatectomy was performed. In addition, multiplex immunohistochemical staining was performed on prostate tumor tissue microarrays to compare the proportions and phenotypes of T cells in the prostate TME of AA and CA patients. Lastly, the immunomodulatory potential of AZD5153, a bivalent Bromodomain 4 (BRD4) inhibitor was investigated on orthotopic prostate tumor-bearing humanized mouse models under racially defined settings, followed by comprehensive flow cytometry immunophenotypic profiling of tumor-infiltrating immune cells in the resected mice prostate tumors at clinical endpoints. Results: Prostate tumors of AA patients harbored higher proportions of CD4+ regulatory T cells (Tregs) and lower proportions of CD8+ T cells relative to CA patients. Furthermore, the immunophenotypic analysis of T cells showed higher expression of immune checkpoint molecules in AA compared to CA patients. Serum analysis revealed cytokine and chemokine expression signatures that are skewed towards a more immunosuppressive profile in AA compared to CA patients. Treatment with AZD5153 led to an increase in the survival time and a more striking reduction in tumor volume of AA-matched prostate tumor-bearing humanized mice relative to CA-matched prostate tumor-bearing humanized mice. A decrease in the proportion of tumor-infiltrating Tregs and a reduction in the expression of immune checkpoint molecules were also observed in prostate tumors from AA-matched humanized mice relative to CA-matched humanized mice. Conclusion: Our findings support the contributory role of racially distinct immunophenotypes and immune signatures in PCa disparity, and highlight the potential immunotherapeutic benefits of BRD4 inhibitors, such as AZD5153 in AA PCa patients. Citation Format: Saheed O. Oseni, Arup Bag, Oluwaseyi Oluwatola, Natalie DeMars, Dennis Adeegbe. The immunological signatures of African American prostate cancer as biological determinants of disease disparity [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A080.

Analysis of Tumor Microenvironment Heterogeneity among Breast Cancer Subtypes to Identify Subtype-Specific Signatures.

Breast cancer is one of the most frequent malignancies in women worldwide. According to 50-gene signature, Prediction Analysis of Microarray 50 (PAM50), breast cancer can be categorized into five molecular subtypes, and these subtypes are highly heterogeneous in different molecular characteristics. However, the landscape of their tumor microenvironment (TME) heterogeneity has not been fully researched. Using the multi-omics dataset of breast cancer from the METABRIC cohort (n = 1699), we conducted extensive analyses of TME-related features to investigate TME heterogeneity in each breast cancer subtype. We then developed a cell-based subtype set enrichment analysis to identify the subtype-specific TME cells, and further evaluate their prognostic effects. Our results illustrate that different breast cancer subtypes exhibit different TME patterns. Basal-like and HER2-enriched subtypes are associated with high immune scores, expression of most immune regulatory targets, and immune cell infiltration, suggesting that these subtypes could be defined as "immune hot" tumors and suitable for immune checkpoint blockade (ICB) therapy. In contrast, Luminal A and Luminal B subtypes are associated with low immune scores and immune cell infiltration, suggesting that these subtypes could be defined as "immune cold" tumors. Additionally, the Normal-like subtype has relatively high levels of both immune and stromal features, which indicates that the Normal-like subtype may be suitable for more diverse treatment strategies. Our study reveals the breast cancer tumor microenvironment heterogeneity across subtypes. The comprehensive analysis of breast cancer TME-related characteristics may help us to adopt a tailored treatment strategy for different subtypes of patients.

Genomic landscape of the immunogenicity regulation in skin melanomas with diverse tumor mutation burden.

Skin melanoma cells are tightly interconnected with their tumor microenvironment (TME), which influences their initiation, progression, and sensitivity/resistance to therapeutic interventions. An immune-active TME favors patient response to immune checkpoint inhibition (ICI), but not all patients respond to therapy. Here, we assessed differential gene expression in primary and metastatic tumors from the TCGA-SKCM dataset, compared to normal skin samples from the GTEx project and validated key findings across 4 independent GEO datasets, as well as using immunohistochemistry in independent patient cohorts. We focused our attention on examining the expression of various immune receptors, immune-cell fractions, immune-related signatures and mutational signatures across cutaneous melanomas with diverse tumor mutation burdens (TMB). Globally, the expression of most immunoreceptors correlated with patient survival, but did not differ between TMBhigh and TMBlow tumors. Melanomas were enriched in "naive T-cell", "effector memory T-cell", "exhausted T-cell", "resting Treg T-cell" and "Th1-like" signatures, irrespective of their BRAF, NF1 or RAS mutational status. Somatic mutations in IDO1 and HLA-DRA were frequent and could be involved in hindering patient response to ICI therapies. We finally analyzed transcriptome profiles of ICI-treated patients and associated their response with high levels of IFNγ, Merck18, CD274, CD8, and low levels of myeloid-derived suppressor cells (MDSCs), cancer-associated fibroblasts (CAFs) and M2 macrophages, irrespective of their TMB status. Overall, our findings highlight the importance of pre-existing T-cell immunity in ICI therapeutic outcomes in skin melanoma and suggest that TMBlow patients could also benefit from such therapies.