Hypoxia Signature Research Articles

The lncRNA AFAP1-AS1 is upregulated in metastatic triple-negative breast tumors and controls hypoxia-activated vasculogenic mimicry and angiogenesis

BackgroundVasculogenic mimicry (VM) is an alternative intratumoral microcirculation system that depends on the capacity of tumor cells to reorganize and grow in three-dimensional (3D) channel architectures like the capillaries formed by endothelial cells. Both VM and angiogenesis may coordinately function to feed cancer cells, allowing tumor growth. Long noncoding RNAs (lncRNAs) regulate critical cellular functions in cancer cells, including cell proliferation, apoptosis, angiogenesis, invasion, and metastasis. The lncRNA, known as actin filament-associated protein 1-antisense RNA 1 (AFAP1-AS1), has been described as an oncogene in diverse types of cancers. However, its role in VM and metastasis in triple-negative breast cancer (TNBC) is unknown.MethodsReverse transcription and quantitative polymerase chain reaction (RT‒qPCR) experiments were performed to evaluate the expression of 10 selected lncRNAs from literature in metastatic and nonmetastatic biopsies from TNBC patients. The expression of AFAP1-AS1 was analyzed in Genotype-Tissue Expression Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets. The AFAP1-AS1 expression was knocked in TNBC Hs578T cells by transfection of specific siRNAs. Channel-like formation assays were performed using 3D cultures over Matrigel in hypoxia-treated Hs578T cancer cells with diminished expression of AFAP1-AS1. The angiogenesis tests were conducted using human umbilical vein endothelial cells (HUVECs) and AFAP1-AS1- silenced Hs578T cells on 3D cell cultures. The presence of VM (CD31-/PAS+) in tumor tissues from TNBC patients with and without metastasis was assessed through immunohistochemistry using endothelial marker CD31 antibodies and periodic acid-Schiff (PAS) staining.ResultsCompared with normal mammary tissues, AFAP1-AS1 expression was higher in breast cancer tissues. Moreover, AFAP1-AS1 expression was upregulated in the TNBC subtype compared to receptor-positive breast tumors. In addition, the expression of AFAP1-AS1 was correlated with the expression of the thirteen genes characteristic of a previously reported hypoxia signature. Interestingly, AFAP1-AS1 was upregulated in primary TNBC tumors from patients who developed metastasis compared with the nonmetastatic group. Functional analysis revealed that the knockdown of AFAP1-AS1 in Hs578T cells significantly impaired the hypoxia-induced VM, accompanied by a decrease in the development of 3D channel networks. Similarly, AFAP1-AS1 knockdown counteracts the angiogenic potential of cancer cells, as indicated by a reduction in the number of polygons, sprouting cells, and nodes in HUVEC cells. Remarkably, an increase in CD31-/PAS + staining of 3D channel networks in primary breast tumors from metastatic patients was found compared with the nonmetastatic group. Finally, we found that the number of blood vessels increased in the nonmetastatic group more than in the metastatic cohort.ConclusionsOur data suggested that AFAP1-AS1 controls both VM and angiogenesis in Hs578T breast cancer cells and that increased metastasis is associated with VM in TNBC patients.

Comprehensive Bioinformatics Analysis Reveals the Potential Role of the hsa_circ_0001081/miR-26b-5p Axis in Regulating COL15A1 and TRIB3 within Hypoxia-Induced miRNA/mRNA Networks in Glioblastoma Cells.

Background/Objectives: The intrinsic molecular heterogeneity of glioblastoma (GBM) is one of the main reasons for its resistance to conventional treatment. Mesenchymal GBM niches are associated with hypoxic signatures and a negative influence on patients' prognosis. To date, competing endogenous RNA (ceRNA) networks have been shown to have a broad impact on the progression of various cancers. In this study, we decided to construct hypoxia-specific microRNA/ messengerRNA (miRNA/mRNA) networks with a putative circular RNA (circRNA) regulatory component using available bioinformatics tools. Methods: For ceRNA network construction, we combined publicly available data deposited in the Gene Expression Omnibus (GEO) and interaction pairs obtained from miRTarBase and circBank; a differential expression analysis of GBM cells was performed with limma and deseq2. For the gene ontology (GO) enrichment analysis, we utilized clusterProfiler; GBM molecular subtype analysis was performed in the Glioma Bio Discovery Portal (Glioma-BioDP). Results: We observed that miR-26b-5p, generally considered a tumor suppressor, was upregulated under hypoxic conditions in U-87 MG cells. Moreover, miR-26b-5p could potentially inhibit TRIB3, a gene associated with tumor proliferation. Protein-protein interaction (PPI) network and GO enrichment analyses identified a hypoxia-specific subcluster enriched in collagen-associated terms, with six genes highly expressed in the mesenchymal glioma group. This subcluster included hsa_circ_0001081/miR-26b-5p-affected COL15A1, a gene downregulated in hypoxic U-87 MG cells yet highly expressed in the mesenchymal GBM subtype. Conclusions: The interplay between miR-26b-5p, COL15A1, and TRIB3 suggests a complex regulatory mechanism that may influence the extracellular matrix composition and the mesenchymal transformation in GBM. However, the precise impact of the hsa_circ_0001081/miR-26b-5p axis on collagen-associated processes in hypoxia-induced GBM cells remains unclear and warrants further investigation.

Single-cell transcriptome analysis reveals evolving tumour microenvironment induced by immunochemotherapy in nasopharyngeal carcinoma.

Combinatory therapeutic strategy containing immunochemotherapy as part of induction therapy components is one of the current trends in the treatment of high-risk metastatic locally advanced nasopharyngeal carcinoma (NPC). However, the mechanism underlying the heterogeneity of response at the single-cell level has not been underexplored. 18 bulks and 11 single-cell RNA sequencing from paired before-treatment and on-treatment samples in patients with treatment-naive high-risk metastatic locally advanced NPCs were obtained. Following quality control, a total of 87191 cells were included in the subsequence bioinformatics analysis. Immunochemotherapy was associated with on-treatment tumour microenvironment (TME) remodelling, including upregulation of anti-TMEs signatures, downregulation of pro-TMEs signatures, reversing CD8+ T exhaustion, and repolarizing proinflammatory TAMs. For the patients achieving a complete response, the cytotoxic activity of CD8+ T cells was stimulated and more interferon-gamma was provided, which would be the key for TAMs proinflammatory repolarization and eventually promote the CD8+ T cells maturation in turn. Among patients who did not reach complete response, differentiation and hypoxia signatures for endothelial cells were elevated after therapy. These patients exhibited higher levels of immune checkpoint genes in malignant cells at the baseline (before treatment), and decreased tumour antigen presentation activity, which may underlie the resistance mechanism to therapy. This study pictures a map of TME modulation following immunochemotherapy-based combination induction therapy and provides potential future approaches. Immunochemotherapy remodeled T cell phenotypes. For the patients achieving complete response, more interferon gamma was provided by CD8+ T cells after therapy, which would be the key for TAMs pro-inflammatory repolarization and eventually promote the CD8+ T cells maturation in turns. Among patients who did not reach complete response, malignant cells exhibited higher level of immune checkpoint genes before therapy, and decreased tumor antigen presentation activity, which may underlie the resistance mechanism to therapy.

Abstract C105: Novel cancer-specific hypoxia signature predicts poor prognosis and highlights racial disparities in breast cancer

Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. TNBC displays exceptional transcriptional heterogeneity, both between patients and intratumorally, and disproportionately affects underserved women. Hypoxia, a state of low oxygen levels, is often present in the solid tumor microenvironment. In TNBC, hypoxia is a key driver of aggressiveness and therapeutic resistance. Past bulk RNA sequencing (RNAseq) studies in cancer research have lacked spatial resolution, failing to uncover precise transcriptional differences within tumor regions. This spatial limitation has been especially problematic for studying transcriptional heterogeneity of the cellular hypoxia response within tumors. By integrating single-cell RNA sequencing and spatial transcriptomic analyses in a TNBC xenograft tumor model, our research has uncovered a novel hypoxia gene signature, specific to cancer cells. Elevated expression of this hypoxia signature predicts poorer prognosis in breast cancer patients, especially within TNBC patients and those of African ancestry. This suggests that hypoxia may play a role in the racial disparities observed in TNBC prognosis, potentially informing treatment strategies. This workflow introduces a novel framework for translating general spatial transcriptomics data into clinically relevant and accurate gene signatures. Citation Format: Kent Schechter, Long C. Nguyen, Geetha P. Yerradoddi, Rania Bassiouni, John D. Carpten, Marsha R. Rosner. Novel cancer-specific hypoxia signature predicts poor prognosis and highlights racial disparities in breast cancer [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 C105.

Proteogenomic characterization of pancreatic neuroendocrine tumors uncovers hypoxia and immune signatures in clinically aggressive subtypes

Pancreatic neuroendocrine tumors (PanNETs) represent well-differentiated endocrine neoplasms with variable clinical outcomes. Predicting patient outcomes using the current tumor grading system is challenging. In addition, traditional systemic treatment options for PanNETs, such as somatostatin analogs or cytotoxic chemotherapies, are very limited. To address these issues, we characterized PanNETs using integrated proteogenomics and identified four subtypes. Two proteomic subtypes showed high recurrence rates, suggesting clinical aggressiveness that was missed by current classification. Hypoxia and inflammatory pathways were significantly enriched in the clinically aggressive subtypes. Detailed analyses revealed metabolic adaptation via glycolysis upregulation and oxidative phosphorylation downregulation under hypoxic conditions. Inflammatory signature analysis revealed that immunosuppressive molecules were enriched in immune hot tumors and might be immunotherapy targets. In this study, we characterized clinically aggressive proteomic subtypes of well-differentiated PanNETs and identified candidate therapeutic targets.

Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer's and Parkinson's disease.

Introduction: This study investigates the role of hypoxia-related genes in the neuroprotective efficacy of Yang Xue oral liquid (YXKFY) in Alzheimer's disease (AD) and Parkinson's disease (PD). Methods and results: Using differential expression and weighted gene co-expression network analysis (WGCNA), we identified 106 and 9 hypoxia-associated genes in AD and PD, respectively, that are implicated in the transcriptomic and proteomic profiles. An artificial intelligence-driven hypoxia signature (AIDHS), comprising 17 and 3 genes for AD and PD, was developed and validated across nine independent cohorts (n = 1713), integrating 10 machine learning algorithms and 113 algorithmic combinations. Significant associations were observed between AIDHS markers and immune cells in AD and PD, including naive CD4+ T cells, macrophages, and neutrophils. Interactions with miRNAs (hsa-miR-1, hsa-miR-124) and transcription factors (USF1) were also identified. Single-cell RNA sequencing (scRNA-seq) data highlighted distinct expression patterns of AIDHS genes in various cell types, such as high expression of TGM2 in endothelial cells, PDGFRB in endothelial and mesenchymal cells, and SYK in microglia. YXKFY treatment was shown to repair cellular damage and decrease reactive oxygen species (ROS) levels. Notably, genes with previously dysfunctional expression, including FKBPL, TGM2, PPIL1, BLVRB, and PDGFRB, exhibited significant recovery after YXKFY treatment, associated with riboflavin and lysicamine. Conclusion: The above genes are suggested to be central to hypoxia and neuroinflammation responses in AD and PD, and are potential key mediators of YXKFY's neuroprotective action.

Identification of a combined hypoxia and lactate metabolism prognostic signature in lung adenocarcinoma

BackgroundIn the tumor microenvironment (TME), a bidirectional relationship exists between hypoxia and lactate metabolism, with each component exerting a reciprocal influence on the other, forming an inextricable link. The aim of the present investigation was to develop a prognostic model by amalgamating genes associated with hypoxia and lactate metabolism. This model is intended to serve as a tool for predicting patient outcomes, including survival rates, the status of the immune microenvironment, and responsiveness to therapy in patients with lung adenocarcinoma (LUAD).MethodsTranscriptomic sequencing data and patient clinical information specific to LUAD were obtained from comprehensive repositories of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A compendium of genes implicated in hypoxia and lactate metabolism was assembled from an array of accessible datasets. Univariate and multivariate Cox regression analyses were employed. Additional investigative procedures, including tumor mutational load (TMB), microsatellite instability (MSI), functional enrichment assessments and the ESTIMATE, CIBERSORT, and TIDE algorithms, were used to evaluate drug sensitivity and predict the efficacy of immune-based therapies.ResultsA novel prognostic signature comprising five lactate and hypoxia-related genes (LHRGs), PKFP, SLC2A1, BCAN, CDKN3, and ANLN, was established. This model demonstrated that LUAD patients with elevated LHRG-related risk scores exhibited significantly reduced survival rates. Both univariate and multivariate Cox analyses confirmed that the risk score was a robust prognostic indicator of overall survival. Immunophenotyping revealed increased infiltration of memory CD4 + T cells, dendritic cells and NK cells in patients classified within the high-risk category compared to their low-risk counterparts. Higher probability of mutations in lung adenocarcinoma driver genes in high-risk groups, and the MSI was associated with the risk-score. Functional enrichment analyses indicated a predominance of cell cycle-related pathways in the high-risk group, whereas metabolic pathways were more prevalent in the low-risk group. Moreover, drug sensitivity analyses revealed increased sensitivity to a variety of drugs in the high-risk group, especially inhibitors of the PI3K-AKT, EGFR, and ELK pathways.ConclusionsThis prognostic model integrates lactate metabolism and hypoxia parameters, offering predictive insights regarding survival, immune cell infiltration and functionality, as well as therapeutic responsiveness in LUAD patients. This model may facilitate personalized treatment strategies, tailoring interventions to the unique molecular profile of each patient’s disease.

Tolerance to Haemophilus influenzae infection in human epithelial cells: Insights from a primary cell-based model.

Haemophilus influenzae is a human respiratory pathogen and inhabits the human respiratory tract as its only niche. Despite this, the molecular mechanisms that allow H. influenzae to establish persistent infections of human epithelia are not well understood. Here, we have investigated how H. influenzae adapts to the host environment and triggers the host immune response using a human primary cell-based infection model that closely resembles human nasal epithelia (NHNE). Physiological assays combined with dualRNAseq revealed that NHNE from five healthy donors all responded to H. influenzae infection with an initial, 'unproductive' inflammatory response that included a strong hypoxia signature but did not produce pro-inflammatory cytokines. Subsequently, an apparent tolerance to large extracellular and intraepithelial burdens of H. influenzae developed, with NHNE transcriptional profiles resembling the pre-infection state. This occurred in parallel with the development of intraepithelial bacterial populations, and appears to involve interruption of NFκB signalling. This is the first time that large-scale, persistence-promoting immunomodulatory effects of H. influenzae during infection have been observed, and we were able to demonstrate that only infections with live, but not heat-killed H. influenzae led to immunomodulation and reduced expression of NFκB-controlled cytokines such as IL-1β, IL-36γ and TNFα. Interestingly, NHNE were able to re-activate pro-inflammatory responses towards the end of the 14-day infection, resulting in release of IL-8 and TNFα. In addition to providing first molecular insights into mechanisms enabling persistence of H. influenzae in the host, our data further indicate the presence of infection stage-specific gene expression modules, highlighting fundamental similarities between immune responses in NHNE and canonical immune cells, which merit further investigation.

Hypoxia-Induced Long Noncoding RNA HIF1A-AS2 Regulates Stability of MHC Class I Protein in Head and Neck Cancer.

Intratumoral hypoxia not only promotes angiogenesis and invasiveness of cancer cells but also creates an immunosuppressive microenvironment that facilitates tumor progression. However, the mechanisms by which hypoxic tumor cells disseminate immunosuppressive signals remain unclear. In this study, we demonstrate that a hypoxia-induced long noncoding RNA HIF1A Antisense RNA 2 (HIF1A-AS2) is upregulated in hypoxic tumor cells and hypoxic tumor-derived exosomes in head and neck squamous cell carcinoma (HNSCC). Hypoxia-inducible factor 1 alpha (HIF1α) was found to directly bind to the regulatory region of HIF1A-AS2 to enhance its expression. HIF1A-AS2 reduced the protein stability of major histocompatibility complex class I (MHC-I) by promoting the interaction between the autophagy cargo receptor neighbor of BRCA1 gene 1 (NBR1) protein and MHC-I, thereby increasing the autophagic degradation of MHC-I. In HNSCC samples, the expression of HIF1A-AS2 was found to correlate with hypoxic signatures and advanced clinical stages. Patients with high HIF1α and low HLA-ABC expression showed reduced infiltration of CD8+ T cells. These findings define a mechanism of hypoxia-mediated immune evasion in HNSCC through downregulation of antigen-presenting machinery via intracellular or externalized hypoxia-induced long noncoding RNA.

Hypoxia and Giardia duodenalis: The Role of Hypoxia-Inducible Factor in Altered Epithelial Glucose Metabolism

The gastrointestinal system experiences frequent oxygenic fluctuations and must be able to maintain barrier integrity during periods of suboptimal oxygen concentration, or hypoxia. Epithelial cells rely on the Hypoxia-Inducible Factor (HIF) complex to activate genes that combat cellular stress and adapt cellular metabolism during hypoxia. Importantly, protozoan parasites can modulate host tissue oxygen tension and HIF activation, yet little is known regarding the relationship between enteric protozoa and hypoxia. This research aims to uncover the role of HIF upon Giardia duodenalis infection, a top cause of global diarrheal disease and an excellent infection model for the study of GI physiology. We hypothesize that HIF-target genes are activated upon Giardia infection, promoting alternative cellular glucose metabolism to sustain bioenergetic homeostasis. Caco-2 colonic epithelial cells were infected with Giardia isolate GS/M (MOI 10) for 1.5 or 4.5 hours under normoxic (21% O2) or hypoxic (~1%O2, STEMCELL hypoxia incubator) conditions to capture the early or peak activation of the oxygen-dependent HIF subunit (HIF-1α). RNA was extracted for assessment of transcriptional alterations of HIF-target genes via reverse transcriptase quantitative polymerase chain reaction. Investigation of HIF-mediated intracellular metabolic changes was carried out via liquid-chromatography mass-spectrometry analysis (hydrophilic-interaction chromatography method) on cocultures supplemented with a hypoxia mimetic (DMOG) or a HIF inhibitor (PX-478). Metabolomics experiments were repeated using Caco-2 cells transfected with sodium-dependent glucose cotransporter 1 (SGLT1), a key glucose transporter in the small intestine where Giardia localizes which is not reliably expressed in Caco-2 cells. Under normoxic conditions, genes that aid in cell stress responses ( VEGFA, ANKRD37, GADD45A) and glycolysis ( HK2, LDHA) are upregulated in Giardia-infected cells in a time-dependent manner (p<0.05). Fewer HIF-target genes are upregulated under hypoxic conditions (e.g., VEGFA, GADD45A, PGK1; p<0.05), indicating Giardia-infected cells exhibit a transcriptional profile similar to hypoxic uninfected cells. Interestingly, HIF1α was upregulated in Giardia-infected cells under hypoxic conditions at 1.5 hours (p<0.05). Analysis of the Caco-2 intracellular metabolome indicated HIF-dependent changes to nucleic acid (e.g., guanosine, inosine, uracil) and amino acid (e.g., glycine, threonine) metabolism. DMOG treatment increased the abundance of glycolytic intermediates (e.g., PEP, DHAP) in both cell lines and inhibited the depletion of the Kreb’s Cycle intermediate aconitate in the Caco-2-SGLT1 transfected cells, confirming the promotion of glycolytic flux by HIF. Taken together, our findings indicate Giardia-infected cells illustrate a hypoxic signature, a novel metabolic cell rescue mechanism in response to enteropathogens. Elucidating the role of HIF during enteric parasitic infections will aid in our understanding of the cellular adaptations underpinning GI pathophysiology, while also shedding light on the potential of HIF as a therapeutic target. Natural Science and Engineering Research Council of Canada. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

The hypoxia signature across skeletal progenitor cells.

The hypoxia signature across skeletal progenitor cells.

Abstract 6124: A comprehensive pan-cancer study nominating NF-κB-mediated TNFA signaling-induced hypoxia as a risk factor in Hispanic cancer progression

Abstract The Hispanic (HA) population is the second largest racial/ethnic group in the United States after non-Hispanic White (NHW). Though the HA population usually has a lower reported incidence of cancers compared to NHW, there are racial disparities exist in the mortality rate of some of the cancers. Factors related to the Social Determinants of Health (SDOH), such as higher poverty rates, less education, and reduced access to health care, are known to increase the risk of diagnosing advanced-stage cancer in HA compared to the NHW population. The contribution of such SDOH in the HA cancer population has been studied in the past years. However, the contribution of biological and genetic mechanisms to HA cancer disparity has not been well understood. Thus, in this study, we performed a comprehensive analysis of different databanks to understand the common genetic and biological factors that contribute to the pan-cancer disparity in the HA population. To identify HA and NHW populations, we used self-reported racial/ethnic information. Analysis of the “All of Us” database suggested a high prevalence of infection-related cancers such as Liver, Stomach, and Cervix Uteri in the HA population compared to the NHW population. SEER database also showed an increased percentage of diagnoses with infection-related cancers and poor survival of the HA population with these cancers compared to the NHW. We then analyzed the TCGA transcriptome data from primary tumors from HA and NHW patients. We only selected cancers with data from at least ten patients in each group. TCGA data confirmed that the tumors from HA cancer patients primarily express high inflammatory and immune-responsive signatures. Specifically, we found a high enrichment of NF-κB induced TNFA signaling in HA tumors. We also observed a significant correlation between TNFA and Hypoxia signature in many HA cancers. Since hypoxia is known to be associated with resistance to radiation and chemotherapy, targeting the increased hypoxia signature in HA tumors may be critical for sensitizing HA patients to cancer therapy. Overall, our pan-cancer analyses suggest an increased prevalence of many infection-related cancers in the HA population. HA tumors are enriched with TNFA, NF-κB, and hypoxic signatures. Specific targeting of these signatures may be critical in managing the HA patients who currently suffer from racial disparity in cancer incidence and survival. Citation Format: Tagari Samanta, Jun Hyoung Park, Benny Abraham Kaipparettu. A comprehensive pan-cancer study nominating NF-κB-mediated TNFA signaling-induced hypoxia as a risk factor in Hispanic cancer progression [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 6124.

Abstract 1107: Prospective observational study to evaluate the efficacy of oxygen saturation endoscopic imaging for radiotherapeutic response in head and neck squamous cell carcinoma

Abstract Background: Radiotherapy (RT) has a pivotal role in the management of head and neck squamous cell carcinoma (HNSCC), providing effective tumor control and functional preservation. Hypoxia is a cause of radioresistance in HNSCC. We have developed an oxygen saturation endoscopic imaging (OXEI) method to assess real-time tissue oxygenation levels. However, the clinical significance of OXEI in patients with HNSCC receiving RT remains unclear. We evaluated the association between pretreatment tumor oxygen saturation (StO2) quantified by OXEI and clinical outcomes of patients with HNSCC receiving RT. Methods: We prospectively recruited patients with HNSCC scheduled to receive RT at 2 institutions. The primary endpoint was the association between pretreatment tumor StO2 and complete response (CR) rate 8 weeks after completion of RT. Secondary endpoints evaluated the impact of StO2 on 1-year overall survival (OS) and progression-free survival (PFS) rates after RT initiation. We also evaluated the cumulative incidence of local failure (LF). To explore the relationship between tumor hypoxia assessed by OXEI and gene expression profile, we performed RNA sequencing of 4 tumor samples collected from 2 patients (2 samples/patient) before RT. The hypoxia score for each sample was calculated by gene set variation analysis based on HNSCC mRNA-based hypoxia signatures. We performed gene set enrichment analysis (GSEA) to evaluate whether the biological pathways (Hallmark, Reactome, and KEGG gene sets) showed significant associations with tumor hypoxia. Results: Of the 50 patients enrolled from March 2019 to February 2022, we analyzed 37 who underwent RT and OXEI. Thirty-six (97%) patients received current platinum-based chemotherapy. The median (range) pretreatment tumor StO2 of 60 (45-84)% was lower than that of normal mucosa, 66 (56-84)% (P < 0.01). Patients with tumor StO2 < 60% were classified as the hypoxia group (n =19), and those with tumor StO2 ≥ 60% as the non-hypoxia group (n =18). The CR rate 8 weeks after RT was not significantly different between the hypoxia and non-hypoxia groups (84% vs. 100%, respectively; P = 0.23). After a median (range) follow-up of 33 (9-45) months, the hypoxia group had worse 1-year PFS (74% vs. 94%, P = 0.017) and OS (89% vs. 100%, P = 0.015) and higher LF rates (21% vs. 6%, P = 0.036) compared with the non-hypoxia group. RNA sequencing confirmed that tumor StO2 reflected expression-based hypoxia scores. GSEA showed upregulation of reactive oxygen species (ROS) and KEAP1-NFE2L2 pathways in hypoxic samples (StO2 of 59%) compared with non-hypoxic samples (StO2 of 70%; adjusted P < 0.01), consistent with the fact that hypoxic stress increases ROS production. Conclusion: Our findings suggest that pretreatment tumor StO2 quantified by OXEI correlates with 1-year PFS, OS, and LF rates of patients with HNSCC receiving RT. Citation Format: Kento Tomizawa, Atsushi Motegi, Hidenari Hirata, Hiroki Yamashita, Hironori Sunakawa, Wataru Okano, Tomohiro Enokida, Takeshi Fujisawa, Sadamoto Zenda, Masaki Nakamura, Hidehiro Hojo, Seiichiro Abe, Madoka Sakuramachi, Hiroshi Igaki, Yutaka Saito, Kazuto Matsuura, Makoto Tahara, Tomonori Yano, Tetsuo Akimoto. Prospective observational study to evaluate the efficacy of oxygen saturation endoscopic imaging for radiotherapeutic response 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 1107.

Abstract 1790: Pyruvate carboxylase regulates tumor progression through central carbon metabolism and immunosuppression

Abstract The tumor microenvironment (TME) is characterized by metabolic reprogramming and immune evasion, essential features in tumor progression. Tumor metabolic dysregulation, particularly the high production of lactate, plays a pivotal role in suppressing antitumor immunity within the TME. Pyruvate carboxylase (PC), responsible for converting pyruvate to oxaloacetate, is a critical determinant for lung metastasis in triple-negative breast cancer (TNBC). Herein we test the hypothesis that PC-mediated regulation of central carbon metabolism controls TME immunosurrveilance. Wild-type C57BL6/J and NSG mice received orthotopic injections of E0771 or M-Wnt tumor cells with shRNA targeting PC or a scramble control. RNA from tumors underwent transcriptomic profiling using Affymetrix Clariom D microarray (n=3-6/group per experiment). Gene set enrichment analysis identified pathways enriched in each condition, including a PC-associated hypoxia signature. Immunohistochemistry with anti-CD3 antibody and full spectrum flow cytometry assessed T cell infiltration and TME immune cell composition. Untargeted metabolomics, extracellular flux analysis, and high-resolution respirometry determined how loss of PC altered cellular metabolism. We found that suppressing PC expression increased primary tumor growth (~2 fold), potently drove immunosuppression, and remodeled cellular metabolism towards lactate production. Injection of PC-suppressed cells increased regulatory T cell levels in wild type mice. Importantly, PC-suppressed cells injected into NSG mice, which lack T, B, and NK cells, demonstrated slower, rather than accelerated, tumor growth. PC-suppression reduced oxygen consumption rate (OCR), but supply of anaplerotic carbon through exogenous malate or oxaloacetate restored OCR. Conversely, both the rate of and reliance on lactate production was increased by PC suppression. Notably, loss of immunosurveillance following downregulation of PC was reversed by inhibiting lactate transport. Additionally, lower PC expression was associated with increased hypoxia in tumors, supporting in vitro evidence of PC-repression by hypoxia. In summary, hypoxia-induced PC suppression emerges as a crucial mechanism through which primary tumors hinder antitumor immunity, partly via increased lactate production. These findings underscore the significance of PC-directed tumor metabolism as an understudied nexus in the interplay between tumor progression and antitumor immunity. Citation Format: Michael F. Coleman, Eylem Kulkoyluoglu Cotul, Alexander J. Pfeil, Alyssa N. Ho, Emily N. Devericks, Muhammad H. Safdar, Hao Chen, Numair Attaar, Violet A. Kiesel, Dorothy Teegarden, Stephen D. Hursting, Michael K. Wendt. Pyruvate carboxylase regulates tumor progression through central carbon metabolism and immunosuppression [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 1790.

Abstract 6857: Evolution of myeloid-mediated mechanisms of immunotherapy resistance at single-cell resolution with prostate cancer progression

Abstract Background: Patients with metastatic castration-resistant prostate cancer (mCRPC) are largely refractory to immune checkpoint inhibitors (ICIs). This resistance is, in part, attributed to the presence of immunosuppressive myeloid cells in tumors. However, attempts to target these cells broadly, such as CSF1R antagonism, have thus far failed clinically primarily due to their heterogeneous nature. Thus, we hypothesized that a more comprehensive understanding of immunosuppressive myeloid subsets and their molecular mechanisms at the single-cell level is critical to enhance the effectiveness of immunotherapy. Methods: We performed single-cell profiling of patient biopsies with either localized, metastatic hormone-sensitive prostate cancer, or mCRPC. We then reverse translated these findings in a syngeneic mouse model of CRPC, where we performed multi-omic single-cell assessment and conducted studies to assess tumor efficacy and gain mechanistic insights. Results: We identified a specific subset of tumor-associated macrophages with elevated hypoxia signatures, including higher SPP1 transcript levels (SPP1hi-TAMs). These macrophages become significantly more abundant as the disease advances, expressing elevated immunosuppressive molecular programs. Notably, CSF1R transcripts were significantly reduced in SPP1hi-TAMs, suggesting their potential role in the clinical ineffectiveness of CSF1R blockade. In a syngeneic mouse CRPC model, we identified an analogous macrophage subset through single-cell profiling and flow cytometry. These macrophages possess the ability to suppress T cell activity in co-culture. Consistent with these findings, adoptive transfer of Spp1hi-TAMs into CRPC promoted ICI resistance and worsened survival in vivo. Importantly, these macrophages proved resistant to anti-CSF1R treatment, underscoring the need to target their immunosuppressive signals as a potential therapeutic approach. Pathway analysis revealed enrichment of gene signatures associated with adenosine signaling in SPP1hi-TAMs both in patients and in mice, implicating this pathway as their immunosuppressive mechanism. Indeed, blocking adenosine signaling using antibodies or pharmacologic inhibitors resulted in a significant reduction in T cell suppression mediated by Spp1hi-TAMs in culture. Furthermore, pharmacologic blockade of adenosine receptors in vivo significantly decreased tumor growth and enhanced the responsiveness of tumor cells to ICI therapies. Conclusions: Our studies demonstrate that SPP1hi-TAMs become prevalent as the disease progresses. They are resistant to CSF1R blockade and play a key role in mediating immunotherapeutic resistance in vivo by activating adenosine signaling pathways. These findings highlight the potential of the associated signals as promising targets for therapeutic intervention. Citation Format: Aram Lyu, Zenghua Fan, Diamond Luong, Ali Setayesh, Alec Starzinski, Laura Valderrábano, Eliezer Van Allen, Lawrence Fong. Evolution of myeloid-mediated mechanisms of immunotherapy resistance at single-cell resolution with prostate cancer progression [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 6857.

Prognostic PET [11C]-acetate uptake is associated with hypoxia gene expression in patients with late-stage hepatocellular carcinoma – a bench to bed study

BackgroundPositron Emission Tomography (PET) with combined [18F]-FDG and [11C]-acetate (dual-tracer) is used for the management of hepatocellular carcinoma (HCC) patients, although its prognostic value and underlying molecular mechanism remain poorly understood. We hypothesized that radiotracer uptake might be associated with tumor hypoxia and validated our findings in public and local human HCC cohorts.MethodsTwelve orthotopic HCC xenografts were established using MHCC97L cells in female nude mice, with 5 having undergone hepatic artery ligation (HAL) to create tumor hypoxia in vivo. Tumors in both Control and HAL-treated xenografts were imaged with [11C]-acetate and [18F]-FDG PET-MR and RNA sequencing was performed on the resected tumors. Semiquantitative analysis of PET findings was then performed, and the findings were then validated on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and patients from our institution.ResultsHAL-treated mice showed lower [11C]-acetate (HAL-treated vs. Control, tumor-to-liver SUV ratio (SUVTLR): 2.14[2.05–2.21] vs 3.11[2.75–5.43], p = 0.02) but not [18F]-FDG (HAL-treated vs. Control, SUVTLR: 3.73[3.12–4.35] vs 3.86[3.7–5.29], p = 0.83) tumor uptakes. Gene expression analysis showed the PET phenotype is associated with upregulation of hallmark hypoxia signature. The prognostic value of the hypoxia gene signature was tested on the TCGA-LIHC cohort with upregulation of hypoxia gene signature associated with poorer overall survival (OS) in late-stage (stage III and IV) HCC patients (n = 66, OS 2.05 vs 1.67 years, p = 0.046). Using a local cohort of late-stage HCC patients who underwent dual-tracer PET-CT, tumors without [11C]-acetate uptake are associated with poorer prognosis (n = 51, OS 0.25 versus 1.21 years, p < 0.0001) and multivariable analyses showed [11C]-acetate tumor uptake as an independent predictor of OS (HR 0.17 95%C 0.06–0.42, p < 0.0001).Conclusions[11C]-acetate uptake is associated with alteration of tumor hypoxia gene expression and poorer prognosis in patients with advanced HCC.

TFRC, associated with hypoxia and immune, is a prognostic factor and potential therapeutic target for bladder cancer

BackgroundBladder cancer is a common malignancy of the urinary system, and the survival rate and recurrence rate of patients with muscular aggressive (MIBC) bladder cancer are not ideal. Hypoxia is a pathological process in which cells acquire special characteristics to adapt to anoxic environment, which can directly affect the proliferation, invasion and immune response of bladder cancer cells. Understanding the exact effects of hypoxia and immune-related genes in BLCA is helpful for early assessment of the prognosis of BLCA. However, the prognostic model of BLCA based on hypoxia and immune-related genes has not been reported.PurposeHypoxia and immune cell have important role in the prognosis of bladder cancer (BLCA). The aim of this study was to investigate whether hypoxia and immune related genes could be a novel tools to predict the overall survival and immunotherapy of BLCA patients.MethodsFirst, we downloaded transcriptomic data and clinical information of BLCA patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A combined hypoxia and immune signature was then constructed on the basis of the training cohort via least absolute shrinkage and selection operator (LASSO) analysis and validated in test cohort. Afterwards, Kaplan–Meier curves, univariate and multivariate Cox and subgroup analysis were employed to assess the accuracy of our signature. Immune cell infiltration, checkpoint and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm were used to investigate the immune environment and immunotherapy of BLCA patients. Furthermore, we confirmed the role of TFRC in bladder cancer cell lines T24 and UMUC-3 through cell experiments.ResultsA combined hypoxia and immune signature containing 8 genes were successfully established. High-risk group in both training and test cohorts had significantly poorer OS than low-risk group. Univariate and multivariate Cox analysis indicated our signature could be regarded as an independent prognostic factor. Different checkpoint was differently expressed between two groups, including CTLA4, HAVCR2, LAG3, PD-L1 and PDCD1. TIDE analysis indicated high-risk patients had poor response to immunotherapy and easier to have immune escape. The drug sensitivity analysis showed that high-risk group patients were more potentially sensitive to many drugs. Meanwhile, TFRC could inhibit the proliferation and invasion ability of T24 and UMUC-3 cells.ConclusionA combined hypoxia and immune-related gene could be a novel predictive model for OS and immunotherapy estimation of BLCA patients and TFRC could be used as a potential therapeutic target in the future.

Hypoxic transcriptomes predict survival and tumor-infiltrating immune cell composition in cutaneous melanoma.

Hypoxia has established associations with aggressive tumor phenotypes in many cancers. However, it is not currently understood whether tumor hypoxia levels map to distinct immune infiltrates in cutaneous melanoma, potentially unveiling novel therapeutic targets. To this end, we leveraged a previously identified seven-gene hypoxia signature to grade hypoxia levels of 460 cutaneous melanomas obtained from the Broad Institute GDAC Firehose portal. CIBERSORTx ( https://cibersortx.stanford.edu/ ) was employed to calculate the relative abundance of 22 mature human hematopoietic populations. Clinical outcomes and immune cell associations were assessed by computational means. Results indicated that patients with high-hypoxia tumors reported significantly worse overall survival and correlated with greater Breslow depth, validating the in-silico methodology. High-hypoxia tumors demonstrated increased infiltration of activated and resting dendritic cells, resting mast cells, neutrophils, and resting NK cells, but lower infiltration of gamma-delta T cells. These data suggest that high tumor hypoxia correlates with lower survival probability and distinct population differences of several tumor-infiltrating leukocytes in cutaneous melanomas.

Abstract A032: Low non-immune stromal cell levels and high hypoxic tumor microenvironments are associated with pathologic complete response in the neoadjuvant I-SPY2 TRIAL

Abstract Background: Non-immune components of the tumor microenvironment (TME) play important roles in cancer. We explore two important components of the TME: non-immune stromal cell populations including fibroblasts, adipocytes, and endothelial cells; and hypoxic conditions. We leverage published gene expression-based biomarkers of stromal cell types and hypoxia, and molecular and clinical data from the I-SPY2 TRIAL (PMID: 35623341) – an adaptive neoadjuvant trial for locally advanced breast cancers. We assess the contribution of stromal cell populations and oxygen-poor environments at pre-treatment in shaping the landscape of immune enrichment and therapeutic response in breast cancers. Methods: We curated 14 stromal and 11 hypoxia gene sets, in addition to 35 immune gene sets from literature. Signatures scores of stromal, hypoxic, and immune TME were calculated from gene expression profiles of pre-treatment tumor samples from I-SPY2 patients (n=987) in the first 9 treatment arms of the trial plus control arms. Correlation of stromal and hypoxia signatures with immune signatures were assessed, and association of TME features with HER2/HR receptor status, I-SPY response-predictive subtype (RPS), and pathological complete response (pCR) were evaluated using non-parametric tests. All p-values were adjusted for multiple testing. Significance levels were defined at adj. p&amp;lt;0.05. Results: Both stromal and hypoxia signatures showed significant differential enrichment across HR/HER2 and RPS subtypes, and association with pCR. Several stromal signatures including adipocytes, endothelial cells, mesenchymal stem cells, and overall stromal score had the lowest enrichment in HR-/HER2- breast cancers, and in the RPS HER2-/immune+ subtype. Moreover, most stromal signatures showed anti-correlation with CD8+ and CD4+ T cell enrichment. Stromal signatures including endothelial cells, smooth muscle cells, and overall score were significantly lower in patients who achieved pCR. Two hypoxia gene sets demonstrated highly significant enrichment in HR- versus HR+ samples regardless of HER2 status. All hypoxia signatures varied significantly across RPS subtypes, with the highest scores in HER2-/Immune-/DRD+, especially relative to HER2-/Immune-/DRD- and HER2+/BP-Luminal subtypes. Hypoxia signatures strongly linked to hypoxia inducible factor (HIF) and angiogenesis via VEGF were positively associated with pCR. These hypoxia signatures showed treatment-specific associations with pCR, specifically in agents targeting mechanisms with known interactions with hypoxia-induced biology: trebananib (angiogenesis inhibitor), ganetespib (HSP90 inhibitor) and veliparib/carboplatin (DNA damage repair inhibitor). Conclusions: Hypoxia and stromal cell gene signatures show breast cancer subtype-specific biology. Relative absence of non-immune stromal cell types is associated with higher immune infiltration and higher pCR rates, while specific hypoxia pathways were associated with response to therapeutic agents targeting hypoxia-related pathways. Citation Format: Kailey Dubinsky, Elene Tsopurashvili, Denise M. Wolf, Zheyun Xu, Silver Al Khafaji Alkhafaji, Anna van Montfort, Christina Yau, Diane Heditsian, Allison Fiscalini, Laura J. Esserman, Laura van ‘t Veer, Rosalyn W. Sayaman. Low non-immune stromal cell levels and high hypoxic tumor microenvironments are associated with pathologic complete response in the neoadjuvant I-SPY2 TRIAL [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A032.

Abstract B067: Identification of Gemcitabine-resistant Populations using scRNA-Sequencing in Triple Negative Breast Cancer Patient-Derived Xenografts

Abstract Despite major advances in the treatment of breast cancer (BC), it remains the most diagnosed and second deadliest cancer among American women. BC consists of distinct clinical subtypes, including estrogen receptor or HER2 receptor-positive and triple-negative breast cancer (TNBC) that lacks these receptors preventing the use of established precision therapies and the standard of care remains neoadjuvant chemotherapy (NACT), followed by surgery, radiation and emerging combinations with immunotherapy. While NACT is effective in some patients, up to 50% of patients are intrinsically unresponsive or acquire resistance. These patients demonstrate the highest rates of recurrence and distant metastasis. It is known that chemotherapies can effectively eliminate proliferating tumor cells, but a small population of drug-tolerant persister (DTPs) cells can remain and are thought to play a key role in relapse and resistance. We hypothesized that chemotherapy influences TNBC tumor plasticity by exerting selective pressures leading to the outgrowth of resistant subpopulations with the greatest survival advantage. To evaluate this hypothesis, we generated in vivo models of disease progression and chemotherapy resistance and investigated the plasticity of tumor cell subpopulations by single-cell RNA sequencing. We developed PDX models from a multi-drug resistant primary TNBC treated with standard-of-care chemotherapy and its patient-matched lung metastasis. To model response and resistance at the metastatic stage, we challenged this metastasis PDX with several cycles of Gemcitabine. We obtained residual disease that relapsed and eventually developed resistance, mirroring the patient response. We performed single-cell RNA sequencing (scRNAseq) of these models using a droplet-based technology from 10X Genomics. This scRNAseq data was used to compare the changes in the proportions of cellular subpopulations in each model. Our data show that the rebound model presents greater similarity to the untreated metastasis, while the resistant model significantly differs in cell population expression profiles. Interestingly, the residual disease demonstrates an intermediated state with similarities to both the untreated metastasis and the resistant model. We identified populations with hypoxic signatures in the primary tumor, its matched metastasis and the residual, rebound and resistant models. Immunohistochemistry and Nanostring GeoMx Digital Spatial Profiler validated these populations in these models. In addition, we have identified other varying populations and are currently investigating their cellular mechanisms and gene expression patterns. Using scRNA-sequencing to understand the clonal expansion of resistant subpopulations following chemotherapy reveals distinctive resistant cell features enabling the identification of the vulnerabilities of these tumors. Citation Format: Sandrine Busque, Constanza Martinez Ramirez, Ariel Madrigal Aguirre, Paul Savage, Anie Monast, Anne-Marie Fortier, Gerardo Zapata, Atilla Omeroglu, Jamil Asselah, Nathaniel Bouganim, Sarkis Meterissian, Francine Tremblay, Ari Meguerditchian, Yasser Riaz Alhosseini, Hamed S. Najafabadi, Hellen Kuasne, Morag Park. Identification of Gemcitabine-resistant Populations using scRNA-Sequencing in Triple Negative Breast Cancer Patient-Derived Xenografts [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B067.