An Eight-Gene Hypoxia Signature Predicts Survival in Pancreatic Cancer and Is Associated With an Immunosuppressed Tumor Microenvironment

Abstract

Intratumoral hypoxia is a widely established element of the pancreatic tumor microenvironment (TME) promoting immune escape, tumor invasion, and progression, while contributing to treatment resistance and poor survival. Despite this critical role, hypoxia is underrepresented in molecular signatures of pancreatic ductal adenocarcinoma (PDA) and concurrent investigations into the hypoxia-immune status are lacking. In this work a literature-based approach was applied to derive an eight-gene hypoxia signature that was validated in fourteen cancer cell lines and in a cohort of PDA. The eight-gene hypoxia signature was significantly associated with overall survival in two distinct PDA datasets and showed independent prognostic value in multivariate analysis. Comparative analysis of tumors according to their hypoxia score (high versus low) determined that tumors with high hypoxia were significantly less enriched in cytotoxic T-cells, and cytolytic activity. In addition, they had lower expression of cytokines and tumor inflammatory markers, pointing to the signature’s ability to discern an immune “cold”, hypoxic TME. Combining the signature with an immune metric highlighted a worse survival probability in patients with high hypoxia and low immune reactivity, indicating that this approach could further refine survival estimates. Hypoxia as determined by our signature, was significantly associated with certain immune checkpoint inhibitors (ICI) biomarkers, suggesting that the signature reflects an aspect of the TME that is worth pursuing in future clinical trials. This is the first work of its kind in PDA, and our findings on the hypoxia-immune tumor contexture are not only relevant for ICI but could also guide combinatorial hypoxia-mediated therapeutic strategies in this cancer type.

Tumor hypoxia: an important regulator of tumor progression or a potential modulator of tumor immunogenicity?

“… 38 The positive correlation between hypoxia and TMB has been further validated in independent studies for hepatocellular carcinoma, 39 gastric cancer 40 and pancreatic cancer. 41 In gastric cancer, TMB positivity was further correlated with higher positive rate of ERO1A protein, a marker of hypoxia, in 73 tumors tested by immunohistochemistry. 40 In addition, lung adenocarcinoma patients classified as high-risk based on a signature of hypoxia-related alternative splicing events have been shown to harbor significantly higher TMB compared to the low-risk group.…”

“…Studies in cancer patient cohorts have similarly correlated the presence of hypoxia with an immunosuppressed TME in breast cancer, 45 , 46 clear cell renal cell carcinoma, 47 colorectal cancer, 48 hepatocellular carcinoma, 49–51 melanoma, 52 osteosarcoma, 53 neuroblastoma 43 and pancreatic cancer, 41 , 54 among others. 55 These studies used hypoxia gene signatures to determine the hypoxic state and immune fraction or gene set enrichment analysis to highlight the immune microenvironment.…”

“… 55 These studies used hypoxia gene signatures to determine the hypoxic state and immune fraction or gene set enrichment analysis to highlight the immune microenvironment. In addition, the coupling of an immune score with a hypoxia score in lung adenocarcinoma, 42 pancreatic cancer, 41 and soft tissue sarcoma 38 revealed significantly lower immune activation in tumors with high hypoxia, compared to their low hypoxia counterparts. Of interest, colorectal tumors classified as immune-cold based on IHC assessment of CD3, CD4, and CD8 were linked to a hypoxic biology and poor prognosis.…”

“…Indeed, on the flipside, studies in pancreatic cancer 41 and lung adenocarcinoma 42 that have simultaneously reported on the TMB, immune TME and hypoxia, found that hypoxia-high tumors harbored higher mutations and exhibited significantly lower immune scores, compared to hypoxia-low tumors. Such discrepancies between studies suggest specific events controlled by hypoxia.…”

“… 39 , 49 , 51 In this line, we recently observed a similar association with PD-L1 in pancreatic tumors, and further found that hypoxia-high tumors displayed significantly lower cytolytic index scores, evocative of T-cell cytolytic dysfunction. 41 Indeed, higher hypoxia scores were enriched in tumors with a low chemokine signature score, indicating inefficient T-cell activation and presumably migration. 41 Clearly a more wholistic approach that considers all these elements is warranted to better isolate the direct impact of hypoxia on the tumor immune microenvironment and its role in resistance to ICB.…”