Myeloid cell-associated resistance to PD-1/PD-L1 blockade in urothelial cancer revealed through bulk and single-cell RNA sequencing

Abstract

Adaptive immunity and tumor-promoting inflammation exist in delicate balance in individual tumor microenvironments; however, the role of this balance in defining sensitivity and resistance to PD-1/PD-L1 blockade therapy in urothelial cancer and other malignancies is poorly understood. We pursued an unbiased systems biology approach using bulk RNA sequencing data to examine pre-treatment molecular features associated with sensitivity to PD-1/PD-L1 blockade in patients with metastatic urothelial cancer and identified an adaptive_immune_response module associated with response and an inflammatory_response module and stromal module associated with resistance. We mapped these gene modules onto single-cell RNA sequencing data demonstrating the adaptive_immune_response module emanated predominantly from T, NK, and B cells, the inflammatory_response module from monocytes/macrophages, and the stromal module from fibroblasts. The adaptive_immune_response:inflammatory_response module expression ratio in individual tumors, reflecting the balance between antitumor immunity and tumor-associated inflammation and coined the 2IR score, best correlated with clinical outcomes and was validated in an independent cohort. Individual monocytes/macrophages with low 2IR scores demonstrated upregulation of proinflammatory genes including IL1B and downregulation of antigen presentation genes, were unrelated to classical M1 versus M2 polarization, and were enriched in pre-treatment peripheral blood from patients with PD-L1 blockade-resistant metastatic urothelial cancer.Single sentence summaryProinflammatory monocytes/macrophages, present in tumor and blood, are associated with resistance to immune checkpoint blockade in urothelial cancer.

Tumor-Associated Macrophages in Bladder Cancer: Biological Role, Impact on Therapeutic Response and Perspectives for Immunotherapy

“…In this study, six different subsets of monocytes/macrophages were found in MIBC tumor, and their gene signatures did not correlate with the classical M1-like versus M2-like signatures. Moreover, the authors also identified another subset of TAM that shares both TAM-like and MDSC-like gene signatures [ 49 ], supporting the theory of the MDSC-to-macrophage differentiation. In the future, determining the origin of TAM (from tissue-resident macrophages, monocytes-derived macrophages or MDSC differentiation) could improve knowledge on TAM diversity and complexity but this is still limited by the lack of specific markers for each subtype.…”

“…Conversely, CD169 + M1-like macrophages in the tumor-draining lymph nodes [ 48 ], but not in the tumor [ 25 ], are positively correlated with a favorable prognosis in MIBC patients. However, single-cell RNA-seq from immune-infiltrating cells revealed the wide diversity of TAMs in MIBC patients [ 49 ]. In this study, six different subsets of monocytes/macrophages were found in MIBC tumor, and their gene signatures did not correlate with the classical M1-like versus M2-like signatures.…”

“…Zeng et al have analyzed the gene expression in the IMvigor210 cohort (Atezolizumab in BCa patients) and they declared that the M1-like TAM signature was a robust biomarker for predicting the prognosis and response to anti-PD-L1 [ 92 ]. Wang and collaborators demonstrated that a pro-tumorigenic inflammation signature was correlated with poor survival in the IMvigor210 and CheckMate275 (Nivolumab in BCa patients) cohorts [ 49 ]. They determine a score where TAMs and monocytes were not defined by the classical M1/M2 signature.…”

“…They determine a score where TAMs and monocytes were not defined by the classical M1/M2 signature. With this scoring, they demonstrated that monocytes with a low score were enriched in the peripheral blood of metastatic BCa patients with resistance to anti-PD-L1 [ 49 ], suggesting that pro-tumorigenic myeloid cells could be a pertinent biomarker for ICI efficiency.…”

Identification of a ZC3H12D-Regulated Competing Endogenous RNA Network for Prognosis of Lung Adenocarcinoma at Single-Cell Level

“…Besides, the scRNA-seq technology provided us an innovative method to reveal the gene expression level in immune cells under different conditions [48,49]. Based on the ScRNA-seq in our study, it showed that ZC3H12D was not homogeneous among different clusters in tumor, but it selectively highly expressed in immune cells.…”