Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy

Abstract

With only a fraction of patients responding to cancer immunotherapy, a better understanding of the entire tumor microenvironment is needed. Using single-cell transcriptomics, we chart the fi broblastic landscape during pancreatic ductal adenocarcinoma (PDAC) progression in animal models. We identify a population of carcinoma-associated fi broblasts (CAF) that are programmed by TGFβ and express the leucine-rich repeat containing 15 (LRRC15) protein. These LRRC15 + CAFs surround tumor islets and are absent from normal pancreatic tissue. The presence of LRRC15 + CAFs in human patients was confi rmed in >80,000 single cells from 22 patients with PDAC as well as by using IHC on samples from 70 patients. Furthermore, immunotherapy clinical trials comprising more than 600 patients across six cancer types revealed elevated levels of the LRRC15 + CAF signature correlated with poor response to anti-PD-L1 therapy. This work has important implications for targeting nonimmune elements of the tumor microenvironment to boost responses of patients with cancer to immune checkpoint blockade therapy. SIGNIFICANCE:This study describes the single-cell landscape of CAFs in pancreatic cancer during in vivo tumor evolution. A TGFβ-driven, LRRC15 + CAF lineage is associated with poor outcome in immunotherapy trial data comprising multiple solid-tumor entities and represents a target for combinatorial therapy.

Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer

“…Correlation network analysis of genes differentially expressed in pseudotime, along each trajectory, was then used to identify pseudotime gene expression modules ( Fig. 2e-f and Supplementary Tables 4&5). Similar to scRNA-seq analysis of human head and neck squamous cell carcinoma 10 and pancreatic adenocarcinoma 11,12 we identified a myofibroblastic-CAF subpopulation (CAF4) with upregulated expression of previously described CAF markers (e.g. ACTA2, POSTN and FAP).…”

“…This is likely due to incomplete understanding of fibroblast heterogeneity and their precise role in tumour progression, which is exemplified by reports of both tumour-promoting and suppressive effects 7 . The diverse roles attributed to fibroblasts may be regulated by distinct subpopulations, such as those previously described in the dermis 8 , fibrotic lesions 9 and in multiple solid cancers [10][11][12] . Cancer associated fibroblast (CAF) subpopulations are known to include myofibroblastic and inflammatory phenotypes 3, 11 . However, the extent of phenotypic diversity and the underlying molecular mechanisms regulating this heterogeneity remain unclear.…”

“…Inflammatory CAFs (iCAFs) have been shown to represent a subpopulation distinct from myofibroblasts in pancreatic cancer 11,12 . We identified a similar inflammatory subpopulation, predominantly found in tumour-adjacent normal tissues (NF3; Fig.…”

Characterizing the tumor microenvironment of metastatic ovarian cancer by single cell transcriptomics

“…Cancer associated fibroblasts mainly function to remodel the extracellular matrix in the tumor microenivironment 57 . Recently, a scRNA-seq study of CAF in pancreatic cancer revealed a LRRC15 + CAF population that correlated with poor response in patients treated with anti-PD-L1 therapy 58 . A few of the fibroblasts in our study also express LRRC15 (data not shown).…”

Identification of Prognosis-Related Genes and Construction of Multi-regulatory Networks in Pancreatic Cancer Microenvironment by Bioinformatics Analysis

“…Recently, increasing evidence has proved that tumor microenvironment plays an essential role in the process of pancreatic cancer (38)(39)(40)(41). Immune cells and stromal cells, the two main types of nonneoplastic components, have been reported to accelerate tumor immune escape and progression (42,43).…”