Spatially resolved transcriptomics reveal the determinants of primary resistance to immunotherapy in NSCLC with mature tertiary lymphoid structures

Effectiveness of immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) has been linked to the presence of mature tertiary lymphoid structures (mTLSs) within the tumor microenvironment (TME). However, only a subset of mTLS-positive NSCLC derives benefit, thus highlighting the need to unravel ICI response determinants. The comprehensive analysis of ICI-treated patients with NSCLC ( n = 509) from the Bergonié Institute Profiling (BIP) study (NCT02534649) reveals that the presence of mTLSs correlates with improved clinical outcomes, independently of programmed death ligand 1 (PD-L1) expression and genomic features. Employing spatial transcriptomics alongside multiplex immunofluorescence (mIF), we show that two distinct subsets of cancer-associated fibroblasts (CAFs) are essential factors in mediating primary resistance to ICIs in mTLS-positive NSCLC. These CAFs are associated with immune exclusion, CD8 + T cell exhaustion, and increased regulatory CD4 + T cell infiltration, underscoring an immunosuppressive TME. Our study highlights the pivotal role of specific CAF subsets in thwarting ICIs, proposing new therapeutic targets to enhance immunotherapy efficacy. • mTLSs are predictive of response to ICIs in NSCLC • Two CAF subsets within the TME are key determinants of primary resistance to ICIs • FAP + αSMA + CAFs correlate with the inflammatory response and exhaustion of CD8 + T cells • MYH11 + αSMA + CAFs favor an immunosuppressive TME with CD4 + Treg cell infiltration Peyraud et al. show that the presence of mTLSs is associated with improved clinical outcome with immunotherapy in NSCLC. However, primary resistance is driven by two distinct subsets of cancer-associated fibroblasts that are associated with immune exclusion, CD8 + T cell exhaustion, and increased regulatory CD4 + T cell infiltration.