Immune-desert tumor microenvironment in SMARCA4-deficient thoracic sarcomas with limited efficacy of immune checkpoint inhibitors.
Authors: Gantzer Justine , Davidson Guillaume , Vokshi Bujamin , Weingertner Noëlle , Bougoüin Antoine , Moreira Marco , Lindner Veronique , Lacroix Guillaume , Mascaux Celine , Chenard Marie Pierre , Davidson Irwin , Kurtz Jean Emmanuel , Sautes-Fridman Catherine , Fridman Wolf-Herman , Malouf Gabriel 
Published: June 2021

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Background: SMARCA4-deficient thoracic sarcomas (SDS) are rare and aggressive sarcomas characterized by inactivating SMARCA4 mutations, with no approved treatment to date. Previous data linking SWI/SNF deficiency with tumor immune microenvironment (TME) are contradictory. While an immunogenic microenvironment and efficacy of immune checkpoint inhibitors (ICI) were described in SMARCA4-deficient small cell carcinoma of the ovary, the TME phenotype of SDS is unknown; in addition, response of patients to ICI is lacking. Methods: All consecutive patients diagnosed with SDS between 2016 and 2019 in Strasbourg University Hospital were included and clinical outcomes collected. Immunostainings for immune cell markers, immune checkpoints and tertiary lymphoid structures (TLS) were assessed on available samples. Validation was performed using an independent transcriptomes dataset of SDS (n = 12), not otherwise specified (NOS) non-small cell lung cancer (NSCLC) with/without SMARCA4 mutations (n = 14) and undifferentiated thoracic sarcoma (n = 5). Finally, chemokines (CXL9 and CXCL10) and PD-L1 expressions were assessed in NSCLC and thoracic fibroblast cell lines, treated with/without interferon gamma (IFNG). Results: Nine patients were identified and had all metastatic disease at presentation, with a median overall survival of 1.8 months (0.3-NR). Among them, 4 received ICI as part of their treatment. Out of 11 evaluated tumors samples, all but one case showed no TLS, consistent with an immune desert TME phenotype charted by low densities of CD3+ T-cells, CD8+ T-cells, CD20+ B-cells from one side and high density of CD68+ macrophage-cells from the other side. Conversely, the unique tumor with TLS aggregate showed an immune-rich TME phenotype associated with high mutational tumor burden. While the patient with TLS harboring tumor showed an exceptional long-lasting response, the 3 remaining patients without TLS had progressive disease at best response to ICI. Using an independent cohort, unsupervised clustering using immune cell scores identified two clusters tightly associated with cell ontogeny of cancer subtypes and immunity; while cluster 1 (C1) was enriched for NOS NSCLC independently from SMARCA4 status (n = 9/10; 90%) (p = 0.001), C2 was enriched for SDS (n = 11/12; 91.7%) (p = 0.005) and undifferentiated thoracic sarcomas (n = 5/5; 100%) (p = 0.0005). Finally, SMARCA4 loss of function experiments revealed upregulation of chemokines (CXL9 and CXCL10) and PD-L1 expression in the NSCLC cell line with no effect on thoracic fibroblast cell line. Conclusions: SDS harbor an immune desert TME phenotype with limited efficacy to ICI, similar to other sarcomas. Our data suggest that TME of SMARCA4-driven tumors might vary according to the cell of origin. Further studies are needed to understand the interplay between SWI/SNF mutations, cell ontogeny and immunity.