Background

ASPS is an ultra-rare soft tissue sarcoma characterized by a translocation gene fusion of TFE3 to ASPSCR1, creating a chimeric ASPSCR1::TFE3 fusion protein that functions as an aberrant transcription factor. Depending on where the ASPSCR1 is joined in-frame of TFE3, it generates one of two oncogenic fusion transcripts, type-1 or 2. ASPS has shown promising responses to ICIs; whether the two fusion isoforms have a differential TIME impacting responses to ICIs is unclear.

Methods

Genomics data for patients (pts) with ASPS were retrieved from multiple databases, including Tempus Inc. and Caris Life Sciences (n=11 and 7 pts, respectively), as well as the GEO database (n=20 pts). Immunogenic signatures (tumor inflammation signature (TIS) and interferon-gamma signature (IFNG) were calculated using single-sample GSEA. Spatial profiling for two in-house samples was done using 10X Visium. Paired biopsy specimens at baseline and cycle 3 day 1 (C3D1) from the ETCTN 10005 trial of single-agent atezolizumab for ASPS were stained using multiplexed immunofluorescence for CD8 T-cells and PD-L1 and RT-PCR was used to discern type 1 vs. type 2 ASPSCR1::TFE3 fusion isoforms (n=35 pts).

Results

Somatic profiling revealed median TMB of <1 for ASPS (Tempus dataset). Pathway enrichment analysis (GEO dataset) revealed upregulation of immunogenic pathways in type 1 fusion tumors (PD-L1/PD-1 checkpoint pathway expression and NK-cell-mediated cytotoxicity). In contrast, type 2 fusion tumors were enriched in autophagy-related and apelin signaling pathways. Immune-cell deconvolution of bulk RNA-seq (GEO dataset) demonstrated significantly higher M1 macrophages and effector-memory CD8+ T-cells in type-1 fusion tumors, observed independently in the Caris and Tempus dataset also. IFNG (p=0.03) and TIS (p=0.07) scores were higher in type 1 fusion tumors compared to type 2 fusion (GEO dataset). Spatial profiling (n=2) showed alveolar macrophages as the predominant component (35%) in ASPS, with macrophages being the main contributor to immunogenic signatures. In the ETCTN10005 trial with response rate of 37%, none of the type 2 fusion tumors (n=5) displayed RECIST responses to atezolizumab. Paired tumor biopsies demonstrated higher median PD-L1+ and CD8+ T-cells (at baseline and C3D1) in type-1 vs. type-2 fusions (table 1).

Conclusions

For the first time, our novel multi-omics analysis reveals that the type-1 fusion isoform in ASPS has an immunologically active TIME, is enriched in M1 macrophages, CD8+ T cells, checkpoint activity pathways, and displays higher CD8+ T-cell infiltration post-ICI compared to the type-2 fusion, likely translating into improved responses to ICIs. Trial funded by NCI Contract No. HHSN261201500003I.

Trial Registration NCT03141684.

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