135 Defining the T cell landscape and neoantigens via T-cell receptor sequencing and gene expression profiling in cutaneous squamous cell carcinoma

Abstract

Background: Immune response is key in defense against cutaneous squamous cell carcinoma (cSCC). We aim to better target T cell killing to treat cancer. Methods: CD8+ tumor infiltrating lymphocytes (TILs) obtained from fresh SCC tumor specimens from immunocompetent (n=5) versus organ transplant recipients (OTRs; n=6) were subject to single-cell RNA profiling and T-cell receptor (TCR) sequencing. Data were analyzed using scSeqR. Results: CD8+ TILs were clustered based on gene expression as follows: effector T cells (GZMA, GZMB, IFN-γ); naïve T cells (CCR7, LEF1, TCF7, IL7R); exhausted T cells (BTLA, CTLA4, PDCD1, TIM3, LAG3); and regulatory T cells (FOXP3, STAT3, TNFSRF). CD8+ TIL clonotypes show potential for response to known and uncharacterized antigens. CD8+ TILs from OTRs exhibited more homogeneous gene expression compared with immunocompetent patients. Regulatory and exhausted T cells were reduced in OTRs. TILs from both OTRs and immunocompetent patients showed clonality. However, more TCR clonotypes were observed in immunocompetent patients (mean = 1140) than OTRs (mean = 544). We analyzed common beta TCR from SCC via multiple bioinformatics-based approaches. Clonotypes common to more than one SCC from immune competent patients included breast cancer-associated keratin 19 and proliferation-associated striatin. OTR clonotypes included tumor-suppressor associated MOB kinase 1A and breast cancer-associated ADAM9. Conclusion: CD8+ TILs from cSCC showed clonotype restriction, implying T cell mediated anti-tumor response. We will refine our understanding of the SCC T cell landscape and identify and screen neoantigens with the goal of developing rational T cell-based cancer therapy.