Decreased cytotoxic T cells and TCR clonality in organ transplant recipients with squamous cell carcinoma

T-cell landscape differences between cutaneous squamous cell carcinoma (cSCC) tumors in immune competent (SCC in IC) and immunocompromised organ transplant recipients (TSCC in OTR) are unclear. We developed an analytical method to define tumor infiltrating lymphocyte (TIL) phenotype in cSCC from immune competent and immune suppressed patients using single-cell TCR sequencing and gene expression data. TSCC exhibits reduced proportions of cytotoxic and naïve TILs and similar numbers of regulatory TILs. Fewer, more heterogeneous TCR clonotypes are observed in TIL from OTR. Most TCR sequences for top ten clonotypes correspond to known antigens, while 24% correspond to putative neoantigens. OTR show increased cSCC events over 12 months possibly due to reduced cytotoxic T-cells. Our novel method of barcoding CD8+ T-cells is the first providing gene expression and TCR sequences in cSCC. Knowledge regarding putative antigens recognized by TCRs with phenotypic function of T-cells bearing those TCRs could facilitate personalized cSCC treatments. CD8+ T cells were obtained from fresh tissue samples via flow cytometry. The sorted cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10-12e3 cells were loaded per channel. Single-cell RNA-Seq libraries were prepared using the following Single Cell 5’ Reagent Kits: Chromiumâ„¢ Single Cell 5’ Library & Gel Bead Kit, PN-1000006 and Chromium Single Cell VDJ enrichment kit for Human T Cells (PN-100000). Libraries were run on a NovaSeq 6000 SP or S1 flow cell (depending on sample numbers) for both 5’ transcriptome data and TCR clonotype determination. We assessed 5 cutaneous squamous cell carcinoma tumors from immunocompetent patients (SCC1-5) and 6 tumors from immunocompromised patients (i.e., organ transplant recipients) (TSCC1-6).