Incorporation of TRDV segments into TCR alpha chains

Abstract

AbstractIn human tumor models we tried to identify and clone the TCR of tumor-reactive T cells enriched in mixed lymphocyte tumor-cell cultures (MLTC). In a particular MLTC, we identified a predominant TCR beta chain using the Beta Mark Vbeta Kit, but a corresponding alpha chain could not be amplified via RT-PCR usingTRAV-specific forward primers. Therefore, we applied 5’RACE to obtain the TCR alpha chain sequences. The 5’RACE product revealed an alpha chain that encompassed 89bp of theTRDV15’UTR, followed by theTRDV1coding sequence joined in frame toTRAJ24. The ORF reaching from theTRDV1start codon to theTRACsegment was intact, suggesting a functional TCR. To analyze this MLTC population in greater depth we conducted 10X VDJ sequencing. CellRanger identified the beta chain known from the Beta Mark analysis, but no corresponding alpha chain in the filtered results. The corresponding TRDV-containing TCR alpha chain could, however, be detected in the “all_contig_annotations” files.In a separate project, we performed TCR sequencing of tumor-infiltrating lymphocytes (TILs) in a murine tumor model. Also here, a predominant clonotype contained a TCR alpha chain joiningTrdv2-2in frame toTraj49.Transfection of both TCR cDNAs resulted in cell surface localization of TCR and CD3 as validated by FACS. Tumor recognition of the human, TRDV1-containing TCR could be demonstrated by IFNgamma ELISpot whereas the murine TCR did not recognize a tumor-derived cell line.TRDV-containing alpha chains have been reported in the literature for two HLA I-restricted TCRs against HIV peptides (Ueno et al, Eur J Immunol, 2003). To determine whether such TDRV-containing TCRs are unique events or whether Vdelta segments are commonly incorporated into TCR alpha chains, we queried the NCBI Sequence Read Archive (SRA) for 10X VDJ data and analyzed 21 human and 23 murine datasets. We found that especiallyTRDV1, Trdv1and to some extentTrdv2-2are more commonly incorporated into TCR alpha chains than someTRAVgenes, making theTRDVsegments a relevant contribution to TCR alpha diversity.For apparently solitary beta chains in 10X VDJ datasets, we suggest to scrutinize the “all_contig_annotations” files as these may contain an accompanying, TRDV-containing alpha chain.