Loss of B cell Tolerance is TCR Dependent [amplicon-seq]
We tested orphan TCR autoreactivity using the peptide MHC-TCR chimeric receptor (MCR) co-culture system.  In this system, cognate antigen recognition leads to TCR specific NFAT activation in MCR reporter cells expressing a mouse I-Ab MHC class II extracellular domain covalently linked to candidate peptides and an intracellular TCR signaling domain.  We used mixed autoimmune bone marrow chimera spleens and kidneys as sources of cDNA to generate a transcriptome-wide library of natural autoantigen peptides .  We cloned this cDNA-derived peptide (CDP) autoantigen library into the MCR retroviral backbone and transduced NFAT reporter cells to make a murine autoantigen MCR reporter library (MCR-Lib). We then used this library to screen orphan TCRs identified by scTCR-seq for autoreactivity. Overall design: Amplicon NGS was performed on PCR-amplified peptide sequences from MCR-Libraries following screening with orphan TCRs