PMID:22058411

[mikessh]

Connelley TK, MacHugh ND, Pelle R, Weir W, Morrison WI. Escape from CD8+ T cell response by natural variants of an immunodominant epitope from Theileria parva is predominantly due to loss of TCR recognition. J Immunol. 2011 Dec 1;187(11):5910-20. doi: 10.4049/jimmunol.1102009. Epub 2011 Nov 4.

[RenskeVroomans]

About to submit this table to the database but wanted to check the following:

• they perform two experiments, one immunisation and one challenge, and sequence T-cells after each. Some sequences are found in both experiments, and so I put these sequences in the database twice, with the clonal frequency of each experiment. Is that ok?
• They generate T cell clones from a limiting dilution after stimulating PBMC for 3 weeks with infected cells. Therefore I filled in "antigen-expressing-targets,limiting-dilution-cloning" in the method.identification field, and TCL in the meta.tissue field.
• They then perform cytotoxicity assays on some T cell clones with variants of the antigen (Tables IV and VI). I think that in principle these data could be put into the database, but what cut-off should I use? Is 11% cytotoxicity against the variant peptide compared to the wildtype peptide sufficient?

Thanks!

[mikessh]

Hi!

1. Yes, its the correct way
2. Correct
3. They say A standard cutoff of .5% specific cytotoxicity was used to define positive clones. In all assays, this was well in excess of 3 SD above the mean spontaneous release value of the respective target cells and was also well in excess of 3 SD above the mean levels of cytotoxicity obtained with MHC-mismatched T. parva-infected and unpulsed T. annulata-infected target cells. So we can follow their definition.

By the way, it looks like CDR3 sequences are incomplete. Can you confirm that this can be fixed by adding C and F/W at both ends? Or they use the N-D-N part only (in that case we will have problems recovering true sequences.

[RenskeVroomans]

The CDR3 sequences indeed look incomplete, but in the paper they do not specify which part of the sequence is included. Should the CI build complain if the CDR3 sequences are incorrect? And should I not add a C and an A at the beginning (the typical start is CAS or CAT or CAW)? Furthermore, the CI build does not recognize BosTaurus (cow).

[mikessh]

The species list is hard-coded, I can change it. I think we have several V/J segments for Bos, don't know if it is possible to check CDR3 sequences.

As noted in another issue - V/J trimmings are random, so if one sees LAPGAT, it can be either CASS LAPGAT NEKLFF or CAS LAPGAT NEKLFF. Absolutely no chance to fix this without real nucleotide sequences :(