Hello everyone, I am looking for help in characterizing the phenotype of a mutation in the TRAV gene ( T Cell receptor alpha variable chain coding gene ).
I want to check how does this mutation affects the T-cells activity in a way connected to an autoimmune disease.
Any suggetions for experiments / ideas on how to further check this?
I have only DNA and RNA samples, I don't have T-cells extracted from patients.
You could first run RNA-Seq on this population compared to controls. Focus on cell surface molecules, secreted proteins and transcription factors. If there are any notable differences then run DNAse-Seq to study epigenetic changes. Without cells, however, it will be difficult to test the significance of all this on cellular function.
Thank you very much I really appreciate it, I have already ran RNA-seq compared to controls ( for a group of 10 patients vs 10 controls ).
can you tell me an example of which are the most connected genes you think that i should check their expression on the RNAseq? David Cameron Wraith
This is nicely described in the following paper: Verhagen, J., Genolet, R., Britton, G.J., Stevenson, B.J., Sabatos-Peyton, C.A., Dyson, J., Luescher, I.F., Wraith, D.C. CTLA-4 controls the thymic development of both conventional and regulatory T cells through modulation of the TCR repertoire. Proc. Natl. Acad. Sci. (USA) (2013) 110: E221-30.
This paper demonstrates how CTLA-4 expression in the thymus controls alpha chain usage and the resulting affinity of the T cell receptors for antigen.
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