Type 1 narcolepsy (T1N) is caused by a hypocretin (HCRT, also called orexin) cell loss. Association with DQB1*06:02/DQA1*01:02 (DQ0602, 98% vs. 25%), T cell receptors (TCR) and other loci indicate autoimmunity. Onset is seasonal and associated with influenza-A, notably pandemic 2009H1N1 (pH1N1) infection and the pH1N1 vaccine Pandemrix. The strong HLA association and unique effects in TCRA and TCRB suggest that autoantigen presentation by DQ0602 to CD4+ T cell is crucial. We surveyed CD4+ T cell binding to autoantigens and flu antigens presented by DQ0602 in narcolepsy versus controls, identifying the immunological basis of narcolepsy.

DQ0602 binding was tested for peptides overlapping RFX4, HCRT and flu HA, NA, PB1and NP sequences.  Reactivity to ~100 tetramers was tested in 6 narcolepsy and 4 controls after expansion of cells in 10-day cultures.  Higher tetramer-peptide specific CD4⁺ T cells was found with HCRT_54-66-NH2, HCRT_86-97-NH2 (HCRT_NH2), pHA_273-287 and NP_17-31, further confirmed for HCRT_NH2 and pHA_273-287 in 77 T1N and 44 DQ0602 controls.  Single cell TCR sequencing after FACS sorting was conducted and public TCR clones transfected into Jurkat76 cells to test for activation after peptide presentation by K562-DQ0602 or RM3-DQ0602 cells. 

Most commonly used public sequences CDR3β-TRBV4-2-CASSQETQGRNYGYTF, CDR3a-TRAV2-CAVETDSWGKLQF-TRAJ24 and TRAV26-1-CIVRSQGGSYIPTF-TRAJ6 were retrieved using both DQ0602-HCRT_NH2 and DQ0602-pHA_273–287 but not DQ0602-NP_17-31 tetramers.  Sharing of clones using TRAJ24 and TRBV4-2 was notable as these exact segments (~0.8% of repertoire) are modulated by rs1154155/rs1483979 and rs1008599, polymorphisms associated with T1N.  Jurkat cells transfected with some clones were activated by HCRT_NH2 and pHA_273–287, suggesting molecular mimicry. As a control, NP_17-31 involved different TCRs, notably TRAV8-6_TRAJ34 with TRBV7-9_TRBJ2-3 and was only activated by NP_17–31.   

Our results provide strong evidence for autoimmunity and molecular mimicry with flu antigens modulated by genetic components in the pathophysiology of T1N.