Supplementary information

List of antibodies used for immunoperoxidase (IP) and immunofluorescence (IF) study

-     Major histo-compatibility (MHC)-class 1: HLA-ABC, W6/32, Dako, Denmark

-     MHC-class 2 antigens (MHC-2): HLA-DP/DQ/DR, CR3/43, Dako)

-     C5b-9 membrane attack complex: aE11; #ab55811, Dako)

-     CD56/neural cell adhesion molecules [NCAM] (regenerating myofibers): #NCL-CD56-1B6, Novocastra, France

-     CD68 (macrophages): KP1, Dako

-     CD3: F7.2.38 #A0452, Dako

-     CD4: 4B12 #ncl-cd41f6, Novocastra

-     CD8: C8/144B #M7103 (IP), Dako; ab4055, Abcam (IF)

-     CD20: L26 #M0755, Dako

-     anti transactivator CIITA: ABF212, Sigma

Assays and primer sequences:

-     (GBP2) Hs00894837_m1

-     (ISG15) Hs00192713_m1

-     (IFNγ) Hs0098291_m1

-     (HLA-DO) Hs00157950_m1

-     (HLA-DP) Hs00157955_m1

-     CIITA forward: CTCCAGTTCCTCGTTGAGCT

-     CIITA reverse: AGGCCGTGGACAGTGAATC

-     HLA-DRB forward: CTCCTGGTCTGCTCTGTGAG

-     HLA-DRB reverse: CTGTTTCCAGCATCACCAGG

-     HLA-DMB forward: AGCATGATCACATTCCTGCC

-     HLA-DMB reverse: TTTGGAGTCCCAGCATCATCC

The relative abundance of each transcript was normalized to the expression level of an endogenous control gene, TATA binding protein (TBP), Hs00427620_m1, TBP forward: AACAACAGCCTGCCACCTTA and TBP reverse: GGGTCAGTCCAGTGCCATAA. The relative quantification value was calculated using the 2^-DDCT method. The normalized fold-change was relative to the mean expression for ten healthy controls.