Table 4.
List of neurodegeneration-associated proteins from which derive MHC class II-binding endogenous peptides in the human B-cell lineage.
| Neurodegeneration-associated proteins | Reported MHC class II restrictions |
|---|---|
| Amyloid beta A4 protein (APP) | HLA class II, HLA-DQ, HLA-DR, HLA-DR3, HLA-DQ7.5, HLA-DQ2.5, HLA-DQ2.2, HLA-DRB1*15:01 (HLA-DR15), HLA-DRB5*01:01 (HLA-DR51), HLA-DRB1*04:05 (HLA-DR4), HLA-DQA1*05:01/DQB1*02:01 (HLA-DQ2.5) |
| Sequestosome-1 (SQSTM1) | HLA class II, HLA-DR, HLA-DQ, HLA-DR1, HLA-DQ7.5, HLA-DQ2.5, HLA-DQ2.2, HLA-DR15/DR51, HLA-DQA1*05:01/DQB1*02:01 (HLA-DQ2.5) |
| Profilin-1 (PFN1) | HLA class II, HLA-DR, HLA-DQ, HLA-DR1, HLA-DR3, HLA-DRB1*04:05 (HLA-DR4), HLA-DR15/DR51 |
| Superoxide dismutase [Cu-Zn] (SOD1) | HLA class II, HLA-DR, HLA-DR1, HLA-DQ7.5, HLA-DQ2.5, HLA-DQ2.2 |
| Transitional endoplasmic reticulum ATPase (VCP) | HLA class II, HLA-DR, HLA-DR1, HLA-DQ7.5, HLA-DQ2.5, HLA-DQ2.2 |
| Lysosomal acid glucosylceramidase (GBA) | HLA class II, HLA-DR, HLA-DQ, HLA-DR1, HLA-DR15, HLA-DRB1*04:05 (HLA-DR4) |
| Presenilin-1 (PSEN1) | HLA class II, HLA-DQ, HLA-DQ2.2, HLA-DR15/DR51, HLA-DRB1*04:05 (HLA-DR4) |
| Ubiquilin-2 (UBQLN2) | HLA class II, HLA-DR1, HLA-DQ7.5, HLA-DQ2.2, HLA-DRB1*04:05 (HLA-DR4) |
| Major prion protein (PRNP) | HLA-DQ, HLA-DR, HLA-DR1, HLA-DQ7.5, HLA-DQ2.2 |
| Vacuolar protein sorting-associated protein 35 (VPS35) | HLA class II, HLA-DR, HLA-DR15/DR51, HLA-DQA1*05:01/DQB1*02:01 (HLA-DQ2.5) |
| Optineurin (OPTN) | HLA-DR1, HLA-DQ7.5, HLA-DQ2.5, HLA-DQ2.2 |
| Protein deglycase DJ-1 (PARK7) | HLA class II, HLA-DR1, HLA-DRB1*04:01 (HLA-DR4), HLA-DRB1*04:05 (HLA-DR4) |
| Progranulin (GRN) | HLA class II, HLA-DQ, HLA-DQ7.5 |
| Spatacsin (SPG11) | HLA-DQ7.5, HLA-DQ2.2 |
| Ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1) | HLA class II, HLA-DR |
| RNA-binding protein FUS (FUS) | HLA class II |
| Probable cation-transporting ATPase 13A2 (ATP13A2) | HLA-DR |
| Heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) | HLA class II |
| Charged multivesicular body protein 2b (CHMP2B) | HLA-DQ7.5 |
| Huntingtin (HTT) | HLA-DR |
| Serine/threonine-protein kinase TBK1 (TBK1) | HLA-DR15/DR51 |
| Presenilin-2 (PSEN2) | HLA-DR15/DR51 |
| Microtubule-associated protein tau (MAPT) | HLA-DR15/DR51 |
The “IEDB-AR” immune epitope database (43) was screened in order to retain only publications reporting on the systematic mass spectrometry identification of endogenous peptides binding MHC-class II molecules in the human B-cell lineage. Only results obtained on human cells of the B-cell lineage in the absence of immunization or stimulation protocols were taken into account. The retrieved list of parent proteins was then crossed with the list of 48 common neurodegeneration-associated proteins we established. The protein names and gene symbols are shown in the left column; the corresponding reported MHC class II restrictions of derived peptides are shown in the right column. When needed, aliases frequently used in the HLA class II genotype/serotype nomenclature are indicated in brackets.