Table 3.
Peptides derived from known tumour-associated antigens exclusively identified in HLA-I eluates from HCC tissues by unbiased MS.
| Antigen | Position | Sequence | HLA type∗ | Donor | HLA† | Tumour‡ | PRM§ |
|---|---|---|---|---|---|---|---|
| GPC3 | 376-384 | AHVEHEETL | B∗38:02 C∗07:01 C∗07:02 |
16 | VG | ||
| GPC3 | 522-541 | FLAELAYDLDV-DDAPGNSQQ | NB | 21 | N/A | ||
| GPC3 | 531-541 | DVDDAPGNSQQ | NB | 21 | VG | ||
| IGF2BP3 | 552-560 | KIQEILTQV | A∗02:01 | 17 | ○ | Brain; breast; Mel; ML; ovarian | VG (1 HCC) |
| MAGEA1 | 278-286 | KVLEYVIKV |
A∗02:01 C∗07:01 |
17 | ○● | Mel; uterine | VG (1 HCC; 1 TF) |
| MAGEA1 | 301-309 | ALREEEEGV | A∗02:01 | 17 | ○ | Mel | VG |
| MAGEB2 | 231-240 | GVYDGEEHSV |
A∗02:01 C∗04:01 |
18 | ○● | Mel; ML; cervix; uterine | VG |
| MAGEC1 | 611-621 | FPQSPLQGEEF | B∗35:02 C∗04:01 |
22 | VG | ||
| MAGEC1 | 1,035-1,043 | FAFGEPREL | A∗68:02 B∗52:01 B∗78:01 C∗16:01 |
19 | ○● | Brain; Mel | VG |
| MAGEC1 | 1,061-1,069 | NSSPPRYEF | A∗68:02 B∗52:01 B∗78:01 C∗16:01 |
19 | Δ | Mel | VG |
| MAGEC2 | 176-184 | DYFPVILKR | A∗33:01 | 19 | VG | ||
| PNMA5 | 61-69 | NAKAVFIEL | A∗68:02 B∗52:01 B∗78:01 C∗16:01 |
19 | ● | Breast | G |
| SSX1 | 23-32 | KAFDDIATYF | B∗57:01 C∗04:01 C∗07:04 |
18 | VG | ||
| SSX1 | 42-50 | YSEKISYVY | A∗01:01 B∗35:02 C∗04:01 C∗07:01 |
22 | N/A |
DDA, data-dependent acquisition; HCC, hepatocellular carcinoma; IEDB, Immune Epitope Database; IFNγ, interferon γ; MS, mass spectrometry; PRM, parallel reaction monitoring; TF, tumour-free.
NB: not predicted to bind donor HLA.
Whether a sequence is reported as HLA ligand and/or epitope in the IEDB or not. For reported sequences, it is indicated whether they are identified exclusively in a new (●), the same (○), or in addition to another (○●) HLA-supertype context as previously reported. Some sequences are reported in the IEDB but lack a specified HLA-type entry (Δ). Peptides in bold are listed as immunogenic in the IEDB (i.e. positive multimer binding and/or IFNγ production).
Tumour types for which this peptide was reported as HLA ligand and/or epitope in the IEDB. Mel: melanoma; ML: myeloid leukaemia.
VG: Peptides with a 'very good match' in the same sample as the DDA hit. The number of very good matches in additional samples is indicated between brackets also stating the tissue type (see Supplementary Materials & methods; Table S7). G: peptide with a good match in the same sample as the DDA hit. N/A: peptides not included in the target list for PRM analyses.