Patient | HLA-type | Vα2.3 | Vβ22 | ||||||
Amino acid sequence | Frequency % | TRAJ | CDR3 length | Amino acid sequence | Frequency % | TRBJ | CDR3 length | ||
1 | DRB1*03,16 | CVVNTPGNTPLVF | 50.93 | 29*01 F | 11 | CASSEQGRGETQYF | 59.8 | 2–5*01 | 12 |
CVVNMGNTGGFKTIF | 49.07 | 9*01 F | 13 | CASSGTSVSTGELFF | 32.1 | 2–2*01 | 13 | ||
2 | DRB1*03,01 | CVVNIGYGNKLVF | 32.75 | 47*01 F | 11 | CASSGPGGRTEAFF | 36.02 | 1–1*01 | 12 |
CVVSVQGAQKLVF | 23.82 | 54*01 F | 11 | CASSEMTRVVFHF | 53.35 | 1–6*01 | 11 | ||
CVVNGLNIGDSGGGADGLTF | 43.43 | 45*01 F | 18 | CASSVITSGELFF | 7.53 | 2–2*01 | 11 | ||
3 | DRB1*03,13 | CVVNNYKLSF | 100 | 20*01 F | 8 | CASSGTGGAGTEAFF | 31.56 | 1–1*01 | 13 |
CASSEDVGRGAAFF | 34.49 | 1–1*01 | 12 | ||||||
CASSGGFEQYF | 33.1 | 2–7*01 | 9 | ||||||
4 | DRB1*03,08 | CVVNMGRGGSNYKLTF | 33.92 | 53*01 F | 14 | CASSGGHGKGEQFF | 50.87 | 2–1*01 | 12 |
CVVGINNRKLIW | 21.48 | 38*01 F | 10 | CASSGAGGRGNEQFF | 31.49 | 2–1*01 | 13 | ||
CVVNVRPGNTPLVF | 44.6 | 29*01 F | 12 | no CDR3 | 14.29 | no J | ─ | ||
5 | DRB1*03,11 | CVVNLAGNQFYF | 80.93 | 49*01 F | 10 | CASSVSTDTQYF | 39.75 | 2–3*01 | 10 |
CVVNPLGGGSYIPTF | 19.07 | 6*01 F | 13 | CASSEFGQGGHEQYF | 60.25 | 2–7*01 | 13 | ||
6 | DRB1*03,04 | CVVKEGSYIPTF | 21.79 | 6*01 F | 10 | CASSIDRSVGEKLFF | 37.69 | 1–4*01 | 13 |
CAVKSGNNRLAF | 14.38 | 7*01 F | 10 | CASSGTARNYGYTF | 60.94 | 1–2*01 | 12 | ||
CVVNMEYGNKLVF | 63.82 | 47*01 F | 11 | ||||||
7 | DRB1*03,13 | CVVIGSGGSQGNLIF | 53.45 | 42*01 F | 13 | CASSAITSNEKLFF | 5.84 | 1–4*01 | 12 |
CVVNLAGNQFYF | 46.55 | 49*01 F | 10 | CASSAGSGQPQHF | 23.47 | 1–5*01 | 11 | ||
CASRPTSGRSDEQFF | 10.35 | 2–1*01 | 13 | ||||||
CASSVLGTAAVTF | 60.35 | 2–6*01 | 11 | ||||||
8 | DRB1*03,08 | CVVISGSARQLTF | 24.38 | 22*01 F | 11 | ||||
CVVNIAGNQFYF | 33.97 | 49*01 F | 10 | ||||||
CVVNPSGTYKYIF | 41.65 | 40*01 F | 11 | ||||||
9 | DRB1*03,13 | CVVNMGNQAGTALIF | 100 | 15*01 F | 13 | ||||
10 | DRB1*03,04 | CVVNGHSNYQLIW | 42.4 | 33*01 F | 12 | ||||
CVVNRATGNQFYF | 57.6 | 49*01 F | 11 | ||||||
11 | DRB1*03,07 | CVVNTGFQKLVF | 100 | 8*01 F | 10 |
Frequency refers to the percentage of reads mapped to every given transcript (isoforms with >10% frequency). In cases where the total percentage is <100%, the remaining sequences were either too short or did not align. The designations TRAJ and TRBJ follow the IMGT (International ImMunoGeneTics Information System) T-cell receptor gene nomenclature. Length of CDR3 region as derived from the IMGT database. All cells were derived from HLA DRB1*03+ patients with bronchoalveolar lavage (BAL) Vα2.3+Vβ22+ CD4+ T-cell expansions. For patients 1–4 and 8–10, mRNA was extracted from fluorescence-activated cell sorting Vα2.3+Vβ22+ T-cells. For patients 5–7 and 11, mRNA was extracted from unsorted BAL cells. For patients 8–11, the amount of product obtained for the Vβ22 chain following PCR amplification was too low to yield reliable sequencing data. Vα2.3 sequences (highlighted in bold font) share the 49*01 J segment and identical or near-identical amino acid sequences.