Table 3.
Identical Clonotypes in Different Sites Indicating Clonal Trafficking Between Subcompartments of the Kidney and Between Kidney and Blood*
| T Cell Receptor β-Chain Structure |
|||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Case | Sample year | Sample Type | Size of Clone (#seq.) | CDR3 Length | CDR3 Region Sequence and Analysis | TRBV Element (BV) | TRBD Element | TRBJ Element | |||||||||||||||||||
| 6 | 2006 | Periglom. | 30 | 12 | TGT | GCC | AGT | AGT | Agg | gGG | GGG | Cag | ggC | TAT | GGC | TAC | ACC | TRBV19 | 1*01 | 1-2*01 | |||||||
| Interstitium | C | A | S | S | R | G | G | Q | G | Y | G | Y | T | (17) | |||||||||||||
| 2006 | Intertubular | 14 | 12 | TGT | GCC | AGT | AGT | Agg | gGG | GGG | Cag | ggC | TAT | GGC | TAC | ACC | TRBV19 | 1*01 | 1-2*01 | ||||||||
| Interstitium | C | A | S | S | R | G | G | Q | G | Y | G | Y | T | (17) | |||||||||||||
| 15 | 2006 | Periglom. | 4 | 12 | TGT | GCC | AGT | AGT | ATt | GGG | ACA | GGC | TCC | TAC | GAG | CAG | TAC | TRBV19 | 1*01 | 2-7*01 | |||||||
| Interstitium | C | A | S | S | I | G | T | G | S | Y | E | Q | Y | (17) | |||||||||||||
| 2006 | Intertubular | 1 | 12 | TGT | GCC | AGT | AGT | ATt | GGG | ACA | GGC | TCC | TAC | GAG | CAG | TAC | TRBV19 | 1*01 | 2-7*01 | ||||||||
| Interstitium | C | A | S | S | I | G | T | G | S | Y | E | Q | Y | (17) | |||||||||||||
| 13 | 2004 | Periglom. | 2 | 13 | TGT | GCC | AGC | Agg | cta | GAC | Aat | gtc | cca | aAC | AAT | GAG | CAG | TTC | TRBV7-3 | 1*01 | 2-1*01 | ||||||
| Interstitium | C | A | S | R | L | D | N | A | P | N | N | E | Q | F | (6S1) | ||||||||||||
| 2004 | Intertubular | 50 | 13 | TGT | GCC | AGC | Agg | cta | GAC | Aat | gtc | cca | aAC | AAT | GAG | CAG | TTC | TRBV7-3 | 1*01 | 2-1*01 | |||||||
| Interstitium | C | A | S | R | L | D | N | A | P | N | N | E | Q | F | (6S1) | ||||||||||||
| 13 | 2008 | Periglom. | 3 | 13 | TGT | GCC | AGC | Agg | cta | GAC | Aat | gtc | cca | aAC | AAT | GAG | CAG | TTC | TRBV7-3 | 1*01 | 2-1*01 | ||||||
| Interstitium | C | A | S | R | L | D | N | A | P | N | N | E | Q | F | (6S1) | ||||||||||||
| 2008 | Tubules | 5 | 13 | TGT | GCC | AGC | Agg | cta | GAC | Aat | gtc | cca | aAC | AAT | GAG | CAG | TTC | TRBV7-3 | 1*01 | 2-1*01 | |||||||
| C | A | S | R | L | D | N | A | P | N | N | E | Q | F | (6S1) | |||||||||||||
| 13 | 2008 | Periglom. | 14 | 19 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 |
| Interstitium | C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | ||||||
| 2008 | Intertubular | 20 | 19 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 | |
| Interstitium | C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | ||||||
| 2008 | Intertubular | 14 | 19 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 | |
| Interstitium | C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | ||||||
| 2008 | Tubules | 6 | 19 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 | |
| C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | |||||||
| 2008 | Glomerulus | 1 | 19 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 | |
| C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | |||||||
| 2002 | PB CD8 | 1 | 17 | TGT | GCC | AGC | AGT | TTA | Ttt | ttg | gcc | aac | cgt | cGG | GAC | AGG | GGt | tCA | GAT | ACG | CAG | TAT | TTT | TRBV28 | 1*01 | 2-3*01 | |
| C | A | S | S | L | F | L | A | N | R | R | D | R | G | S | D | T | Q | Y | F | (3) | |||||||
| 13 | 2008 | Glomerulus | 1 | 15 | TGT | GCC | AGC | AGC | TTa | ttc | cgt | GGG | ACA | GGG | caa | ACC | GGG | GAG | CTG | TTT | TTT | TRBV5-1 | 1*01 | 2-2*01 | |||
| C | A | S | S | L | F | R | G | T | G | Q | T | G | E | L | F | F | (5S1) | ||||||||||
| 2008 | Intertubular | 4 | 15 | TGT | GCC | AGC | AGC | TTa | ttc | cgt | GGG | ACA | GGG | caa | ACC | GGG | GAG | CTG | TTT | TTT | TRBV5-1 | 1*01 | 2-2*01 | ||||
| Interstitium | C | A | S | S | L | F | R | G | T | G | Q | T | G | E | L | F | F | (5S1) | |||||||||
| 8 | 2003 | Kidney | 2 | 8 | TGT | GCC | AGC | Agc | CGG | Ggc | gtg | TAC | GAG | CAG | TAC | TRBV28 | 2*01 | 2-7*01 | |||||||||
| Biopsy | C | A | S | S | R | G | V | Y | E | Q | Y | (3) | |||||||||||||||
| 2003 | PB CD8 | 8 | 8 | TGT | GCC | AGC | Agc | CGG | Ggc | gtg | TAC | GAG | CAG | TAC | TRBV28 | 2*01 | 2-7*01 | ||||||||||
| C | A | S | S | R | G | V | Y | E | Q | Y | (3) | ||||||||||||||||
| 16 | 2002 | Kidney | 1 | 9 | TGC | GCC | AGC | AGC | CCG | GGA | ata | ggt | ACT | GAA | GCT | TTC | TRBV4 | 2*02 | 1-1*01 | ||||||||
| Biopsy | C | A | S | S | P | G | I | G | T | E | A | F | (7S1) | ||||||||||||||
| 2002 | PB CD8 | 19 | 9 | TGC | GCC | AGC | AGC | CCG | GGA | ata | ggt | ACT | GAA | GCT | TTC | TRBV4 | 2*02 | 1-1*01 | |||||||||
| C | A | S | S | P | G | I | G | T | E | A | F | (7S1) | |||||||||||||||
*
The IMGT CDR3 length is shown in terms of number of amino acids. The nucleotide sequence of the CDR3 region, arranged in codons, is represented in upper case when the nucleotides are germline encoded. The germline D element residues are underlined. Non-germline encoded N and P diversity nucleotides are represented as lower case letters. The single letter amino acid code for each codon is indicated. The TRBV designation for the variable element is shown along with the Arden et al. designation in parentheses.