Background
Methods
Clinical samples
Immunohistochemical staining
Statistical analysis
Flow cytometry
Copy number analysis
Fluorescent in situ hybridization
Whole exome sequencing
Variant calling and annotation
HLA typing
Neoepitope generation and filtering
Results
PD-1 and PD-L1 expression patterns
IHC score | PD-1 | PD-L1 |
---|---|---|
Negative 0 | 0 | 3 (2) |
Rare 1 | 9 (5)a | 4 (2) |
Low 2 | 17 (13) | 15 (11) |
Moderate 3 | 17 (12) | 12 (9) |
High 4 | 10 (8) | 12 (7) |
Very high 5 | 1 (1) | 8 (8) |
Genomic lesions in resected TNBCs
Sample | MYC | EGFR | AKT2 | FGFR2 | JAK2 |
---|---|---|---|---|---|
TNBC-2 | + | ||||
TNBC-4 | +++++ | ++ | |||
TNBC-7 | ++ | +++++ | |||
TNBC-8 | ++ | ||||
TNBC-11 | ++ | ++++ | |||
TNBC-13 | +++ | ++ | |||
TNBC-16 | ++ | ||||
TNBC-17 | + | ||||
TNBC-18 | ++ | ++ | +++ | ||
TNBC-19 | ++ | ||||
TNBC-20 | ++ | ||||
TNBC-23 | ++ | ++ | |||
TNBC-27 | ++ | ||||
TNBC-29 | +++ | ||||
TNBC-30 | ++ | ||||
TNBC-36 | ++ | ++ | |||
TNBC-39 | + | ++ | |||
TNBC-43 | ++ | ++ | |||
TNBC-44 | +++++ | ++ | |||
TNBC-47 | +++ | ||||
TNBC-49 | +++ | ++ | |||
TNBC-50 | +++++ | ||||
TNBC-51 | ++ | + | |||
TNBC-53 | ++ | ++ | ++ |
CNVs and treatment-naïve TNBCs with increased PD-L1 expression
Sample | Ploidy | EGFR | JAK2 | AKT2 | MYC | FGFR2 | PD-L1 (IHC) | Neoadjuvant |
---|---|---|---|---|---|---|---|---|
TNBC-6 | 4.0 | 5 T | – | |||||
TNBC-9 | 4.0 | 5 T | – | |||||
TNBC-14 | 3.1 | +++ | ++ | 5 T | – | |||
TNBC-21 | 2.8 | 5 T | – | |||||
TNBC-24 | 2.5 | 5 T | – | |||||
TNBC-33 | 3.6 | 5 T | – | |||||
TNBC-37 | NB | 5 T | – | |||||
TNBC-40 | 3.4 | 4 NT | – | |||||
TNBC-16 | 3.2 | ++ | 4 T | – | ||||
TNBC-23 | 3.6 | ++ | ++ | 4 T/NT | – | |||
TNBC-44 | 4.1 | +++++ | ++ | 4 T | – | |||
TNBC-46 | ND | 4 T/NT | – | |||||
TNBC-50 | 2.0 | +++++ | 4 T/NT | – | ||||
TNBC-55 | 3.0 | ++ | ++ | 4 NT | – | |||
TNBC-5 | 3.0 | ++ | 4 T | + | ||||
TNBC-8 | 3.3 | ++ | 4 NT | + | ||||
TNBC-29 | 4.0 | ++ | 4 T | + | ||||
TNBC-36 | 2.0 | ++ | ++ | 4 T/NT | + | |||
TNBC-43 | 3.2 | +++ | 4 T/NT | + | ||||
TNBC-18 | 4.2 | ++ | +++ | ++ | 1 NT | – | ||
TNBC-30 | 3.1 | ++ | 1 NT | – | ||||
TNBC-4 | 3.2 | ++ | +++++ | 1 NT | + | |||
TNBC-7 | 3.8 | ++ | +++++ | 1 NT | + | |||
TNBC-51 | 3.5 | ++ | ++ | 0 | + | |||
TNBC-20 | 3.4 | ++ | 0 | – | ||||
TNBC-56 | ND | 0 | – |
CNVs and treatment-naïve TNBCs with reduced PD-L1 expression
DNA repair pathway lesions
Sample | Gene lesion | PD-1 | PD-L1 | Neoadjuvant |
---|---|---|---|---|
TNBC-8 | MSH2F289C | 2 | 4 NT | + |
TNBC-53 | MLH3−/− | 3 | 3 NT | + |
TNBC-30 | CHEK2−/− | 1 | 1 NT | – |
TNBC-31 | BRIP1−/− | 3 | 2 NT | – |
TNBC-24 | BRCAmut | 4 | 5 T | – |
TNBC-27 | FBXW7S398F | 2 | 3 NT | + |
TNBC-29 | PRKDCQ75R | 2 | 4 T | + |
TNBC-17 | ALKBH5P303Q | 1 | 2 NT | – |
TNBC-36 | DCLRE1C656_671del16 | 3 | 4 T/NT | + |
TNBC-54 | TBD | 2 | 2 T/NT | + |
TNBC-51 | TBD | 1 | 0 | + |
TNBC-23 | TBD | 3 | 4 T/NT | – |
PTEN/PIK3CA
TNBC | PD-1 | PD-L1 | Tumor/Non-tumor | PTEN/PIK3CA | Neoadjuvant |
---|---|---|---|---|---|
TNBC-1 | 2 | 2 | T/NT | PTEN−/−1 | – |
TNBC-8 | 2 | 3 | NT | PTEN−/− | + |
TNBC-10 | 2 | 3 | T/NT | PTEN−/− | + |
TNBC-11 | 1 | 2 | T/NT | PTEN−/− | – |
TNBC-34 | 2 | 3 | NT | PIK3CAH1047R | – |
TNBC-35 | 1 | 2 | NT | PTEN−/− | + |
TNBC-55 | 2 | 4 | NT | PTEN−/− | – |
Mutation load and predicted neoepitopes
TNBC case | Number of neoepitopes (ann < 500) | Non-synonymous mutations | Synonymous mutations | Stop gain | Stop loss |
---|---|---|---|---|---|
TNBC-27 | 129 | 23 | 19 | 1 | 0 |
TNBC-29 | 413 | 61 | 30 | 3 | 0 |
TNBC-44 | 388 | 50 | 45 | 5 | 0 |
TNBC-2 | 70 | 21 | 5 | 1 | 0 |
TNBC-49 | 69 | 54 | 54 | 0 | 0 |
TNBC-8 | 557 | 64 | 29 | 4 | 0 |
TNBC-25 | 148 | 16 | 9 | 0 | 0 |
TNBC-34 | 243 | 33 | 20 | 2 | 0 |
TNBC-38 | 187 | 26 | 25 | 4 | 0 |
TNBC-47 | 88 | 41 | 13 | 1 | 0 |
TNBC-36 | 1368 | 137 | 55 | 9 | 0 |
TNBC-17 | 1116 | 137 | 65 | 8 | 1 |