Introduction
Materials and methods
Patients, response criteria, and samples
Gene expression profiling
Statistical analysis methods
Results
Gene expression differences between responding and non-responding breast cancer tumours treated with chemotherapy are subtle and time dependent
Characteristics | NEO cohort (50) | NEO cohort PT-TM pairs (23) | p value | I-SPY 1 PT-T2 pairs (36) | p value |
---|---|---|---|---|---|
Median age at diagnosis | 50.8 | 50.1 | 0.8 | 47 | |
Tumour grade | 0.52 | 0.58 | |||
1 | 0 (0%) | 0 (0%) | 1 (3%) | ||
2 | 22 (44%) | 12 (52%) | 20 (55%) | ||
3 | 28 (56%) | 11 (48%) | 15 (42%) | ||
Hormone receptor status | 0.24 | 0.66 | |||
Positive | 23 (46%) | 14 (61%) | 24 (67%) | ||
Negative | 27 (54%) | 9 (39%) | 12 (33%) | ||
HER2 status | 0.87 | 0.64 | |||
Positive | 10 (20%) | 5 (22%) | 6 (17%) | ||
Negative | 40 (80%) | 18 (78%) | 30 (83%) |
Responding and non-responding tumours are more different upon exposure to chemotherapy
AAGAB is a promising potential novel on-treatment biomarker of response to chemotherapy
Response accuracy | Response AUC | Outcome (log-rank) | ||||
---|---|---|---|---|---|---|
NEO | I-SPY | NEO | I-SPY | NEO | I-SPY | |
On-treatment | ||||||
AAGAB |
100%
| 78% | 1.00 | 0.63 |
0.048
|
0.0036
|
ZNF165 |
88%
| 54% | 0.91 | 0.57 | 0.26 | 0.70 |
KRTCAP3 |
79%
| 52% | 0.85 | 0.56 | 0.81 | 0.49 |
RFC2 |
79%
| 40% | 0.85 | 0.35 | 0.51 | 0.44 |
C20orf151 |
70%
| NA | 0.75 | NA | 0.36 | NA |
ARF5 |
70%
| 43% | 0.75 | 0.36 |
0.0038
| 0.20 |
BSPRY |
70%
| 48% | 0.75 | 0.49 | 0.47 | 0.19 |
NGRN |
58%
| NA | 0.66 | Na | 0.53 | Na |
CHST7 |
29%
| 46% | 0.21 | 0.52 | 0.65 | 0.40 |
SLC18B1 |
25%
| Na | 0.18 | NA | 0.55 | NA |
Pre-treatment | ||||||
IGF1R |
74%
| 63% | 0.76 | 0.69 | 0.36 | 0.11 |
CTNNB1 |
71%
| 49% | 0.73 | 0.46 | 0.60 | 0.40 |
SLC20A2 |
71%
| 56% | 0.72 | 0.57 | 0.063 | 0.56 |
HMGCL |
68%
| 47% | 0.67 | 0.45 | 0.10 | 0.97 |
ST6GALNAC5 |
68%
| 52% | 0.69 | 0.53 | 0.6 | 0.28 |
AAGAB |
65%
| 57% | 0.65 | 0.58 | 0.71 | 0.20 |
C1orf51 |
62%
| NA | 0.61 | NA | 0.12 | NA |
KRTCAP3 |
62%
| 54% | 0.63 | 0.57 | 0.78 | 0.78 |
SETDB2 |
50%
| 49% | 0.48 | 0.51 | 0.29 | 0.15 |
FADS2 |
29%
| 48% | 0.27 | 0.5 | 0.14 | 0.73 |