| Literature DB >> 31921107 |
Javier Pérez-Pena1, Janos Tibor Fekete2,3,4, Raquel Páez5,6, Mariona Baliu-Piqué1, José Ángel García-Saenz1, Vanesa García-Barberán1, Aránzazu Manzano1, Pedro Pérez-Segura1, Azucena Esparis-Ogando7, Atanasio Pandiella7, Balázs Gyorffy2,3,4, Alberto Ocana1,5,6.
Abstract
Limited therapeutic options exist for the treatment of patients with triple negative breast cancer (TNBC). Neoadjuvant chemotherapy is currently the standard of care treatment in the early stages of the disease, although reliable biomarkers of response have been scarcely described. In our study we explored whether immunologic signatures associated with inflamed tumors or hot tumors could predict the outcome to neoadjuvant chemotherapy. Publicly available transcriptomic data of more than 2,000 patients were evaluated. ROC plots were generated to assess the response to therapy. Cox proportional hazards regression was computed. Kaplan-Meier plots were drawn to visualize the survival differences. Higher expression of IDO1, CXCL9, CXCL10, HLA-DRA, HLA-E, STAT1, and GZMB were associated with a higher proportion without relapse in the first 5 y after chemotherapy in TNBC. The expression of these genes was associated with a high presence of CD8 T cells in responder patients using the EPIC bioinformatic tool. The strongest effect was observed for STAT1 (p = 1.8e-05 and AUC 0.69, p = 2.7e-06). The best gene-set signature to predict favorable RFS was the combination of IDO1, LAG3, STAT1, and GZMB (HR = 0.28, CI = 0.17-0.46, p = 9.8 E-08, FDR = 1%). However, no influence on pathological complete response (pCR) was observed. Similarly, no benefit was identified in any other tumor subtype: HER2 or estrogen receptor positive. In conclusion, we describe a set of immunologic genes that predict the outcome to neoadjuvant chemotherapy in TNBC, but not pCR, suggesting that this non-time to event endpoint is not a good surrogate marker to detect the long term outcome for immune activated tumors.Entities:
Keywords: chemotherapy treated patients; immunotherapy; outcome; transcriptomic signature; triple negative breast cancer
Year: 2019 PMID: 31921107 PMCID: PMC6930158 DOI: 10.3389/fimmu.2019.02802
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Table of genes included in the four immunological signatures used for our analyses.
| HLA | |
| IFN gamma signature | |
| Expanded immune gene signature | |
| Cytotoxic T lymphocyte (CTL) level signature |
Figure 1Results of immune related genes that predict better outcome in chemotherapy treated TNBC patients. Box-plots comparing responders (higher proportion without relapse in the first 5 years after) vs. non-responders using a Mann-Whitney test and the Area Under the Curve (AUC) [p-values, the strongest cutoff, the False Positive Rate (FPR), and the True Positive Rate (TPR)], were calculated for each gene for: (A) INF gamma signature, (B) expanded immune gene signature, and (C) CTL level signature. All the p-values are significant at FDR < 10%.
Figure 2Overexpression of immune related genes that predict outcome (RFS) in early stage chemotherapy treated TNBC patients. Kaplan-Meier plots show survival differences. (A) INF gamma signature, (B) expanded immune gene signature, and (C) CTL level signature. Correlation to survival was analyzed when using the gene expression as a continuous variable in the Cox regression (yellow box).
ROC analysis results of all the potential combinations for those genes that predicted individually a statistical significance response to chemotherapy in terms of recurrence at 5 years.
| IDO1 + CXCL9 | 0.678 | 8.10E-05 |
| IDO1 + CXCL10 | 0.647 | 1.16E-03 |
| IDO1 + HLA-DRA | 0.634 | 3.10E-03 |
| IDO1 + IRF9 | 0.631 | 3.89E-03 |
| IDO1 + CXCL13 | 0.665 | 2.69E-04 |
| IDO1 + HLA-E | 0.647 | 1.13E-03 |
| IDO1 + LAG3 | 0.628 | 4.60E-03 |
| IDO1 + STAT1 | 0.696 | 1.50E-05 |
| IDO1 + GZMB | 0.634 | 2.99E-03 |
| CXCL9 + CXCL10 | 0.663 | 3.21E-04 |
| CXCL9 + HLA-DRA | 0.660 | 4.00E-04 |
| CXCL9 + IRF9 | 0.682 | 5.50E-05 |
| CXCL9 + CXCL13 | 0.672 | 1.42E-04 |
| CXCL9 + HLA-E | 0.671 | 1.56E-04 |
| CXCL9 + LAG3 | 0.675 | 1.09E-04 |
| CXCL9 + STAT1 | 0.697 | 1.40E-05 |
| CXCL9 + GZMB | 0.672 | 1.45E-04 |
| CXCL10 + HLA-DRA | 0.649 | 9.51E-04 |
| CXCL10 + IRF9 | 0.655 | 5.94E-04 |
| CXCL10 + CXCL13 | 0.656 | 5.59E-04 |
| CXCL10 + HLA-E | 0.650 | 9.46E-04 |
| CXCL10 + LAG3 | 0.646 | 1.28E-03 |
| CXCL10 + STAT1 | 0.677 | 9.00E-05 |
| CXCL10 + GZMB | 0.644 | 1.46E-03 |
| HLA-DRA + IRF9 | 0.624 | 6.32E-03 |
| HLA-DRA + CXCL13 | 0.635 | 2.85E-03 |
| HLA-DRA + HLA-E | 0.621 | 7.34E-03 |
| HLA-DRA + LAG3 | 0.620 | 7.74E-03 |
| HLA-DRA + STAT1 | 0.666 | 2.35E-04 |
| HLA-DRA + GZMB | 0.627 | 4.94E-03 |
| IRF9 + CXCL13 | 0.662 | 3.53E-04 |
| IRF9 + HLA-E | 0.632 | 3.56E-03 |
| IRF9 + LAG3 | 0.615 | 1.12E-02 |
| IRF9 + STAT1 | 0.694 | 1.90E-05 |
| IRF9 + GZMB | 0.644 | 1.46E-03 |
| CXCL13 + HLA-E | 0.649 | 9.51E-04 |
| CXCL13 + LAG3 | 0.666 | 2.34E-04 |
| CXCL13 + STAT1 | 0.687 | 3.50E-05 |
| CXCL13 + GZMB | 0.656 | 5.79E-04 |
| HLA-E + LAG3 | 0.622 | 7.09E-03 |
| HLA-E + STAT1 | 0.688 | 3.30E-05 |
| HLA-E + GZMB | 0.631 | 3.85E-03 |
| LAG3 + STAT1 | 0.694 | 1.70E-05 |
| LAG3 + GZMB | 0.619 | 8.25E-03 |
| STAT1 + GZMB | 0.694 | 1.70E-05 |
| IDO1 + STAT1 + GZMB | 0.696 | 1.40E-05 |
| 0.697 | 1.30E-05 | |
| CXCL10 + STAT1 + GZMB | 0.675 | 1.11E-04 |
| HLA-DRA + STAT1 + GZMB | 0.670 | 1.74E-04 |
| IRF9 + STAT1 + GZMB | 0.693 | 2.00E-05 |
| CXCL13 + STAT1 + GZMB | 0.689 | 3.00E-05 |
| HLA-E + STAT1 + GZMB | 0.689 | 2.90E-05 |
| LAG3 + STAT1 + GZMB | 0.695 | 1.60E-05 |
| 0.699 | 1.10E-05 | |
| IDO1 + STAT1 + GZMB + CXCL10 | 0.678 | 8.70E-05 |
| IDO1 + STAT1 + GZMB + HLA-DRA | 0.676 | 9.80E-05 |
| IDO1 + STAT1 + GZMB + IRF9 | 0.692 | 2.10E-05 |
| IDO1 + STAT1 + GZMB + CXCL13 | 0.694 | 1.90E-05 |
| IDO1 + STAT1 + GZMB + HLA-E | 0.690 | 2.50E-05 |
| 0.697 | 1.40E-05 | |
| 0.699 | 1.10E-05 | |
| IDO1 + STAT1 + GZMB + LAG3 + CXCL10 | 0.678 | 8.70E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA | 0.677 | 9.30E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + IRF9 | 0.692 | 2.10E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + CXCL13 | 0.694 | 1.80E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-E | 0.690 | 2.60E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 | 0.685 | 4.30E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL10 | 0.678 | 8.70E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + IRF9 | 0.680 | 7.20E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + HLA-E | 0.674 | 1.20E-04 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL13 | 0.681 | 6.20E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL10 | 0.681 | 6.20E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + IRF9 | 0.687 | 3.50E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + HLA-E | 0.683 | 5.30E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 | 0.690 | 2.50E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + CXCL10 | 0.686 | 4.00E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + IRF9 | 0.689 | 2.90E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + HLA-E | 0.687 | 3.60E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + IRF9 + CXCL10 | 0.687 | 3.50E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + IRF9 + HLA-E | 0.688 | 3.30E-05 |
| IDO1 + STAT1 + GZMB + LAG3 + HLA-DRA + CXCL9 + CXCL13 + IRF9 + HLA-E + CXCL10 | 0.685 | 4.10E-05 |
The combinations more closely related to better chemotherapy response are displayed in orange-red colors; the combinations related to a better chemotherapy response to a lesser extent are displayed in yellow-green colors.
Figure 3Association of immune related signatures (including the genes with the highest AUC) and relapse free survival for early stage TNBC.
Figure 4Expression of immune related gene does not predict better outcome (RFS) in patients treated with anti-HER2 or endocrine therapies. Box-plots comparing responders (relapse free survival) vs. non-responders using a Mann-Whitney test in anti-HER2 (A) and endocrine therapy (B) treated breast cancer patients. All genes have an FDR > 10%, except for CXCL9 and CXCL10.