Phosphoproteomic analysis of neoadjuvant breast cancer suggests that increased sensitivity to paclitaxel is driven by CDK4 and filamin A

Precision oncology research is challenging outside the contexts of oncogenic addiction and/or targeted therapies. We previously showed that phosphoproteomics is a powerful approach to reveal patient subsets of interest characterized by the activity of a few kinases where the underlying genomics is complex. Here, we conduct a phosphoproteomic screening of samples from HER2-negative female breast cancer receiving neoadjuvant paclitaxel (N = 130), aiming to find candidate biomarkers of paclitaxel sensitivity. Filtering 11 candidate biomarkers through 2 independent patient sets (N = 218) allowed the identification of a subgroup of patients characterized by high levels of CDK4 and filamin-A who had a 90% chance of achieving a pCR in response to paclitaxel. Mechanistically, CDK4 regulates filamin-A transcription, which in turn forms a complex with tubulin and CLIP-170, which elicits increased binding of paclitaxel to microtubules, microtubule acetylation and stabilization, and mitotic catastrophe. Thus, phosphoproteomics allows the identification of explainable factors for predicting response to paclitaxel.

Abstract PD2-09: High-throughput phosphoproteomics (HTPS) in neoadjuvant (NEO) breast cancer (BC) reveals clusters of extreme sensitivity to paclitaxel (T)

Background: NGS has elucidated the mutational landscape in BC. However, the correlation between mutational landscapes and complex phenotypic traits such as drug response is yet unclear. The genomic and transcriptomic aberrations coalesce into a diverse number of phosphorylation-driven patterns of activation of the proteome. These patterns are and associated to clinical outcomes of interest. The specific nature of the phosphopeptides in a profile versus another can be driven by a small number of activated kinases. In the past we relied on mass-spectrometry-based HTPS to build a kinase-based classification of triple-negative breast cancer (TNBC, Nat. Comms, in press), which is more parsimonious than gene-centered classifications and uncovers new actionable targets. We implemented this methodology to find predictors of response to T in early BC.

Methods: Training set: fresh baseline and day+15 tumor biopsies form a trial in NEO HER2-negative BC (N=139) that randomized patients to T (80 mg/m2 weekly x12) plus placebo or nintedanib (150 mg b.i.d) were processed with a hybrid ion trap-orbitrap mass spectrometer after TiO2 phospho-enrichment. Phosphoprofiles were compared pair-wise according to the following factors: day 0 versus day + 15, standard versus experimental arm, pathologic response Symmans/Pusztai (Symmans) 0/1 vs 2/3. Kinases driving each phosphoprofile were solved by an in silico algorithm termed kinase-set enrichment analysis (KSEAS). Validation set: an in-house designed and previously validated mass-spectrometry-to-immunohistochemistry translation algorithm was used to validate the kinases enriched in the profiles from the baseline samples of patients achieving Symmans 0/1 (pCR) or Symmans=3 in the training set. Probes against those kinases were validated in an independent dataset of 160 HER2-negative patients receiving NEO T followed by AC. H-score of each activated kinase was divided in quartiles (Q1 to Q4), and upper-quartiles (Q1) of each kinase were tested in a multivariate logistic regression model to predict pCR adjusted by T, N, age, G, ER/PR and Ki67.

Results: >2.5 millions of spectra were captured, identifying >35000 unique phosphopeptides mapping to >2500 unique proteins per sample. Training set: KSEAS revealed that a high activity of CDK4 and pP70S6K drove the baseline phosphoprofiles of the patients obtaining pCR in the T arm, whereas pSTAT3, pSrc and BARD drove that of the patients achieving Symmans= 3. In the validation set, H-score cut-offs for Q1 were 1.21, 0.69, 0.79, 1.64 and 1.54 for pP70S6K, CDK4, pSTAT3, pSrc and BARD. TNBC patients with Q1 pP70S6K or Q1 CDK4 achieved pCR in 100% of the cases (versus 45% in Q2-4). In the HR+ cases, the pCR rate for Q1 patients was 50% and 61% respectively. In the multivariate model (all patients), having Q1 pP70S6K or CDK4 multiplied by 2.3- and 3.6-fold, respectively, the probability of achieving pCR (P<0.05). Regarding Symmans=3, BARD and pSTAT3 lost significance in the validation but not pSrc (2.5-fold less probability of pCR, P<0.005).

Conclusions: HTPS is a useful tool to find associations with complex traits. TNBC and HR+ patients with high pP70S6K or CDK4 receiving NEO T-based chemotherapy achieve very high rates of pCR.

Citation Format: Quintela-Fandino M, Lluch A, Manso L, Calvo I, Cortes J, Garcia-Saenz JA, Zagorac I, Tapial-Martinez P, Gomez-Lopez G, Fustero C, Muñoz J, Gonzalez-Cortijo L, Mouron S. High-throughput phosphoproteomics (HTPS) in neoadjuvant (NEO) breast cancer (BC) reveals clusters of extreme sensitivity to paclitaxel (T) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD2-09.

Abstract OT2-07-02: CNIO-BR-009 trial: Targeting mitochondrial metabolism with ME-344 in breast cancer upon bevacizumab-induced vascular normalization: A phase 0 randomized clinical trial

Background: Antiangiogenic agents have shown activity in breast cancer; however their use should be optimized. One potential solution is designing rational combinations based on blocking specific mechanisms of resistance. We previously published that tumors exposed to bevacizumab (BEV) can either experience vascular pruning (followed by increased tumor hypoxia) or vascular normalization (followed by a switch to mitochondrial metabolism). FDG-PET can monitor which pattern is occurring as early as 8 days after the first dose (Mol Oncol; 10: 704-18). We have also shown that when vascular normalization occurs, tumors become highly sensitive to mitochondrial inhibitors (Cell Rep 2016; 15: 1-14). ME-344 is a mitocondrial respiration inhibitor that has recently completed phase I. We sought to test the pharmacodynamic effects of ME-344 and its effects in Ki67 and cleaved caspase 3 (CC3) after single-dose BEV in treatment-naive early HER2-negative breast cancer patients, and whether the effects are restricted or not to those patients experiencing vascular normalization as predicted by FDG-PET.

Trial design

Placebo-controlled, two-arm, randomized, multicentric phase 0 trial. Treatment-naive HER2-negative breast cancer patients undergo a breast FDG-PET and a baseline tumor biopsy (frozen and paraffinized cores), followed by a single (15 mg/kg) BEV dose. FDG-PET is repeated on day +8. Patients are then randomized to three ME-344 (10 mg/kg) doses or placebo (days +8, +15 and +22). A second biopsy is then harvested, ending trial procedures. Patients can then follow surgery or neoadjuvant treatment according to their physician's criterion. Serial paraffinized biopsies are used to measure Ki67 and CC3; frozen biopsies are used for measuring mitochondrial activity with SDH enzymo-histochemistry (EHC) and assessing vessel architecture. Toxicity is graded with NCI CTC AE V4.03 criteria.

Eligibility criteria

1) Women >18 year old; 2) diagnosed of HER2-negative breast cancer; 3) patients must be treatment-naive; 4) ECOG 0/1; 5) lack of neuropathy; 6) primary tumor > 1cm .

Specific aims

Primary:

1) To study the effects in cell replication and cell death as a surrogate measure of efficacy of ME-344 added to BEV in treatment-naive breast cancer.

2) To determine if FDG-PET accurately detects patients experiencing vascular normalization early after BEV dosing.

3) To observe the effects of ME-344 in mitochondrial activity at the tumor level by performing SDH EHC.

4) To assess if ME-344 efficacy (measured by changes in CC3 and Ki67) is restricted or not to those patients experiencing vascular normalization and mitochondrial switch.

Secondary:

5) To study the tolerability of the combination of BEV plus ME-344.

Statistical methods

The sample size is calculated on the basis of the expected change in Ki-67 staining in the primary tumors in patients receiving ME-344 (-10% on average). With an α and β errors of 5% and 20% respectively, the minimum number of patients necessary to observe a 10% decrease is 20 per arm. Changes in CC3, KI67, SDH activity and FDG-PET SUV will be compared with intra-subject measurements and Z-scores.

Accrual: 13 of 40 planned patients.

Contact: acsalgado86@gmail.com

Citation Format: Cortes A, Apala JV, Malon D, Guerra J, Gion-Cortes M, Manso L, Hornedo J, Gonzalez-Cortijo L, Mouron S, Quintela-Fandino M. CNIO-BR-009 trial: Targeting mitochondrial metabolism with ME-344 in breast cancer upon bevacizumab-induced vascular normalization: A phase 0 randomized clinical trial [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr OT2-07-02.

Abstract OT3-01-02: CNIO-BR-008 trial: Reversion of T-cell exhaustion caused by chronic treatment with hypoxia-inducing antiangiogenic treatment by durvalumab in HER2-negative breast cancer: A pilot proof-of-concept trial

Background: The role of immune checkpoints in tumor progression is less relevant in breast cancer than in other malignancies. However, in preclinical experimentation we found a niche for immune checkpoint inhibitors. In an immunocompetent model of HER2-negative breast cancer (MMTV-PyMT) we observed that antiangiogenic agents may induce either a tumor normoxic or hypoxic adaptation. Normoxic adaptation leads to a therapeutically exploitable dependence on mitochondrial metabolism (Cell Rep 2016; 15: 1-14). Hypoxic adaptation (usually caused by monoclonal antibody type antiangiogenics) induces an increase in PGE2 and PGA synthesis, followed by a switch of the tryptophan metabolism from 5HIAA to kinurenine that culminates in differentiation of naive T-cells to Tregs and expression of PD-L1 in the hypoxic areas. The exhausted T-cell response observed in this model can be restored with PD-L1 inhibitors. We sought to prove the relevance of T-cell exhaustion an its reversibility by the anti-PD-L1 antibody durvalumab in patients receiving chronic bevacizumab (Bev).

Trial design

Single-arm, prospective, multicentric, phase II open-label trial. Patients receiving Bev maintenance after a chemotherapy+Bev regimen administered in the first line of metastatic disease that experience disease progression (PD) during maintenance will be candidates. The treatment will start by adding durvalumab (10 mg/kg q2w) to the ongoing Bev (15 mg/kg q3 w). Patients will undergo serial tumor biopsies, tumor-cfDNA sequencing (baseline and progression), and immunophenotyping (baseline and q4w). RECIST/I-RECIST and NCI CTC AE V4.03 criteria will be used for assessing disease response and toxicity.

Elegibility criteria

Women >18 year old diagnosed of HER2-negative advanced breast cancer; 2) have received chemotherapy plus Bev for the first line treatment and experienced PR, CR or SD, 3) followed by maintenance with three-weekly Bev in monotherapy for at least 6 weeks before diagnosis of PD. 4) Concurrent hormonal therapy is allowed for ER+ patients, but reception of previous immunotherapy is precluded. 5) Adequate organ function defined according to standard parameters.

Specific aims

Primary:

1) To determine the relative percentages of innate and adaptive immune cell subpopulations and ascertain the status of T-cell function and polarization by multiparametric flow cytometry in patients with acquired resistance against Bev

2) To assess the reversibility of the abnormalities evidenced in (1) by durvalumab

3) To determine the disease control rate of the combination, and its relationship with (1) and (2)

Secondary:

4) To determine potential tumor neoantigens generated by chronic tumor hypoxia secondary to the antiangiogenic treatment.

Statistical methods

The sample size is calculated on the basis of the expected change in the Treg percentage in peripheral blood (10%), with an alpha and beta errors of 5% and 20% respectively. The minimum number of patients necessary to observe a 10% decrease is 25. Changes in lymphocytes will be compared with intra-subject measurements and Z-scores.

Accrual: 2 of 25 (target accrual) patients have been recruited.

Contact info: mquintela@cnio.es.

Citation Format: Quintela-Fandino M, Manso L, Mouron S, Lopez-Acosta JF, García-Saenz JA, Holgado E, Pascual-Martinez T, Medicna L, Guerra J, Gonzalez-Cortijo L, Mañes S. CNIO-BR-008 trial: Reversion of T-cell exhaustion caused by chronic treatment with hypoxia-inducing antiangiogenic treatment by durvalumab in HER2-negative breast cancer: A pilot proof-of-concept trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-01-02.

Abstract P4-21-16: Phase III trial to evaluate patient´s preference for subcutaneous versus intravenous trastuzumab administration in patients with HER2 positive advanced breast cancer (ABC) under IV trastuzumab (IV-t) treatment for at least 4 months. ChangHER-SC study (GEICAM/2012-07)

Background: Patients with HER2-positive ABC, receive anti-HER2 treatment for several months or even years. IV-t is administered weekly or 3-weekly, mandating patients to visit the hospital on a regular basis to receive infusions. This has inconveniences for patients and increase treatment costs. Subcutaneous administration could improve convenience of trastuzumab therapy. This study was designed to evaluate patient's preference for IV-t or SC trastuzumab (SC-t) in ABC patients.

Methods:This is a phase III, open label, multicenter study inpatients with HER2 positive ABC, receiving IV-t for at least 4 months and without evidence of disease progression. Patients received 600 mg of SC-t, either from a vial or from a single injection device (SID), every 3 weeks for 4 cycles. Before starting SC-t, patients received an additional IV-t cycle. Patients were randomized 1:1 to arm A, receiving 2 cycles of SC-t with vial followed by 2 cycles with SID or arm B, receiving the opposite sequence. After cycle 4, patients decided to continue with IV-t or SC-t till disease progression. Stratification criteria were the associated therapy (Chemotherapy, Hormone-therapy or none) and its administration route (IV, oral or none). Patients completed a questionnaire of experiences and preferences at three time points: before starting SC-t, after cycle 2 and after cycle 4. Health Care Professionals completed a satisfaction questionnaire every 5 patients. The primary objective was to evaluate patient´s preference for IV-t or SC-t (after cycle 2) and, secondary objectives were, to evaluate patient´s preference between the two SC-t administrations (vial or SID) after cycle 4, Health Care Professional satisfaction, associated costs of the administration options (Time and Motion pharmacoeconomic study) and safety.

Results: From September-13 to July-15, 166 patients were randomized (81 arm A, 85 arm B) in 26 Spanish sites from GEICAM. Median age was 60 years (35-93), 88% of patients were postmenopausal and 123 and 42 had an ECOG PS of 0 and 1, respectively. The median duration of prior IV-t for ABC was 1.8 years (range: 0.3-14). Patients received a median of 2 previous lines of Chemotherapy and/or Hormone-therapy (range: 1-9). Twenty patients were receiving pertuzumab at inclusion. According to patient questionnaires completed after cycle 2, 137 patients preferred the SC-t (66 arm A, 71 arm B), 11 the IV-t (6 arm A, 5 arm B), 11 didn't have a preference (4 arm A, 7 arm B), and 7 didn't answer (3 progressed, 2 withdrew participation before cycle 2 and 2 unknown reason). Three of the 11 patients choosing IV-t were receiving IV treatment as accompanying therapy; after cycle 4 five of these 11 patients finally continued with SC-t, 5 with IV-t and 1 progressed. From the 11 patients without any preference 7 received SC-t, 2 receive IV-t and 2 progressed; from the 137 patients preferring SC-t, 125 actually received it, 3 received IV-t and 9 progressed.

Conclusions: Our study shows that 82.5% of patients preferred the SC-t over the IV-t. Treatment choice was not influenced by the accompanying therapy.

Citation Format: Ciruelos EM, Montaño Á, Rodríguez CA, González-Flores E, Lluch A, Garrigós L, Quiroga V, Antón A, Malón D, Chacón JI, Velasco M, Gonzalez-Cortijo L, Jolis L, Pascual T, Amigo Y, Casas M, Cámara MC, Carrasco E, Casas A. Phase III trial to evaluate patient´s preference for subcutaneous versus intravenous trastuzumab administration in patients with HER2 positive advanced breast cancer (ABC) under IV trastuzumab (IV-t) treatment for at least 4 months. ChangHER-SC study (GEICAM/2012-07) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-21-16.

Abstract OT3-02-07: A phase II study to compare fulvestrant (F) 500mg plus placebo versus (vs) F 500mg plus palbociclib (P) as first line treatment for postmenopausal women with hormone receptor (HR)-positive advanced breast cancer (BC) sensitive to endocrine therapy (ET). “The FLIPPER study” (GEICAM/2014-12)

Background: Delaying/overcoming resistance to ET in HR-positive HER2-negative BC patients (pts) is a major need to futhrt improve safe and efficacious treatment options. F is a selective estrogen receptor (ER) downregulator currently indicated for the treatment of HR-positive metastatic BC in postmenopausal women with disease progression following anti-estrogen therapy. In FIRST trial F 500mg improved median time to progression (TTP) over anastrozole (23.4 vs 13.1 months, respectively) in untreated metastatic BC. P is a selective reversible inhibitor of cyclin-dependent kinase 4/6. FDA granted its accelerated approval based on progression-free survival (PFS) in combination with letrozole for postmenopausal women with ER-positive and HER2-negative advanced BC as initial ET (PALOMA-1). In another study, after progression to ET, P in combination with F resulted in longer PFS than F alone (PALOMA-3).

The high median TTP achieved with F alone (FIRST) coupled with the significant benefit of adding P to F (PALOMA-3) suggest that F 500mg in combination with P in the first-line setting may significantly improve long-term disease control.

Trial Design:This is an international, randomized, double-blind, multicentre phase II study comparing F 500mg in combination with P vs F 500mg plus placebo as first line therapy in postmenopausal women with HR-positive, HER2-negative metastatic BC who have received ≥5 years of adjuvant ET for early disease and remained disease free for >12 months following its completion or have “de novo” metastatic disease. HR and HER2 status will be based on central testing on the most recent tumour biopsy. Patients will be randomized 1:1. The primary objective is to compare the efficacy of both treatment arms in terms of PFS at 1 year according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 by investigator assessment. As secondary efficacy objectives,PFS, Objective Response Rate (ORR), Clinical Benefit Rate (CBR), Overall Survival (OS), and 1-year and 2-year survival probabilities, have been considered. Other secondary objectives include the comparison of safety, tolerability and health-related quality of life between the treatment arms. As exploratory objectives, the identification of promising biomarkers related with response to study therapy and primary/acquired drug resistance. Pts will be stratified by the site of disease (visceral vs non-visceral) and disease presentation at study entry (recurrent disease vs metastatic “de novo”). With a sample size of 190 pts, the analysis would have 80% power to detect a difference between both treatment arms, assuming PFS proportions of 0.545 and 0.695, respectively. This study is sponsored by GEICAM and Cancer Trials Ireland (formerly ICORG) is also participating. Recruitment started in February 2016 with 14 pts included. Analysis of the primary endpoint is planned for Q1 2018. ClinicalTrials.gov identifier:NCT02690480.

Citation Format: Moreno F, Martínez-Jañez N, Garau I, Guerra JA, Alarcón J, Bermejo B, Gonzalez-Cortijo L, Bueno C, Lao J, Bezares S, Rosell L, Blanch A, Caballero R, Carrasco E, Rojo F, Martín M, O'Connor M, Hernando A, Albanell J. A phase II study to compare fulvestrant (F) 500mg plus placebo versus (vs) F 500mg plus palbociclib (P) as first line treatment for postmenopausal women with hormone receptor (HR)-positive advanced breast cancer (BC) sensitive to endocrine therapy (ET). “The FLIPPER study” (GEICAM/2014-12) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OT3-02-07.