Abstract P2-08-02: Interaction of PIK3CA mutation subclasses with response to preoperative treatment with the PI3K inhibitor pictilisib in patients with estrogen receptor-positive breast cancer

Background: Although preclinical data suggest that combining PI3K inhibitors with endocrine therapy may overcome resistance, results from randomized clinical trials have failed to identify a subgroup of patients that derive a substantial benefit. This preoperative window study assessed whether adding the PI3K inhibitor pictilisib can increase the anti-tumor effects of anastrozole in primary breast cancer and aimed to identify the most appropriate patient population for combination therapy.

Methods: In this randomized, open-label, phase 2 study, 167 postmenopausal women with newly diagnosed, operable, ER-positive, HER2-negative breast cancers were recruited. Participants were randomly allocated (2:1, favoring the combination) to two-weeks of preoperative treatment with anastrozole 1 mg once daily or the combination of anastrozole 1mg with pictilisib 260 mg once daily. The primary endpoint was inhibition of tumor cell proliferation, as measured by change in Ki-67 protein expression between tumor samples taken before and at the end of treatment. Secondary endpoints include induction of apoptosis (Caspase3) and safety. Comprehensive biomarkers analyses included targeted NGS of a comprehensive cancer panel of >400 genes (Ampliseq Comprehensive Cancer panel), copy number variation analyses, and pre- and post-treatment reverse-phase protein arrays (RPPA) and RNA profiling (NanoString nCounter platform).

Results:There was significantly greater geometric mean Ki67 suppression of 82.5% (90% CI, 78.3%-85.8%) for the combination vs 70.7% (61.0%-78.0%) for anastrozole [geometric mean ratio (combination/ anastrozole) 0.60 (0.58-0.85);p=0.01]. Higher baseline Ki67, Luminal B status and/or negative PR status were associated with increased benefit from adding pictilisib. A significant interaction was observed between PIK3CA mutation subtypes [helical domain mutations (HD), kinase domain mutations (KD), wildtype (WT)] and mean Ki67 suppression; the combination/anastrozole geometric mean ratio of Ki67 suppression was 0.48 (0.27-0.84; p=0.02) for patients with HD mutations and 0.63 (0.39–1.0; p=0.05) for patients with PIK3Ca WT, compared to 1.17 (0.57–2.41; p=0.64) for patients with KD mutations. This was largely due to patients with HD mutations showing a particularly poor response to anastrozole alone [mean Ki67 suppression 53.9% (9.5%-76.5%)], that was reversed by the addition of pictilisib [mean Ki-67 suppression 78.1% (71.0%-83.4%)]. On the other hand, patients with KD mutations responded well to anastrozole alone [mean Ki-67 suppression 77.7% (57.0%-88.4%)] and showed no benefit from the addition of pictilisib [mean Ki-67 suppression 73.9% (59.8%-83.0%)]. There was no significant difference in induction of apoptosis between treatment groups. Comprehensive pre- and post-treatment biomarkers analyses will be presented.

Conclusions: Adding pictilisib to anastrozole significantly increases the anti-proliferative response to preoperative treatment with anastrozole. A significant interaction was observed between PIK3CA mutation subtypes, with patients with helical domain mutations showing a particularly poor response to anastrozole alone that was reversed by the addition of pictilisib.

Citation Format: Schmid P, Pinder S, Wheatley D, Zummit C, Macaskill EJ, Hu J, Price R, Bundred N, Hadad S, Shia A, Sarker S-J, Lim L, Mousa K, O'Brien C, Wilson TR, Lackner MR, Gendreau S, Gazinska P, Korbie D, Trau M, Mainwaring P, Thompson A, Purushotham A. Interaction of PIK3CA mutation subclasses with response to preoperative treatment with the PI3K inhibitor pictilisib in patients with estrogen receptor-positive breast cancer [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 P2-08-02.

Abstract P1-15-21: The molecular characterisation of early and advanced breast cancer in a Middle-Eastern breast cancer cohort treated with neo/adjuvant anthracycline+/-taxane-based chemotherapy

Neoadjuvant therapy for breast cancer enables improved conservative operative approaches for breast cancer with similar survival. In addition, it may be used to define clinical as well as molecular systemic therapy sensitivity, aid molecular subtyping analysis of residual disease as well as incorporating potential mechanisms of resistance. Breast cancer in women in the Middle East is characterized by younger median age, more advanced stage at presentation and a higher proportion of patients with triple-negative disease. Recently, Symmans et al. published the results of neoadjuvant anthracycline+/-taxane-based chemotherapy demonstrating a strong association between residual cancer burden (RCB) and overall survival. In this and other cohorts e.g. TCGA, ICGC molecular data of pts from the Middle-East is under-represented.

Aim:

The aim of this project was to define the above parameters in a cohort of women treated with systemic therapy from June 2016 to October 2017 in a Middle Eastern breast cancer referral centre treated in the neo/adjuvant setting. In the neoadjuvant setting we are examining the association between primary biopsy and pathological response tissue (RCB criteria) integrating molecular pathology using massive parallel sequencing (MPS) analyses.

Methodology:

We designed a custom 1000 gene panel using Illumina IDT capture-based assay design and sequenced tumour samples to greater than 500X coverage. Sequencing analysis and variant calling were performed using Broad GAKT best practice; BWA, Mutect2, Oncotator pipeline.

Results:

We present a cohort of 57 pts with median age of 45(26-66), presenting with clinical stage I 2(4%), stageII 30(53%), stage III 25(44%) breast cancer for neoadjuvant (20) or adjuvant (37) anthracycline +/- taxane-based chemotherapy. Standard immunohistochemical (IHC) analysis revealed ER-pos PR-pos HER2-neg 38(67%) ER-pos PR-neg HER2-neg 2(4%) ER-neg PR-neg HER2-pos 3(5%), ER-pos PR-pos HER2-pos 5(9%), TNBC 9(16%). In the neoadjuvant cohort (20) pts, 7 were clinical stage II and 12 stage 3 at presentation. Anthracycline+/-taxane-based chemotherapy achieved pCR/RCB 0 7(35%), RCB I 3(15%), RBC II 4(20%), RCB III 6(30%). All Her2 positive patients received concurrent taxane-trastuzumab.

Implications:

Predictive molecular expression algorithms for response to systemic chemotherapy in the neoadjuvant setting have been published (Hatzis JAMA 2011; Masuda Clin Ca Res 2013).Molecular characterisation of RCB after neoadjuvant chemotherapy has looked at DNA mutations (Jiang PLOS Med 2016) and RNA expression (Lehmann J PLOS One 2016; Echavarria Clin Ca Res 2018). Integration of both provides insight into mechanisms of sensitivity and relapse using pathway analysis. We present genomic data on 20 of the neoadjuvant samples with sufficient quality DNA analysed using a custom designed 1000 gene panel using Illumina IDT capture-based assay design to greater than 500X coverage. The most commonly aberrant genes TP53, PIK3CA, GATA3, KMT2Dwere observed, with notable differences in PAX3, BRCA2, CHD2, FGFR4. Using integrated comprehensive tumour molecular comparisons pre- and post-treatment in the neoadjuvant patients and circulating tumour DNA analyses of the whole cohort will be presented.

Citation Format: Dawood S, Korbie D, Pheasant M, Kazim H, Al Hamadi A, Lloyd C, Dent R, Mainwaring PN. The molecular characterisation of early and advanced breast cancer in a Middle-Eastern breast cancer cohort treated with neo/adjuvant anthracycline+/-taxane-based chemotherapy [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 P1-15-21.

Extracellular vesicles as circulating cancer biomarkers: opportunities and challenges

Extracellular vesicles (EVs) are small, lipid-bound particles containing nucleic acid and protein cargo which are excreted from cells under a variety of normal and pathological conditions. EVs have garnered substantial research interest in recent years, due to their potential utility as circulating biomarkers for a variety of diseases, including numerous types of cancer. The following review will discuss the current understanding of the form and function of EVs, their specific role in cancer pathogenesis and their potential for non-invasive disease diagnosis and/or monitoring. This review will also highlight several key issues for this field, including the importance of implementing robust and reproducible sample handling protocols, and the challenge of extracting an EV-specific biomarker signal from a complex biological background.

Abstract P4-05-16: Quality metric study of real-time targeted massive parallel sequencing (MPS) (ampliseq comprehensive cancer panel (CCP)) and bioinformatics in early breast cancer (EBC) using life technologies ion proton system

We undertook a prospective quality assurance and metric study in 26 women with early breast cancer (EBC) in order to identify issues that may interfere with real-time integration of massive parallel sequencing (MPS) with clinical and pathology parameters for clinical decision making.

Pre-operatively, patients underwent formal informed consent process with the aid of bespoke multimedia (iPad) technology to educate patients on a) the logistical aims of the trial b) somatic and hereditary genomics c) privacy and off target (non-cancer) issues.

On Day 1, seven patients (27%) underwent WLE & SNB, 17 (65%) WLE & AXLND, 2 (7%) Mastectomy & SNB.

Samples (tumour and normal) were collected fresh into Qiagen PaxGene Tissue Container preserving both morphology and biomolecules of the sample with lysis of tissues overnight.

Day 2&3; DNA extraction was performed using the Qiagen DSP kit over 1 hour.

DNA MPS CCP was performed on Life technologies Proton P1 chip using in-house modification of manufacturers protocol. The average time taken to run CCP includes 2 days library preparation; 4 hour sequencing run, 8 hours primary analysis for generating read alignments and sequencing files. The Ampliseq protocol required modifications with respect to template input amount and cycling parameters in order to increase the fidelity of library preparation. Limitations in sequencing depth and read qualities with the current technologies lend themselves to approximately 5-6 samples/sequencing run/day if 500x read depth per amplicon is desired.

Days 4-6 manually curated bioinformatics against publicly available mutation databases (e.g. COSMIC, ENSEMBL etc.)

Day 7 communication of results

Molecular Pathology results

The median age was 57, (32-84), 18 (72%) were postmenopausal. Histopathology invasive ductal 22 (84%), invasive lobular 2 (8%) metaplastic 2 (8%).

TNM Staging: T1b 5 (19%), T1c 9 (35%) T2 12 (46%); N0 23 (88%), N1mi 1 (4%), N1a 1 (4%), N2a 1 (4%).

Hormone receptors antibodies: ER (Roche SP1) Strong 20 (77%), Moderate 1 (4%), Weak 1 (4%), Negative 4 (15%); PR (Roche 1E2) Strong 11 (42%), Moderate 10 (38%), Weak 0 (0%), Negative 5 (19%); HER2 IHC (Ventana 4B5) Strong 1 (4%), Moderate 6 (23%), Weak 6 (23%), Negative 13 (50%); HER2 SISH (Ventana inform single probe); 1 SISH positive (mean copy number 29.6); 4 patients (15%) triple negative.

Molecular aberrations identified included oncogenes TP53 2 (8%), PIK3CA 12 (46%) HRAS 2 (8%), AKT1 1 (4%); tumour suppressor genes MLL3 2 (8%), MSH6 1 (4%), ARID1A 1 (4%), and in the germline in tumour suppressor genes EPHB6 1 (4%) and LTK 1 (4%).

Significant technical and bioinformatic challenges were encountered during the development of this metric study including Ampliseq protocol modification and parameter tuning for variant calling algorithm.

In summary, many challenges face the clinical laboratory developing high throughput MPS using desktop MPS. To date this is the first publication of the new Ion Proton P1 chips in development for real-time clinical decision making. Copy-number variation (CNV), RNA-Seq, Methyl-Seq data will be available for presentation at San Antonio.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-16.