Metadata and data files supporting the related article: PIK3CA and MAP3K1 alterations imply luminal A status and are associated with clinical benefit from pan-PI3K inhibitor buparlisib and letrozole in ER+ metastatic breast cancer

In this study, the authors analysed next generation sequencing data from a targeted panel of known recurrently mutated genes in breast cancer in a cohort of patients from two phase Ib trials of buparlisib and alpelisib, each in combination with the aromatase inhibitor letrozole

Data access: Datasets in Prism file format (and accompanying .txt file versions of these datasets) supporting figures 1, 2, 3 and 4 of the published article as described in Nixon et. al.xlsx are publicly available in the figshare repository (https://doi.org/10.6084/m9.figshare.9700373) as part of this data record. Next-generation sequencing MSK-IMPACT data generated during this study, are publicly available in cBioPortal at https://identifiers.org/cbioportal:brca_mskcc_2019. NanoString normalized linear count data are publicly available in Supplementary dataset 2 of the published article. The datasets analysed during this study are publicly available in cBioPortal at https://identifiers.org/cbioportal:cellline_ccle_broad (CCLE analysis) and https://identifiers.org/cbioportal:brca_tcga_pub (TCGA analysis and PIK3CA-GS analysis). Patient-derived xenograft and drug treatment data analysed in this study are publicly available in supplementary dataset 1 of the published article. The latter were originally derived from supplementary table 1 of the following published article: https://doi.org/10.1038/nm.3954.

Study approval: Approval for the study was obtained from the ethics committees (IRB#101057, Vanderbilt University Medical Center) of the participating institutions and regulatory authorities. All patients gave written informed consent. The study followed the Declaration of Helsinki and Good Clinical Practice guidelines.

Study aims and methodology: The goal of this analysis was to determine possible biomarkers aside from PIK3CA mutations status that were associated with clinical benefit to buparlisib and alpelisib, each in combination with the aromatase inhibitor letrozole. Patients in both trials were endocrine refractory (at least 1 line of prior failed endocrine therapy), representing an area of therapy that could be greatly impacted by new treatment options.

The authors performed correlative molecular characterization of primary and metastatic tissue from patients enrolled in a phase Ib study combining buparlisib (NVP-BKM-120), a pan-PI3K inhibitor, with letrozole in estrogen receptor-positive (ER+), human epidermal growth factor-2 (HER2)-negative, metastatic breast cancer. The study involved analysing next generation sequencing data from a targeted panel of known recurrently mutated genes in cancer in a cohort of patients from two phase Ib trials of buparlisib and alpelisib, each in combination with the aromatase inhibitor letrozole.

Patients: The patients described in this study had histologically confirmed ER-positive/human epidermal growth factor receptor 2-negative metastatic breast cancer refractory to at least one line of endocrine therapy in the metastatic setting or diagnosed with metastatic breast cancer during or within 1 year of adjuvant endocrine therapy. All patients were treated with buparlisib or alpelisib.

MSK-IMPACT targeted next generation sequencing (tNGS) profiling for 341 genes was carried out using pre-study biopsy (where available) material or archival tissue from 33 patients subsequently enrolled and treated according to the study protocol. This was done to determine potential genomic correlates with clinical benefit to buparlisib and letrozole in metastatic ER+ breast cancer patients.

MAP3K1 siRNA knockdown in the following cell lines: MCF7, T47D and BT483. The authors also generated T47D cells stably expressing short-hairpin RNA (shRNA) targeting MAP3K1. Real-time Polymerase Chain Reaction was carried out to determine the levels of mRNA knock down in the aforementioned cell lines. Following knockdown of MAP3K1, cells were treated with buparlisib, and cell viability assays were carried out. Using a custom-designed NanoString code set targeting the PAM50 geneset, the authors ascertained the molecular subtype by testing the association to luminal A or luminal B PAM50 centroids.

Please read the published article for more details on the methodology and on the analyses of publicly available datasets (CCLE analysis, TCGA analysis, PIK3CA-GS analysis and analysis of patient-derived xenograft inhibitor data).

Datasets supporting the figures in the published article: Data file names, data file formats and persistent links to datasets generated and analysed during this study, are described in the Excel file Nixon et. al.xlsx.

Software needed to access the datasets: All the files in Prism (.pzfx) file format in this data record can only be accessed using the GraphPad Prism 5 software or a later version of the software.