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<br><b>Data access:</b> Datasets in <b>Prism file format</b> (and accompanying <b>.txt file versions</b> 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 (<b>https://doi.org/10.6084/m9.figshare.9700373</b>) as part of this data record. Next-generation sequencing MSK-IMPACT data generated during this study, are publicly available in cBioPortal at <b>https://identifiers.org/cbioportal:brca_mskcc_2019</b>. 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 <b>https://identifiers.org/cbioportal:cellline_ccle_broad</b> (CCLE analysis) and <b>https://identifiers.org/cbioportal:brca_tcga_pub</b> (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: <b>https://doi.org/10.1038/nm.3954</b>.<br><b>Study approval</b>: 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.<br><b>Study aims and methodology:</b> The goal of this analysis was to determine possible biomarkers aside from <i>PIK3CA </i>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.<br>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.<br><i>Patients:</i> 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.<br><i>MSK-IMPACT targeted next generation sequencing</i> (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.<br><i>MAP3K1 siRNA knockdown</i> in the following cell lines: MCF7, T47D and BT483. The authors also generated T47D cells stably expressing short-hairpin RNA (shRNA) targeting MAP3K1. <i>Real-time Polymerase Chain Reaction</i> was carried out to determine the levels of mRNA knock down in the aforementioned cell lines. Following knockdown of <i>MAP3K1</i>, cells were treated with buparlisib, and <i>cell viability assays</i> were carried out. Using a custom-designed <i>NanoString</i> code set targeting the PAM50 geneset, the authors ascertained the molecular subtype by testing the association to luminal A or luminal B PAM50 centroids.<br>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).<br><b>Datasets supporting the figures in the published article: </b>Data file names, data file formats and persistent links to datasets generated and analysed during this study, are described in the Excel file <b>Nixon et. al.xlsx.</b><b><br></b><b>Software needed to access the datasets:</b> All the files in Prism (.<b>pzfx</b>) file format in this data record can only be accessed using the GraphPad Prism 5 software or a later version of the software.<br>

本研究中，研究者针对两项分别将buparlisib与alpelisib联合芳香化酶抑制剂来曲唑（letrozole）的Ib期临床试验队列中的乳腺癌患者，对其已知复发性突变癌症基因靶向测序面板的下一代测序（next generation sequencing, NGS）数据进行了分析。<br><b>数据获取：</b>本数据记录中，支撑已发表论文图1、2、3、4的Prism文件格式（及配套的.txt格式文件版本）数据集，已公开存放在figshare知识库（https://doi.org/10.6084/m9.figshare.9700373）中，相关信息详见Nixon et. al.xlsx文件。本研究产生的下一代测序MSK-IMPACT数据，已公开存放在cBioPortal平台，链接为https://identifiers.org/cbioportal:brca_mskcc_2019。NanoString标准化线性计数数据已公开存放在已发表论文的补充数据集2中。本研究分析的其他数据集可在cBioPortal平台获取，对应链接分别为https://identifiers.org/cbioportal:cellline_ccle_broad（CCLE分析，即癌细胞系百科全书Cancer Cell Line Encyclopedia分析）与https://identifiers.org/cbioportal:brca_tcga_pub（TCGA分析，即癌症基因组图谱The Cancer Genome Atlas分析，以及PIK3CA基因特征分析）。本研究分析的患者来源异种移植瘤及药物治疗数据，已公开存放在已发表论文的补充数据集1中，该部分数据最初来源于下述已发表论文的补充表1：https://doi.org/10.1038/nm.3954。<br><b>研究伦理审批：</b>本研究已获得参与机构的伦理委员会（范德堡大学医学中心，IRB#101057）及监管机构的批准。所有患者均签署书面知情同意书，本研究遵循《赫尔辛基宣言》及《药物临床试验质量管理规范》（Good Clinical Practice, GCP）指南。<br><b>研究目标与方法：</b>本分析的目标是探寻除PIK3CA突变状态外，与buparlisib、alpelisib分别联合来曲唑治疗临床获益相关的潜在生物标志物。两项试验中的患者均为内分泌治疗难治性人群（至少接受过一线内分泌治疗失败），该领域亟需新型治疗方案的突破。<br>研究者对两项Ib期临床试验队列中的患者样本进行了相关性分子表征分析，这两项试验分别为buparlisib（NVP-BKM-120，一种泛PI3K抑制剂（pan-PI3K inhibitor））联合来曲唑治疗雌激素受体阳性（estrogen receptor-positive, ER+）、人表皮生长因子受体2阴性（human epidermal growth factor receptor 2-negative, HER2-）转移性乳腺癌的研究。本研究的核心分析内容为：针对乳腺癌中已知复发性突变癌症基因的靶向测序面板的下一代测序数据，该分析覆盖了上述两项Ib期试验的患者队列。<br><i>患者：</i>本研究纳入的患者经组织学确诊为ER+/HER2-转移性乳腺癌，且满足以下任一条件：在转移性疾病治疗阶段至少接受过一线内分泌治疗失败；在辅助内分泌治疗期间或结束后1年内确诊为转移性乳腺癌。所有入组患者均接受了buparlisib或alpelisib治疗。<br><i>MSK-IMPACT靶向下一代测序（tNGS）：</i>本研究对33例符合入组标准并按研究方案接受治疗的患者，采用研究前活检组织（若可获取）或存档组织进行了涵盖341个基因的MSK-IMPACT靶向NGS测序，旨在明确转移性ER+乳腺癌患者接受buparlisib联合来曲唑治疗的临床获益相关潜在基因组关联因素。<br><i>细胞功能实验：</i>研究者在MCF7、T47D及BT483细胞系中进行了MAP3K1的小干扰RNA（small interfering RNA, siRNA）敲低实验，同时构建了稳定表达靶向MAP3K1的短发夹RNA（short hairpin RNA, shRNA）的T47D细胞株。通过实时定量聚合酶链反应（Real-time Polymerase Chain Reaction）检测上述细胞系中MAP3K1的mRNA敲低效率。在MAP3K1敲低后，研究者用buparlisib处理细胞并进行细胞活力检测。研究者还使用针对PAM50基因集的定制化NanoString编码集，通过与管腔A型、管腔B型PAM50质心的关联分析，确定了样本的分子亚型。<br>如需了解研究方法及公开数据集（CCLE分析、TCGA分析、PIK3CA-GS分析及患者来源异种移植瘤抑制剂数据的分析）的更多细节，请参阅已发表论文。<br><b>支撑论文图表的数据集：</b>本研究产生并分析的数据集的文件名、文件格式及永久链接，详见Excel文件Nixon et. al.xlsx。<br><b>数据集访问所需软件：</b>本数据记录中所有Prism格式（.pzfx）的文件，仅可通过GraphPad Prism 5或更高版本软件打开。