Data from: Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction

Dataset Description

This record is a collection of Whole-genome sequencing (WGS), RNA sequencing (RNA-seq), NanoString's nCounter® Breast Cancer 360 (BC360) Panel and cell viability assay data, generated as part of the study “Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction" by Chen et al., 2022.

The WGS dataset contains raw sequencing data (BAM files) from tumor scraping cells (TSCs) at the time of surgical resection, derived whole-tumor cell (WTC) cultures from each patient's specimen, and normal skin biopsy for germline control, from five (5) breast cancer (BC) patients. Genomic DNA samples were isolated by using the QIAamp DNA mini kit (QIAGEN). The library was prepared by using Illumina TruSeq PCR-free (350 bp) according to the manufacturer’s protocol. The bulk DNA samples were then sequenced by Illumina Hiseq X and processed via the Science for Life Laboratory CAW workflow version 1.2.362 (Stockholm, Sweden; https://github.com/SciLifeLab/Sarek).

The RNA-seq dataset contains raw sequencing data (fastq files) from the TSC pellets at the time of surgical resection, and the pellets of derived WTC cultures with or without tamoxifen metabolites treatment (1 nM 4OHT and 25 nM Z-Endoxifen), from 16 BC patients. 2000 ng RNA was extracted using the RNeasy mini kit (QIAGEN) from each sample, and 1 μg of total RNA was used for rRNA depletion using RiboZero (Illumina). Stranded RNA-seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit (Illumina), and paired-end sequencing was performed on HiSeq 2500 with a 2 x 126 setup using the Science for Life Laboratory platform (Stockholm, Sweden).

The NanoString's nCounter® BC360 Panel dataset contains normalized data from FFPE tissue samples of 43 BC patients. RNA was extracted from the macrodissected sections using the High Pure FFPET RNA Isolation Kit (Roche) following the manufacturer's protocols. Then, 200 ng of RNA per sample were loaded and further analyzed according to the manufacturer’s recommendation on a NanoString nCounter® system using the Breast Cancer 360 code set, which is comprised of 18 housekeeping genes and 752 target genes covering key pathways in tumor biology, microenvironment, and immune response. Raw data was assessed using several quality assurance (QA) metrics to measure imaging quality, oversaturation, and overall signal-to-noise ratio. All samples satisfying QA metric checks were background corrected (background thresholding) using the negative probes and normalized with their mean minus two standard deviations. The background-corrected data were then normalized by calculating the geometric mean of five housekeeper genes, namely ACTB, MRPL19, PSMC4, RPLP0, and SF3A1.

The cell viability assay dataset for the main study contains drug sensitivity score (DSS) values for each of the tested drugs derived from the WTC spheroids of 45 BC patients. For patient DP-45, multiple regions were sampled to establish WTCs and perform drug profiling. For the neoadjuvant setting validation study, DSS values correspond to WTCs of 15 BC patients. For the drug profiling assay, each compound covered five concentrations ranging from 10 μM to 1 nM (2 μM to 0.2 nM for trastuzumab and pertuzumab) in 10-fold dilutions and was dispensed using the acoustic liquid handling system Echo 550 (Labcyte Inc) to make spotted 384-well plates. For the neoadjuvant setting validation assay, we updated the cyclophosphamide into its active metabolite form 4-hydroperoxy cyclophosphamide (4-OOH-cyclophosphamide). Each relevant compound covered eight concentrations ranging from 10 μM to 1 nM (2 μM to 0.2 nM for trastuzumab and pertuzumab) and was dispensed using the Tecan D300e Digital Dispenser (Tecan) to make spotted 384-well plates. In both experiment settings, a total volume of 40 nl of each compound condition was dispensed into each well, for limiting the final DMSO concentration to 0.1% during the treatment period. Further details on the cell viability assay, as well as the DSS estimation are available in the Materials & Methods part of Chen et al., 2022.