GSE129353
Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
To study the interaction between mutated clones using interspecies competition and mathematical models Methods: RNA was extracted from 3-D cultures after 48 hours of growth in spheroids using manufacturer protocol (Qiagen) and sequenced in duplicate using Illumina NextSeq500. libraries were prepared from 500ng of purified RNA using Illumina TruSeq preparation kits.  Sequence reads that passed quality filters were aligned to the UCSC mm9 reference genome and quanitifed using STAR (v2.5.1b). Normalized read counts (FPKM) were calculated using cufflinks and transcriptome profiling was analyzed using DESeq2. We determined that previously sensitive cancer cell clones within heterogeneous tumors will induce drug resistant phenotypes among neighboring cells while under drug pressure Non-mutational drug resistance can arise through drug-induced mechanisms augmented in heterogeneous tumors. Overall design: Wild-type and Dicer1-mutated cell lines were analyzed for transcriptomic variation by RNA sequencing using Illumina NextSeq500.