Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Mouse orthotopic transplantation MSA2 12 samples single cell RNA-Seq

ABSTRACT: The goal of this experiment is to examine the effect of STING agonism and interferon signalling in repressing tumour growth through a signalling interplay between cells. Murine tumour organoid lines where orthotopically transplanted into the pancreas of wild-type mice. Tumour bearing mice were treated with the STING agonist MSA-2 or vehicle control. The tumours were dissected and dissociated to single cell for single-cell RNA-sequencing.

INSTRUMENT(S): 10x Chromium v3, Illumina NovaSeq X, FACS Aria-III

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-MTAB-14940 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP170483

REPOSITORIES: biostudies-arrayexpress

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Project description:Genetic and non-genetic heterogeneity within cancer cell populations represents a major challenge to anti-cancer therapies. We currently lack robust methods to determine how pre-existing and adaptive features affect cellular responses to therapies. Here, by conducting clonal fitness mapping and transcriptional characterization using expressed barcodes and single-cell RNA-sequencing, we have developed TraCe-seq, a method that captures at clonal resolution the origin, fate, and differential early adaptive transcriptional programs of cells in a complex population in response to distinct treatments. We used TraCe-seq to benchmark how next-generation dual EGFR inhibitors-degraders compare to standard EGFR kinase inhibitors in EGFR-mutant lung cancer cells. To QC the TraCe-seq strategy, single-cell RNA-seq libraries were generated from a variety of human cancer cell lines transduced with the TraCe-seq library to validate the TraCe-seq strategy. Specifically, 5 different cell lines (PC9, MCF-10A, MDA-MB-231, NCI-H358, and NCI-H1373) were each transduced with a unique TraCe-seq barcode. The transduced cells were selected with puromycin only, dissociated to single cell suspensions, and then mixed together. The complex mixture of the 5 cell lines was profiled by 10X scRNA-seq. Furthermore, transduced NCI-H1373 cells were sorted by FACS to enrich for the top 50% of eGFP positive cells, and sorted cells were cultured briefly and used to construct scRNA-seq libraries and profiled by 10x scRNA-seq. To carry out the full TraCe-seq experiment, ~600 PC9 cells carrying unique TraCe-seq barcodes were expanded over 12 doublings to establish the barcoded population. A subset of the barcoded PC9 population was used to generate scRNA-seq libraries and profiled by 10x scRNA-seq prior to treatment to establish a baseline transcription profile for each barcoded clone. The rest of the cells were then treated for four days with 1 µM erlotinib, 1 µM GNE-069, or 1 µM GNE-104 respectively. scRNA-seq libraries were then generated form the treated cells and profiled by 10x scRNA-seq.

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Mouse orthotopic transplantation MSA2 12 samples single cell RNA-Seq

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