Occult Polyclonality of Preclinical Pancreatic Cancer Models Drives In Vitro Evolution

Authors

Maria E Monberg
Heather Geiger
Jaewon J Lee
Roshan Sharma
Alexander Semaan
Vincent Bernard
Justin Wong
Fang Wang
Shaoheng Liang
Daniel B Swartzlander
Bret M Stephens
Matthew H G Katz
Ken Chen
Nicolas Robine
Paola A Guerrero
Anirban Maitra

Publication Date

6-25-2022

Journal

Nature Communications

Abstract

Heterogeneity is a hallmark of cancer. The advent of single-cell technologies has helped uncover heterogeneity in a high-throughput manner in different cancers across varied contexts. Here we apply single-cell sequencing technologies to reveal inherent heterogeneity in assumptively monoclonal pancreatic cancer (PDAC) cell lines and patient-derived organoids (PDOs). Our findings reveal a high degree of both genomic and transcriptomic polyclonality in monolayer PDAC cell lines, custodial variation induced by growing apparently identical cell lines in different laboratories, and transcriptomic shifts in transitioning from 2D to 3D spheroid growth models. Our findings also call into question the validity of widely available immortalized, non-transformed pancreatic lines as contemporaneous "control" lines in experiments. We confirm these findings using a variety of independent assays, including but not limited to whole exome sequencing, single-cell copy number variation sequencing (scCNVseq), single-nuclei assay for transposase-accessible chromatin with sequencing, fluorescence in-situ hybridization, and single-cell RNA sequencing (scRNAseq). We map scRNA expression data to unique genomic clones identified by orthogonally-gathered scCNVseq data of these same PDAC cell lines. Further, while PDOs are known to reflect the cognate in vivo biology of the parental tumor, we identify transcriptomic shifts during ex vivo passage that might hamper their predictive abilities over time. The impact of these findings on rigor and reproducibility of experimental data generated using established preclinical PDAC models between and across laboratories is uncertain, but a matter of concern.

Keywords

Carcinoma, Pancreatic Ductal, Cell Line, Tumor, DNA Copy Number Variations, Humans, Pancreas, Pancreatic Neoplasms, Reproducibility of Results, Pancreatic cancer, Genome informatics, Pancreatic cancer, Tumour heterogeneity, Cancer genomics

DOI

10.1038/s41467-022-31376-3

PMID

35752636

PMCID

PMC9233687

PubMedCentral® Posted Date

6-25-2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes