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| Status |
Public on Apr 28, 2022 |
| Title |
Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Our findings reveal a high degree of both genomic and transcriptomic heterogeneity in established and globally utilized PDAC cell lines, custodial variation induced by growing apparently identical PDAC cell lines in different laboratories, and profound 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. Further, while patient-derived organoids (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.
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| Overall design |
Single cell RNA (11 samples), single nuclei ATAC (2 samples), and single cell copy number variation (9 samples)sequencing analysis of pancreatic cancer cell lines and 2 passages of a patient-derived organoid.
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| Web link |
https://www.biorxiv.org/content/10.1101/2021.04.13.439717v1
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| Contributor(s) |
Monberg ME, Geiger H, Sharma R, Lee JJ, Semaan A, Stephens BM, Bernard V, Swartzlander DB, Chen K, Katz MH, Robine N, Maitra A, Guerrero PA, Wang F, Liang S, Wong J |
| Citation(s) |
35752636 |
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| Submission date |
Apr 26, 2021 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Anirban Maitra |
| E-mail(s) |
AMaitra@mdanderson.org
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| Organization name |
The University of Texas MD Anderson Cancer Center
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| Department |
Translational Molecular Pathology
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| Lab |
Maitra laboratory
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| Street address |
6565 MD Anderson Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA725211 |
| SRA |
SRP316396 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE173339_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BED, CSV, H5, TAR) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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