Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
Data files
Sep 15, 2023 version files 836.39 MB
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README.md
993 B
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tumors.csv
836.39 MB
Abstract
Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the interactions between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged—the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context—and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.
README: Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
This csv provides information about the 13,926,734 tumors that are the basis of all main manuscript figures.
Description of the data and file structure
The columns, with descriptions, are as follows:
- "oncogene": the CRE-inducible oncogene allele in the mouse germline driving tumor growth.
- "is_cas9_present": whether a CRE-inducible Cas9 allele is present in the mouse germline.
- "is_tp53_floxed": whether Trp53 is flanked by LoxP sites in the mouse germline.
- "study_duration_wks": the duration of tumor growth measured in weeks.
- "mouse_id": a unique id for each mouse.
- "sg_rna": the sgRNA present in this tumor.
- "tumor_size_cells": the estimated size of the tumor measured in absolute number of cells.
- "tumor_read_count": the number of raw NGS reads corresponding to this tumor.
Code/Software
Methods described in manuscript.
Methods
See manuscript methods.