Functional genomic dissection of lung cancer in vivo

Tumor suppressor pathways are critical regulators of many different aspects of cancer development, including tumor initiation and growth. Identifying tumor suppressor genes, the pathways they control, and their interactions with other genetic alterations is essential for understanding tumorigenesis. While cancer genomics has revealed important tumor suppressor genes, many remain uncharacterized and there is a growing appreciation that genes and pathways that are not highlighted in cancer genomic studies can be fundamentally important in cancer. The function of putative tumor suppressor genes on cancer growth has been investigated mostly using cell lines and mouse models. Cell lines lack a natural microenvironment and have near optimal growth, while genetically engineered mouse model recapitulate human tumors but are limited in scale. Thus, a comprehensive approach to assess tumor suppressor gene function is lacking. To overcome these limitations, we integrated genetically engineered mouse model, multiplexed CRISPR-based genome editing, and tumor barcoding to assess multiple genotypes on lung tumor initiation and growth in parallel. We hypothesize that many uncharacterized tumor suppressor genes exist, and their effects are highly dependent on genomic context. Our preliminary data and novel in vivo models make us well-positioned to achieve these goals. In Aim 1 we will use CRISPR/Cas9 genome editing and tumor barcoding in a KRAS-driven mouse model to inactivate ~10,000 genes and quantify their effects on lung tumor initiation and growth. We will identify key genetic determinants of lung carcinogenesis and generate novel insights into the molecular mechanisms underlying tumor initiation and growth. In Aim 2, we will determine how tumor suppressor genes function across various oncogenic contexts, using multiplexed in vivo genetic epistasis experiments in EGFR-, KRAS-, and BRAF-driven lung tumors. Finally, in Aim 3, we will use somatic genome editing, diverse oncogene-driven lung cancer models, and in vivo Perturb- seq to study the molecular effects of single and combined tumor suppressor gene inactivation. This will provide a molecular framework to understand the effects of novel tumor suppressor genes and begin to uncover the molecular logic that drives the pattern of genomic alterations in human cancer. The unprecedented scale and resolution of these data will have a broad impact on our understanding of lung tumorigenesis with potential implications for tumor suppression across other cancer types. These innovative, multidisciplinary, and highly quantitative approaches will fundamentally improve our understanding of the pathways and biological processes that drive lung tumorigenesis in the physiologic in vivo setting and begin the systematic deconvolution of gene function during tumorigenesis. Project Number: 1R01CA308157-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Monte Winslow (+1 co-PI) | Institution: STANFORD UNIVERSITY, STANFORD, CA | Award Amount: $635,340 | Activity Code: R01 | Study Section: Cancer Genetics Study Section[CG] View on NIH RePORTER: https://reporter.nih.gov/project-details/11273975