Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis
Ameen A. Salahudeen,
Jose A. Seoane,
Kanako Yuki,
Amanda T. Mah,
Amber R. Smith,
Kevin Kolahi,
Sean M. De la O,
Daniel J. Hart,
Jie Ding,
Zhicheng Ma,
Sammy A. Barkal,
Navika D. Shukla,
Chuck H. Zhang,
Michael A. Cantrell,
Arpit Batish,
Tatsuya Usui,
David E. Root,
William C. Hahn,
Christina Curtis,
Calvin J. Kuo
Affiliations
Ameen A. Salahudeen
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA; University of Illinois at Chicago College of Medicine, Department of Medicine, Division of Hematology and Oncology, Chicago, IL 60612, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA; University of Illinois Cancer Center, Chicago, IL 60612, USA; Corresponding author
Jose A. Seoane
Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA; Cancer Computational Biology Group, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; Corresponding author
Kanako Yuki
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Amanda T. Mah
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Amber R. Smith
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Kevin Kolahi
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Sean M. De la O
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Daniel J. Hart
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Jie Ding
Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA
Zhicheng Ma
Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA
Sammy A. Barkal
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Navika D. Shukla
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Chuck H. Zhang
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Michael A. Cantrell
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Arpit Batish
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
Tatsuya Usui
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA
David E. Root
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
William C. Hahn
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Department of Medical Oncology, 450 Brookline Avenue, Boston, MA 02215, USA
Christina Curtis
Stanford University School of Medicine, Department of Medicine, Divisions of Oncology, Stanford, CA 94305, USA; Stanford University School of Medicine, Department of Medicine, Divisions of Genetics, Stanford, CA 94305, USA
Calvin J. Kuo
Stanford University School of Medicine, Department of Medicine, Divisions of Hematology, Stanford, CA 94305, USA; Corresponding author
Summary: Somatic copy number gains are pervasive across cancer types, yet their roles in oncogenesis are insufficiently evaluated. This inadequacy is partly due to copy gains spanning large chromosomal regions, obscuring causal loci. Here, we employed organoid modeling to evaluate candidate oncogenic loci identified via integrative computational analysis of extreme copy gains overlapping with extreme expression dysregulation in The Cancer Genome Atlas. Subsets of “outlier” candidates were contextually screened as tissue-specific cDNA lentiviral libraries within cognate esophagus, oral cavity, colon, stomach, pancreas, and lung organoids bearing initial oncogenic mutations. Iterative analysis nominated the kinase DYRK2 at 12q15 as an amplified head and neck squamous carcinoma oncogene in p53−/− oral mucosal organoids. Similarly, FGF3, amplified at 11q13 in 41% of esophageal squamous carcinomas, promoted p53−/− esophageal organoid growth reversible by small molecule and soluble receptor antagonism of FGFRs. Our studies establish organoid-based contextual screening of candidate genomic drivers, enabling functional evaluation during early tumorigenesis.
