Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells

Antonella F M Dost; Aaron L Moye; Marall Vedaie; Linh M Tran; Eileen Fung; Dar Heinze; Carlos Villacorta-Martin; Jessie Huang; Ryan Hekman; Julian H Kwan; Benjamin C Blum; Sharon M Louie; Samuel P Rowbotham; Julio Sainz de Aja; Mary E Piper; Preetida J Bhetariya; Roderick T Bronson; Andrew Emili; Gustavo Mostoslavsky; Gregory A Fishbein; William D Wallace; Kostyantyn Krysan; Steven M Dubinett; Jane Yanagawa; Darrell N Kotton; Carla F Kim

doi:10.1016/j.stem.2020.07.022

Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells

Cell Stem Cell. 2020 Oct 1;27(4):663-678.e8. doi: 10.1016/j.stem.2020.07.022. Epub 2020 Sep 4.

Authors

Antonella F M Dost¹, Aaron L Moye¹, Marall Vedaie², Linh M Tran³, Eileen Fung⁴, Dar Heinze⁵, Carlos Villacorta-Martin⁶, Jessie Huang², Ryan Hekman⁷, Julian H Kwan⁷, Benjamin C Blum⁷, Sharon M Louie¹, Samuel P Rowbotham¹, Julio Sainz de Aja¹, Mary E Piper⁸, Preetida J Bhetariya⁹, Roderick T Bronson¹⁰, Andrew Emili¹¹, Gustavo Mostoslavsky⁵, Gregory A Fishbein¹², William D Wallace¹³, Kostyantyn Krysan³, Steven M Dubinett¹⁴, Jane Yanagawa¹⁵, Darrell N Kotton¹⁶, Carla F Kim¹⁷

Affiliations

¹ Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
² Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
³ Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA.
⁴ Department of Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA.
⁵ Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; Section of Gastroenterology and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
⁶ Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA.
⁷ Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
⁸ Harvard T.H. Chan School of Public Health, Department of Biostatistics, Boston, MA 02115, USA.
⁹ Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard T.H. Chan School of Public Health, Department of Biostatistics, Boston, MA 02115, USA.
¹⁰ Rodent Histopathology Core, Harvard Medical School, Boston, MA 02115, USA.
¹¹ Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biology, Boston University, Boston, MA 02215, USA.
¹² Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA 90095, USA.
¹³ Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA.
¹⁴ Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
¹⁵ Department of Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: [email protected].
¹⁶ Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA. Electronic address: [email protected].
¹⁷ Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [email protected].

Abstract

Mutant KRAS is a common driver in epithelial cancers. Nevertheless, molecular changes occurring early after activation of oncogenic KRAS in epithelial cells remain poorly understood. We compared transcriptional changes at single-cell resolution after KRAS activation in four sample sets. In addition to patient samples and genetically engineered mouse models, we developed organoid systems from primary mouse and human induced pluripotent stem cell-derived lung epithelial cells to model early-stage lung adenocarcinoma. In all four settings, alveolar epithelial progenitor (AT2) cells expressing oncogenic KRAS had reduced expression of mature lineage identity genes. These findings demonstrate the utility of our in vitro organoid approaches for uncovering the early consequences of oncogenic KRAS expression. This resource provides an extensive collection of datasets and describes organoid tools to study the transcriptional and proteomic changes that distinguish normal epithelial progenitor cells from early-stage lung cancer, facilitating the search for targets for KRAS-driven tumors.

Keywords: KRAS; alveolar; developmental programs; early-stage lung cancer; iPSC; loss of differentiation; organoid; single-cell RNA sequencing; stage IA lung adenocarcinoma; tumor progression.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Humans
Induced Pluripotent Stem Cells*
Lung
Mice
Organoids*
Proteomics
Proto-Oncogene Proteins p21(ras) / genetics

Substances

KRAS protein, human
Proto-Oncogene Proteins p21(ras)

Abstract

Publication types

MeSH terms

Substances

Grants and funding