Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

Anne C Rios; Bianca D Capaldo; François Vaillant; Bhupinder Pal; Ravian van Ineveld; Caleb A Dawson; Yunshun Chen; Emma Nolan; Nai Yang Fu; 3DTCLSM Group; Felicity C Jackling; Sapna Devi; David Clouston; Lachlan Whitehead; Gordon K Smyth; Scott N Mueller; Geoffrey J Lindeman; Jane E Visvader

doi:10.1016/j.ccell.2019.02.010

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

Cancer Cell. 2019 Apr 15;35(4):618-632.e6. doi: 10.1016/j.ccell.2019.02.010. Epub 2019 Mar 28.

Authors

Anne C Rios¹, Bianca D Capaldo², François Vaillant², Bhupinder Pal², Ravian van Ineveld³, Caleb A Dawson², Yunshun Chen⁴, Emma Nolan², Nai Yang Fu²; 3DTCLSM Group⁵; Felicity C Jackling², Sapna Devi⁶, David Clouston⁷, Lachlan Whitehead⁸, Gordon K Smyth⁹, Scott N Mueller⁶, Geoffrey J Lindeman¹⁰, Jane E Visvader¹¹

Affiliations

¹ Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands. Electronic address: a.c.rios@prinsesmaximacentrum.nl.
² Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia.
³ Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
⁴ Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
⁵ 3D Tissue Clearing and Lightsheet Microscopy Group, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia.
⁶ Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3050, Australia; The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3000, Australia.
⁷ TissuPATH, Melbourne, VIC 3149, Australia.
⁸ Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
⁹ Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia.
¹⁰ Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Department of Medicine, The University of Melbourne, Parkville, VIC 3010, Australia.
¹¹ Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: visvader@wehi.edu.au.

PMID: 30930118
DOI: 10.1016/j.ccell.2019.02.010

Abstract

Breast tumors are inherently heterogeneous, but the evolving cellular organization through neoplastic progression is poorly understood. Here we report a rapid, large-scale single-cell resolution 3D imaging protocol based on a one-step clearing agent that allows visualization of normal tissue architecture and entire tumors at cellular resolution. Imaging of multicolor lineage-tracing models of breast cancer targeted to either basal or luminal progenitor cells revealed profound clonal restriction during progression. Expression profiling of clones arising in Pten/Trp53-deficient tumors identified distinct molecular signatures. Strikingly, most clones harbored cells that had undergone an epithelial-to-mesenchymal transition, indicating widespread, inherent plasticity. Hence, an integrative pipeline that combines lineage tracing, 3D imaging, and clonal RNA sequencing technologies offers a comprehensive path for studying mechanisms underlying heterogeneity in whole tumors.

Keywords: 3D imaging; EMT; Elf5; breast cancer; cell-of-origin; clonal competition; lineage tracing; luminal progenitor; plasticity; tumor suppressor.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biomarkers, Tumor / genetics
Biomarkers, Tumor / metabolism
Breast Neoplasms / genetics
Breast Neoplasms / metabolism
Breast Neoplasms / pathology*
Cell Line, Tumor
Cell Lineage* / genetics
Cell Plasticity* / genetics
Epithelial-Mesenchymal Transition* / genetics
Female
Gene Expression Regulation, Neoplastic
Genetic Heterogeneity
Humans
Imaging, Three-Dimensional*
Mice, Inbred C57BL
Mice, Inbred NOD
Mice, SCID
Mice, Transgenic
Microscopy, Confocal*
Sequence Analysis, RNA
Single-Cell Analysis / methods*
Transcriptome
Tumor Burden

Substances

Biomarkers, Tumor