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Abraham MJ, Goncalves C, McCallum P, Gupta V, Preston SEJ, Huang F, Chou H, Gagnon N, Johnson NA, Miller WH, Mann KK, Del Rincon SV. Tunable PhenoCycler imaging of the murine pre-clinical tumour microenvironments. Cell Biosci 2024; 14:19. [PMID: 38311785 PMCID: PMC10840224 DOI: 10.1186/s13578-024-01199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND The tumour microenvironment (TME) consists of tumour-supportive immune cells, endothelial cells, and fibroblasts. PhenoCycler, a high-plex single cell spatial biology imaging platform, is used to characterize the complexity of the TME. Researchers worldwide harvest and bank tissues from mouse models which are employed to model a plethora of human disease. With the explosion of interest in spatial biology, these panoplies of archival tissues provide a valuable resource to answer new questions. Here, we describe our protocols for developing tunable PhenoCycler multiplexed imaging panels and describe our open-source data analysis pipeline. Using these protocols, we used PhenoCycler to spatially resolve the TME of 8 routinely employed pre-clinical models of lymphoma, breast cancer, and melanoma preserved as FFPE. RESULTS Our data reveal distinct TMEs in the different cancer models that were imaged and show that cell-cell contacts differ depending on the tumour type examined. For instance, we found that the immune infiltration in a murine model of melanoma is altered in cellular organization in melanomas that become resistant to αPD-1 therapy, with depletions in a number of cell-cell interactions. CONCLUSIONS This work presents a valuable resource study seamlessly adaptable to any field of research involving murine models. The methodology described allows researchers to address newly formed hypotheses using archival materials, bypassing the new to perform new mouse studies.
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Affiliation(s)
- Madelyn J Abraham
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | | | - Paige McCallum
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Vrinda Gupta
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Samuel E J Preston
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Fan Huang
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Hsiang Chou
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Clinical Research Unit, Jewish General Hospital, Montreal, QC, Canada
| | - Natascha Gagnon
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Nathalie A Johnson
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Clinical Research Unit, Jewish General Hospital, Montreal, QC, Canada
| | - Wilson H Miller
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Clinical Research Unit, Jewish General Hospital, Montreal, QC, Canada.
| | - Koren K Mann
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
| | - Sonia V Del Rincon
- Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
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7
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Gurkar AU, Gerencser AA, Mora AL, Nelson AC, Zhang AR, Lagnado AB, Enninful A, Benz C, Furman D, Beaulieu D, Jurk D, Thompson EL, Wu F, Rodriguez F, Barthel G, Chen H, Phatnani H, Heckenbach I, Chuang JH, Horrell J, Petrescu J, Alder JK, Lee JH, Niedernhofer LJ, Kumar M, Königshoff M, Bueno M, Sokka M, Scheibye-Knudsen M, Neretti N, Eickelberg O, Adams PD, Hu Q, Zhu Q, Porritt RA, Dong R, Peters S, Victorelli S, Pengo T, Khaliullin T, Suryadevara V, Fu X, Bar-Joseph Z, Ji Z, Passos JF. Spatial mapping of cellular senescence: emerging challenges and opportunities. NATURE AGING 2023; 3:776-790. [PMID: 37400722 PMCID: PMC10505496 DOI: 10.1038/s43587-023-00446-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Cellular senescence is a well-established driver of aging and age-related diseases. There are many challenges to mapping senescent cells in tissues such as the absence of specific markers and their relatively low abundance and vast heterogeneity. Single-cell technologies have allowed unprecedented characterization of senescence; however, many methodologies fail to provide spatial insights. The spatial component is essential, as senescent cells communicate with neighboring cells, impacting their function and the composition of extracellular space. The Cellular Senescence Network (SenNet), a National Institutes of Health (NIH) Common Fund initiative, aims to map senescent cells across the lifespan of humans and mice. Here, we provide a comprehensive review of the existing and emerging methodologies for spatial imaging and their application toward mapping senescent cells. Moreover, we discuss the limitations and challenges inherent to each technology. We argue that the development of spatially resolved methods is essential toward the goal of attaining an atlas of senescent cells.
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Affiliation(s)
- Aditi U Gurkar
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ana L Mora
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Anru R Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine and Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Anthony B Lagnado
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | | | - David Furman
- Buck Institute for Research on Aging, Novato, CA, USA
- Stanford 1000 Immunomes Project, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, Pilar, Argentina
| | - Delphine Beaulieu
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diana Jurk
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth L Thompson
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Fei Wu
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Fernanda Rodriguez
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Grant Barthel
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Hao Chen
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hemali Phatnani
- Columbia University Irving Medical Center and New York Genome Center, Columbia University, New York, NY, USA
| | | | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeremy Horrell
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Joana Petrescu
- Columbia University Irving Medical Center and New York Genome Center, Columbia University, New York, NY, USA
| | - Jonathan K Alder
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Laura J Niedernhofer
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Manoj Kumar
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, USA
| | - Melanie Königshoff
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marta Bueno
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Miiko Sokka
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | | | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Oliver Eickelberg
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Qianjiang Hu
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Quan Zhu
- University of California, San Diego, CA, USA
| | - Rebecca A Porritt
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Runze Dong
- Department of Biochemistry, Institute for Protein Design and Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Samuel Peters
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Stella Victorelli
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Thomas Pengo
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Timur Khaliullin
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA
| | - Vidyani Suryadevara
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, USA
| | - Xiaonan Fu
- Department of Biochemistry, Institute for Protein Design and Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhicheng Ji
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine and Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - João F Passos
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA.
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