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Bouchard G, Zhang W, Li I, Ilerten I, Bhattacharya A, Li Y, Trope W, Shrager JB, Kuo C, Tian L, Giaccia AJ, Plevritis SK. The colocatome as a spatial -omic reveals shared microenvironment features between tumour-stroma assembloids and human lung cancer. bioRxiv 2023:2023.09.11.557278. [PMID: 37745466 PMCID: PMC10515823 DOI: 10.1101/2023.09.11.557278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Computational frameworks to quantify and compare microenvironment spatial features of in-vitro patient-derived models and clinical specimens are needed. Here, we acquired and analysed multiplexed immunofluorescence images of human lung adenocarcinoma (LUAD) alongside tumour-stroma assembloids constructed with organoids and fibroblasts harvested from the leading edge (Tumour-Adjacent Fibroblasts;TAFs) or core (Tumour Core Fibroblasts;TCFs) of human LUAD. We introduce the concept of the "colocatome" as a spatial -omic dimension to catalogue all proximate and distant colocalisations between malignant and fibroblast subpopulations in both the assembloids and clinical specimens. The colocatome expands upon the colocalisation quotient (CLQ) through a nomalisation strategy that involves permutation analysis and thereby allows comparisons of CLQs under different conditions. Using colocatome analysis, we report that both TAFs and TCFs protected cancer cells from targeted oncogene treatment by uniquely reorganising the tumour-stroma cytoarchitecture, rather than by promoting cellular heterogeneity or selection. Moreover, we show that the assembloids' colocatome recapitulates the tumour-stroma cytoarchitecture defining the tumour microenvironment of LUAD clinical samples and thereby can serve as a functional spatial readout to guide translational discoveries.
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Affiliation(s)
- Gina Bouchard
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Weiruo Zhang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Irene Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ilayda Ilerten
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Asmita Bhattacharya
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuanyuan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Winston Trope
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Calvin Kuo
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford, CA 94305, USA
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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Lanz MC, Zatulovskiy E, Swaffer MP, Zhang L, Ilerten I, Zhang S, You DS, Marinov G, McAlpine P, Elias JE, Skotheim JM. Increasing cell size remodels the proteome and promotes senescence. Mol Cell 2022; 82:3255-3269.e8. [PMID: 35987199 PMCID: PMC9444988 DOI: 10.1016/j.molcel.2022.07.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/06/2022] [Accepted: 07/25/2022] [Indexed: 01/10/2023]
Abstract
Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.
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Affiliation(s)
- Michael C Lanz
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, Stanford, CA 94305, USA
| | | | | | | | - Ilayda Ilerten
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dong Shin You
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Georgi Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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