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Zorbas C, Soenmez A, Léger J, De Vleeschouwer C, Lafontaine DL. Detecting material state changes in the nucleolus by label-free digital holographic microscopy. EMBO Rep 2024:10.1038/s44319-024-00134-5. [PMID: 38654122 DOI: 10.1038/s44319-024-00134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Ribosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension human cells. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images. Holograms containing cell optical thickness information allowed us to define a novel index which we used to distinguish nucleoli whose material state had been modulated optogenetically by blue-light-induced protein aggregation. Nucleoli whose function had been impacted by drug treatment or depletion of ribosomal proteins could also be distinguished. We explored the potential of the technology to detect other natural and pathological condensates, such as those formed upon overexpression of a mutant form of huntingtin, ataxin-3, or TDP-43, and also other cell assemblies (lipid droplets). We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli and other cell assemblies, including their material state, without any staining.
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Affiliation(s)
- Christiane Zorbas
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Aynur Soenmez
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium
| | - Jean Léger
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Christophe De Vleeschouwer
- ICTEAM-ELEN, Fonds de la Recherche Scientifique (F.R.S./FNRS), UCLouvain, B-1348, Louvain-la-Neuve, Belgium
| | - Denis Lj Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark campus, B-6041, Gosselies, Belgium.
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Verhoeven J, Jacobs KA, Rizzollo F, Lodi F, Hua Y, Poźniak J, Narayanan Srinivasan A, Houbaert D, Shankar G, More S, Schaaf MB, Dubroja Lakic N, Ganne M, Lamote J, Van Weyenbergh J, Boon L, Bechter O, Bosisio F, Uchiyama Y, Bertrand MJ, Marine JC, Lambrechts D, Bergers G, Agrawal M, Agostinis P. Tumor endothelial cell autophagy is a key vascular-immune checkpoint in melanoma. EMBO Mol Med 2023; 15:e18028. [PMID: 38009521 DOI: 10.15252/emmm.202318028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Tumor endothelial cells (TECs) actively repress inflammatory responses and maintain an immune-excluded tumor phenotype. However, the molecular mechanisms that sustain TEC-mediated immunosuppression remain largely elusive. Here, we show that autophagy ablation in TECs boosts antitumor immunity by supporting infiltration and effector function of T-cells, thereby restricting melanoma growth. In melanoma-bearing mice, loss of TEC autophagy leads to the transcriptional expression of an immunostimulatory/inflammatory TEC phenotype driven by heightened NF-kB and STING signaling. In line, single-cell transcriptomic datasets from melanoma patients disclose an enriched InflammatoryHigh /AutophagyLow TEC phenotype in correlation with clinical responses to immunotherapy, and responders exhibit an increased presence of inflamed vessels interfacing with infiltrating CD8+ T-cells. Mechanistically, STING-dependent immunity in TECs is not critical for the immunomodulatory effects of autophagy ablation, since NF-kB-driven inflammation remains functional in STING/ATG5 double knockout TECs. Hence, our study identifies autophagy as a principal tumor vascular anti-inflammatory mechanism dampening melanoma antitumor immunity.
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Affiliation(s)
- Jelle Verhoeven
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Kathryn A Jacobs
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Francesca Rizzollo
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Francesca Lodi
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Yichao Hua
- Laboratory of Tumor Microenvironment and Therapeutic Resistance Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joanna Poźniak
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Adhithya Narayanan Srinivasan
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Diede Houbaert
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Gautam Shankar
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Sanket More
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marco B Schaaf
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolina Dubroja Lakic
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Maarten Ganne
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jochen Lamote
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Johan Van Weyenbergh
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Louis Boon
- Polpharma Biologics, Utrecht, The Netherlands
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mathieu Jm Bertrand
- VIB Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jean Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Madhur Agrawal
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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