1
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Simó C, Serra-Casablancas M, Hortelao AC, Di Carlo V, Guallar-Garrido S, Plaza-García S, Rabanal RM, Ramos-Cabrer P, Yagüe B, Aguado L, Bardia L, Tosi S, Gómez-Vallejo V, Martín A, Patiño T, Julián E, Colombelli J, Llop J, Sánchez S. Urease-powered nanobots for radionuclide bladder cancer therapy. Nat Nanotechnol 2024; 19:554-564. [PMID: 38225356 PMCID: PMC11026160 DOI: 10.1038/s41565-023-01577-y] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 01/17/2024]
Abstract
Bladder cancer treatment via intravesical drug administration achieves reasonable survival rates but suffers from low therapeutic efficacy. To address the latter, self-propelled nanoparticles or nanobots have been proposed, taking advantage of their enhanced diffusion and mixing capabilities in urine when compared with conventional drugs or passive nanoparticles. However, the translational capabilities of nanobots in treating bladder cancer are underexplored. Here, we tested radiolabelled mesoporous silica-based urease-powered nanobots in an orthotopic mouse model of bladder cancer. In vivo and ex vivo results demonstrated enhanced nanobot accumulation at the tumour site, with an eightfold increase revealed by positron emission tomography in vivo. Label-free optical contrast based on polarization-dependent scattered light-sheet microscopy of cleared bladders confirmed tumour penetration by nanobots ex vivo. Treating tumour-bearing mice with intravesically administered radio-iodinated nanobots for radionuclide therapy resulted in a tumour size reduction of about 90%, positioning nanobots as efficient delivery nanosystems for bladder cancer therapy.
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Affiliation(s)
- Cristina Simó
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine in St. Louis, St Louis, MO, USA
| | - Meritxell Serra-Casablancas
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Ana C Hortelao
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Valerio Di Carlo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Sandra Guallar-Garrido
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Sandra Plaza-García
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Rosa Maria Rabanal
- Unitat de Patologia Murina i Comparada, Department of Animal Medicine and Surgery, Veterinary Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pedro Ramos-Cabrer
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Balbino Yagüe
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Laura Aguado
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- Laboratory of Neuroimaging and Biomarkers of Inflammation, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Biomedical Sciences, Faculty Of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa Gómez-Vallejo
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Abraham Martín
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Laboratory of Neuroimaging and Biomarkers of Inflammation, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Biomedical Engineering Department, Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, The Netherlands
| | - Esther Julián
- Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Jordi Llop
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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2
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Basu S, Martínez-Cristóbal P, Frigolé-Vivas M, Pesarrodona M, Lewis M, Szulc E, Bañuelos CA, Sánchez-Zarzalejo C, Bielskutė S, Zhu J, Pombo-García K, Garcia-Cabau C, Zodi L, Dockx H, Smak J, Kaur H, Batlle C, Mateos B, Biesaga M, Escobedo A, Bardia L, Verdaguer X, Ruffoni A, Mawji NR, Wang J, Obst JK, Tam T, Brun-Heath I, Ventura S, Meierhofer D, García J, Robustelli P, Stracker TH, Sadar MD, Riera A, Hnisz D, Salvatella X. Rational optimization of a transcription factor activation domain inhibitor. Nat Struct Mol Biol 2023; 30:1958-1969. [PMID: 38049566 PMCID: PMC10716049 DOI: 10.1038/s41594-023-01159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 11/21/2022] [Accepted: 10/23/2023] [Indexed: 12/06/2023]
Abstract
Transcription factors are among the most attractive therapeutic targets but are considered largely 'undruggable' in part due to the intrinsically disordered nature of their activation domains. Here we show that the aromatic character of the activation domain of the androgen receptor, a therapeutic target for castration-resistant prostate cancer, is key for its activity as transcription factor, allowing it to translocate to the nucleus and partition into transcriptional condensates upon activation by androgens. On the basis of our understanding of the interactions stabilizing such condensates and of the structure that the domain adopts upon condensation, we optimized the structure of a small-molecule inhibitor previously identified by phenotypic screening. The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and potentially even to design, small molecules that target the activation domains of oncogenic transcription factors.
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Affiliation(s)
- Shaon Basu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paula Martínez-Cristóbal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Frigolé-Vivas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mireia Pesarrodona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michael Lewis
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elzbieta Szulc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - C Adriana Bañuelos
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stasė Bielskutė
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jiaqi Zhu
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Levente Zodi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Jordann Smak
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Harpreet Kaur
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Cristina Batlle
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Verdaguer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain
| | - Alessandro Ruffoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nasrin R Mawji
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jun Wang
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jon K Obst
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Teresa Tam
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Berlin, Germany
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, USA
| | - Travis H Stracker
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, Spain.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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3
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Herrera A, Menendez A, Ochoa A, Bardia L, Colombelli J, Pons S. Neurogenesis redirects β-catenin from adherens junctions to the nucleus to promote axonal growth. Development 2023; 150:dev201651. [PMID: 37519286 PMCID: PMC10482005 DOI: 10.1242/dev.201651] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Here, we show that, in the developing spinal cord, after the early Wnt-mediated Tcf transcription activation that confers dorsal identity to neural stem cells, neurogenesis redirects β-catenin from the adherens junctions to the nucleus to stimulate Tcf-dependent transcription in a Wnt-independent manner. This new β-catenin activity regulates genes implicated in several aspects of contralateral axon growth, including axon guidance and adhesion. Using live imaging of ex-vivo chick neural tube, we showed that the nuclear accumulation of β-catenin and the rise in Tcf-dependent transcription both initiate before the dismantling of the adherens junctions and remain during the axon elongation process. Notably, we demonstrated that β-catenin activity in post-mitotic cells depends on TCF7L2 and is central to spinal commissural axon growth. Together, our results reveal Wnt-independent Tcf/β-catenin regulation of genes that control the growth and guidance of commissural axons in chick spinal cord.
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Affiliation(s)
- Antonio Herrera
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Anghara Menendez
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Andrea Ochoa
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Sebastian Pons
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain
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4
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Navaridas R, Vidal-Sabanés M, Ruiz-Mitjana A, Perramon-Güell A, Megino-Luque C, Llobet-Navas D, Matias-Guiu X, Egea J, Encinas M, Bardia L, Colombelli J, Dolcet X. Transient and DNA-free in vivo CRISPR/Cas9 genome editing for flexible modeling of endometrial carcinogenesis. Cancer Commun (Lond) 2023; 43:620-624. [PMID: 36762520 PMCID: PMC10174088 DOI: 10.1002/cac2.12409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Affiliation(s)
- Raúl Navaridas
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Maria Vidal-Sabanés
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Anna Ruiz-Mitjana
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Aida Perramon-Güell
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Cristina Megino-Luque
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - David Llobet-Navas
- Molecular Mechanisms and Experimental Therapy in Oncology-Oncobell Program, Bellvitge Biomedical Research Institute, 'L'Hospitalet de Llobregat, Barcelona, Spain.,Cancer Networking Biomedical Research Center, Institute of Health Carlos III, Madrid, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Bellvitge Hospital, University of Barcelona, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Pathology, Arnau de Vilanova Hospital, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain.,Cancer Networking Biomedical Research Center, Institute of Health Carlos III, Madrid, Spain
| | - Joaquim Egea
- Molecular Developmental Neurobiology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Mario Encinas
- Developmental and Oncogenic Signalling Group, Department of Experimental Medicine, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
| | - Lídia Bardia
- Advanced Digital Microscopy Core Facility, Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Julien Colombelli
- Advanced Digital Microscopy Core Facility, Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Dolcet
- Oncological Pathology Group, Department of Basic Medical Sciences, University of Lleida, Biomedical Research Institute of Lleida, Lleida, Spain
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Tosi S, Bardia L, Barallobre MJ, Muñoz-Barrutia A, Soto-Montenegro ML, Colombelli J. MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy. F1000Res 2021; 9:1308. [PMID: 33763206 PMCID: PMC7953913 DOI: 10.12688/f1000research.27112.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection.
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Affiliation(s)
- Sébastien Tosi
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
| | - Maria Jose Barallobre
- Department of Developmental Biology, Instituto de Biología Molecular de Barcelona, CSIC, Barcelona, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - María Luisa Soto-Montenegro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER de Salud Mental (CIBERSAM), Madrid, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
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6
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Tosi S, Lladó A, Bardia L, Rebollo E, Godo A, Stockinger P, Colombelli J. AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy. Front Bioinform 2021; 1:627626. [PMID: 36303768 PMCID: PMC9581036 DOI: 10.3389/fbinf.2021.627626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/02/2021] [Indexed: 01/22/2023] Open
Abstract
We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution, an action that would be impractical by user operation. For fixed samples, the software can dramatically reduce the amount of data acquired and the acquisition duration in situations where statistically few targets of interest are observed per field of view. AutoScanJ is compatible with motorized fluorescence microscopes controlled by Leica LAS AF/X or Micro-Manager. The software is straightforward to set up and new custom image analysis workflows to detect targets of interest can be simply implemented and shared with minimal efforts as independent ImageJ macro functions. We illustrate five different application scenarios with the system ranging from samples fixed on micropatterned surfaces to live cells undergoing several rounds of division. The target detection functions for these applications are provided and can be used as a starting point and a source of inspiration for new applications. Overall, AutoScanJ helps to optimize microscope usage by autonomous operation, and it opens up new experimental avenues by enabling the real-time detection and selective imaging of transient events in live microscopy.
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Affiliation(s)
- Sébastien Tosi
- Institute for Research in Biomedicine, IRB Barcelona, Barcelona Institute of Science and Technology, BIST, Barcelona, Spain
- *Correspondence: Sébastien Tosi,
| | - Anna Lladó
- Institute for Research in Biomedicine, IRB Barcelona, Barcelona Institute of Science and Technology, BIST, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine, IRB Barcelona, Barcelona Institute of Science and Technology, BIST, Barcelona, Spain
| | - Elena Rebollo
- Molecular Imaging Platform, Molecular Biology institute of Barcelona IBMB-CSIC, Barcelona, Spain
| | - Anna Godo
- Genetics of Male Fertility Group, Cell Biology Unit, Faculty of Biosciences, Autonomous University of Barcelona, Bellaterra, Spain
| | - Petra Stockinger
- Center for Genomic Regulation, CRG, Barcelona Institute of Science and Technology, BIST, Barcelona, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine, IRB Barcelona, Barcelona Institute of Science and Technology, BIST, Barcelona, Spain
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7
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Tosi S, Bardia L, Barallobre MJ, Muñoz-Barrutia A, Soto-Montenegro ML, Colombelli J. MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy. F1000Res 2020; 9:1308. [PMID: 33763206 PMCID: PMC7953913 DOI: 10.12688/f1000research.27112.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 03/23/2024] Open
Abstract
We introduce MosaicExplorerJ, an ImageJ macro to stitch 3D tiles from terabyte-size microscopy datasets organized on a regular 2D grid. As opposed to existing software, stitching does not require any prior information on the actual positions of the tiles, or conversion of raw TIFF images to a multi-resolution format for interactive exploration and fast processing. MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-sided lightsheet illumination and dual-sided camera detection.
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Affiliation(s)
- Sébastien Tosi
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
| | - Maria Jose Barallobre
- Department of Developmental Biology, Instituto de Biología Molecular de Barcelona, CSIC, Barcelona, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - María Luisa Soto-Montenegro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Salud Mental (CIBERSAM), Madrid, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine - IRB Barcelona, the Barcelona Institute for Science and Technology - BIST, Barcelona, Spain
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8
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Tosi S, Bardia L, Filgueira MJ, Calon A, Colombelli J. LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data. Bioinformatics 2020; 36:2634-2635. [PMID: 31860062 DOI: 10.1093/bioinformatics/btz945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Open source software such as ImageJ and CellProfiler greatly simplified the quantitative analysis of microscopy images but their applicability is limited by the size, dimensionality and complexity of the images under study. In contrast, software optimized for the needs of specific research projects can overcome these limitations, but they may be harder to find, set up and customize to different needs. Overall, the analysis of large, complex, microscopy images is hence still a critical bottleneck for many Life Scientists. We introduce LOBSTER (Little Objects Segmentation and Tracking Environment), an environment designed to help scientists design and customize image analysis workflows to accurately characterize biological objects from a broad range of fluorescence microscopy images, including large images exceeding workstation main memory. LOBSTER comes with a starting set of over 75 sample image analysis workflows and associated images stemming from state-of-the-art image-based research projects. AVAILABILITY AND IMPLEMENTATION LOBSTER requires MATLAB (version ≥ 2015a), MATLAB Image processing toolbox, and MATLAB statistics and machine learning toolbox. Code source, online tutorials, video demonstrations, documentation and sample images are freely available from: https://sebastients.github.io. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sébastien Tosi
- Institute for Research in Biomedicine--IRB Barcelona, The Barcelona Institute for Science and Technology-BIST
| | - Lídia Bardia
- Institute for Research in Biomedicine--IRB Barcelona, The Barcelona Institute for Science and Technology-BIST
| | - Maria Jose Filgueira
- Department of Developmental Biology, Instituto de Biología Molecular de Barcelona, CSIC, and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08028 Barcelona, Spain
| | - Alexandre Calon
- Cancer Research Programme, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine--IRB Barcelona, The Barcelona Institute for Science and Technology-BIST
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9
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Pittolo S, Lee H, Lladó A, Tosi S, Bosch M, Bardia L, Gómez-Santacana X, Llebaria A, Soriano E, Colombelli J, Poskanzer KE, Perea G, Gorostiza P. Reversible silencing of endogenous receptors in intact brain tissue using 2-photon pharmacology. Proc Natl Acad Sci U S A 2019; 116:13680-13689. [PMID: 31196955 PMCID: PMC6613107 DOI: 10.1073/pnas.1900430116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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] [Indexed: 01/12/2023] Open
Abstract
The physiological activity of proteins is often studied with loss-of-function genetic approaches, but the corresponding phenotypes develop slowly and can be confounding. Photopharmacology allows direct, fast, and reversible control of endogenous protein activity, with spatiotemporal resolution set by the illumination method. Here, we combine a photoswitchable allosteric modulator (alloswitch) and 2-photon excitation using pulsed near-infrared lasers to reversibly silence metabotropic glutamate 5 (mGlu5) receptor activity in intact brain tissue. Endogenous receptors can be photoactivated in neurons and astrocytes with pharmacological selectivity and with an axial resolution between 5 and 10 µm. Thus, 2-photon pharmacology using alloswitch allows investigating mGlu5-dependent processes in wild-type animals, including synaptic formation and plasticity, and signaling pathways from intracellular organelles.
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Affiliation(s)
- Silvia Pittolo
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Hyojung Lee
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Lladó
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Miquel Bosch
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Lídia Bardia
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Xavier Gómez-Santacana
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), 08034 Barcelona, Spain
| | - Amadeu Llebaria
- Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), 08034 Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology, and Immunology, University of Barcelona (UB), 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Network Center of Biomedical Research in Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Kira E Poskanzer
- Department of Biochemistry & Biophysics, University of California, San Francisco (UCSF), CA 94158
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94158
| | - Gertrudis Perea
- Cajal Institute, Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002 Madrid, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, 08028 Barcelona, Spain;
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Network Center of Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 50015 Zaragoza, Spain
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