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3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy. Commun Biol 2022; 5:447. [PMID: 35551498 PMCID: PMC9098858 DOI: 10.1038/s42003-022-03390-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/21/2022] [Indexed: 12/17/2022] Open
Abstract
The combination of optical tissue transparency with immunofluorescence allows the molecular characterization of biological tissues in 3D. However, adult human organs are particularly challenging to become transparent because of the autofluorescence contributions of aged tissues. To meet this challenge, we optimized SHORT (SWITCH-H2O2-antigen Retrieval-TDE), a procedure based on standard histological treatments in combination with a refined clearing procedure to clear and label portions of the human brain. 3D histological characterization with multiple molecules is performed on cleared samples with a combination of multi-colors and multi-rounds labeling. By performing fast 3D imaging of the samples with a custom-made inverted light-sheet fluorescence microscope (LSFM), we reveal fine details of intact human brain slabs at subcellular resolution. Overall, we proposed a scalable and versatile technology that in combination with LSFM allows mapping the cellular and molecular architecture of the human brain, paving the way to reconstruct the entire organ.
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2
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Mascadri F, Bolognesi MM, Pilla D, Cattoretti G. Rejuvenated Vintage Tissue Sections Highlight Individual Antigen Fate During Processing and Long-term Storage. J Histochem Cytochem 2021; 69:659-667. [PMID: 34541944 PMCID: PMC8504260 DOI: 10.1369/00221554211047287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Antigen-bearing proteins become progressively unavailable to immunodetection after prolonged storage of routine sections, exposed to a variety of agents, such as moisture, oxygen, and temperature. By proteomic analysis, the antigens are retained in the sections and definitely in the tissue block, pointing to fixation-independent, storage time–dependent protein modifications. Based on previous experience, we hypothesized that a combined exposure to a reducing agent and to chemicals favoring protein conformation changes would reverse the masking in aged sections. Disaccharides, lactose and sucrose, and a surfactant, added to a standard antigen retrieval buffer, reverse the negative changes in aged sections. Furthermore, they provide enhanced access to antigens in freshly cut sections, but not universally, revealing additional factors, besides heat and calcium chelation, required for antigen retrieval of individual proteins:
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Affiliation(s)
- Francesco Mascadri
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
| | - Maddalena M Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
| | - Daniela Pilla
- Department of Pathology, ASST Monza, Ospedale San Gerardo, Monza, Italy
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy.,Department of Pathology, ASST Monza, Ospedale San Gerardo, Monza, Italy
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3
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Debackere K, Marcelis L, Demeyer S, Vanden Bempt M, Mentens N, Gielen O, Jacobs K, Broux M, Verhoef G, Michaux L, Graux C, Wlodarska I, Gaulard P, de Leval L, Tousseyn T, Cools J, Dierickx D. Fusion transcripts FYN-TRAF3IP2 and KHDRBS1-LCK hijack T cell receptor signaling in peripheral T-cell lymphoma, not otherwise specified. Nat Commun 2021; 12:3705. [PMID: 34140493 PMCID: PMC8211700 DOI: 10.1038/s41467-021-24037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of non-Hodgkin lymphomas with poor prognosis. Up to 30% of PTCL lack distinctive features and are classified as PTCL, not otherwise specified (PTCL-NOS). To further improve our understanding of the genetic landscape and biology of PTCL-NOS, we perform RNA-sequencing of 18 cases and validate results in an independent cohort of 37 PTCL cases. We identify FYN-TRAF3IP2, KHDRBS1-LCK and SIN3A-FOXO1 as new in-frame fusion transcripts, with FYN-TRAF3IP2 as a recurrent fusion detected in 8 of 55 cases. Using ex vivo and in vivo experiments, we demonstrate that FYN-TRAF3IP2 and KHDRBS1-LCK activate signaling pathways downstream of the T cell receptor (TCR) complex and confer therapeutic vulnerability to clinically available drugs.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Line, Tumor
- Cell Membrane/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Forkhead Box Protein O1/genetics
- Forkhead Box Protein O1/metabolism
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Intracellular Signaling Peptides and Proteins/metabolism
- Kaplan-Meier Estimate
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins c-fyn/genetics
- Proto-Oncogene Proteins c-fyn/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Seq
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/metabolism
- bcl-X Protein/antagonists & inhibitors
- bcl-X Protein/metabolism
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Affiliation(s)
- Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Michael Broux
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Gregor Verhoef
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Carlos Graux
- Mont-Godinne University Hospital, Yvoir, Belgium
| | - Iwona Wlodarska
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Gaulard
- Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - Daan Dierickx
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium.
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.
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New Dimensions of Antigen Retrieval Technique: 28 Years of Development, Practice, and Expansion. Appl Immunohistochem Mol Morphol 2019; 27:715-721. [DOI: 10.1097/pai.0000000000000778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Bombelli S, Meregalli C, Scalia C, Bovo G, Torsello B, De Marco S, Cadamuro M, Viganò P, Strada G, Cattoretti G, Bianchi C, Perego RA. Nephrosphere-Derived Cells Are Induced to Multilineage Differentiation when Cultured on Human Decellularized Kidney Scaffolds. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:184-195. [PMID: 29037855 DOI: 10.1016/j.ajpath.2017.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023]
Abstract
In end-stage chronic kidney disease, the option of organ transplantation is limited because of the scarce availability of kidneys. The combination of stem cell research, regenerative medicine, and tissue engineering seems a promising approach to produce new transplantable kidneys. Currently, the possibility to repopulate naturally obtained scaffolds with cells of different sources is advancing. Our aim was to test, for the first time, whether the nephrosphere (NS) cells, composed by renal stem/progenitor-like cells, were able to repopulate different nephron portions of renal extracellular matrix scaffolds obtained after decellularization of human renal tissue slices. Our decellularization protocol enabled us to obtain a completely acellular renal scaffold while maintaining the extracellular matrix structure and composition in terms of collagen IV, laminin, and fibronectin. NS cells, cultured on decellularized renal scaffolds with basal medium, differentiated into proximal and distal tubules as well as endothelium, as highlighted by histology and by the specific expression of epithelial cytokeratin 8.18, proximal tubular CD10, distal tubular cytokeratin 7, and endothelial von Willebrand factor markers. Endothelial medium promoted the differentiation toward the endothelium, whereas epithelial medium promoted the differentiation toward the epithelium. NS cells seem to be a good tool for scaffold repopulation, paving the way for experimental investigations focused on whole-kidney reconstruction.
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Affiliation(s)
- Silvia Bombelli
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | - Chiara Meregalli
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | - Carla Scalia
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | - Giorgio Bovo
- Urology Unit, Bassini Hospital, Cinisello Balsamo, Italy
| | - Barbara Torsello
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | - Sofia De Marco
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | | | - Paolo Viganò
- Urology Unit, Bassini Hospital, Cinisello Balsamo, Italy
| | - Guido Strada
- Urology Unit, Bassini Hospital, Cinisello Balsamo, Italy
| | - Giorgio Cattoretti
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy; Anatomo-Pathology Unit, San Gerardo Hospital, Monza, Italy
| | - Cristina Bianchi
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy
| | - Roberto A Perego
- School of Medicine and Surgery, Milano-Bicocca University, Monza, Italy.
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6
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Bolognesi MM, Manzoni M, Scalia CR, Zannella S, Bosisio FM, Faretta M, Cattoretti G. Multiplex Staining by Sequential Immunostaining and Antibody Removal on Routine Tissue Sections. J Histochem Cytochem 2017; 65:431-444. [PMID: 28692376 PMCID: PMC5533273 DOI: 10.1369/0022155417719419] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multiplexing, labeling for multiple immunostains in the very same cell or tissue section in situ, has raised considerable interest. The methods proposed include the use of labeled primary antibodies, spectral separation of fluorochromes, bleaching of the fluorophores or chromogens, blocking of previous antibody layers, all in various combinations. The major obstacles to the diffusion of this technique are high costs in custom antibodies and instruments, low throughput, and scarcity of specialized skills or facilities. We have validated a method based on common primary and secondary antibodies and diffusely available fluorescent image scanners. It entails rounds of four-color indirect immunofluorescence, image acquisition, and removal (stripping) of the antibodies, before another stain is applied. The images are digitally registered and the autofluorescence is subtracted. Removal of antibodies is accomplished by disulfide cleavage and a detergent or by a chaotropic salt treatment, this latter followed by antigen refolding. More than 30 different antibody stains can be applied to one single section from routinely fixed and embedded tissue. This method requires a modest investment in hardware and materials and uses freeware image analysis software. Multiplexing on routine tissue sections is a high throughput tool for in situ characterization of neoplastic, reactive, inflammatory, and normal cells.
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Affiliation(s)
- Maddalena Maria Bolognesi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Marco Manzoni
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Carla Rossana Scalia
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Stefano Zannella
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC)
| | - Francesca Maria Bosisio
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC).,Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium (FMB)
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy (MF)
| | - Giorgio Cattoretti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (MMB, MM, CRS, SZ, FMB, GC).,Department of Pathology, Azienda Socio-Sanitaria Territoriale Monza, Monza, Italy (GC)
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7
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Abstract
Germinal centers are short-lived microanatomical compartments with essential roles in adaptive immunity. These lymphoid structures can be identified in secondary lymphoid organs using both flow cytometry and immunohistological analyses, but only the latter provides useful architectural and spatial information. Here we describe how to use immunofluorescence and immunohistochemistry with specific antibodies to precisely highlight the cellular and architectural features of germinal centers, both in human and mouse secondary lymphoid organs, and to study their normal development and disturbance in disease.
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Affiliation(s)
- David Dominguez-Sola
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, Box 1044A, New York, NY, 10029, USA.
- The Tisch Cancer Institute & Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Giorgio Cattoretti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca (UNIMIB), Via Cadore 48, 20900, Monza, Italy.
- Anatomia Patologica, Azienda Ospedaliera San Gerardo, Via Pergolesi 33, 20900, Monza, Italy.
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8
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Scalia CR, Boi G, Bolognesi MM, Riva L, Manzoni M, DeSmedt L, Bosisio FM, Ronchi S, Leone BE, Cattoretti G. Antigen Masking During Fixation and Embedding, Dissected. J Histochem Cytochem 2016; 65:5-20. [PMID: 27798289 DOI: 10.1369/0022155416673995] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Antigen masking in routinely processed tissue is a poorly understood process caused by multiple factors. We sought to dissect the effect on antigenicity of each step of processing by using frozen sections as proxies of the whole tissue. An equivalent extent of antigen masking occurs across variable fixation times at room temperature. Most antigens benefit from longer fixation times (>24 hr) for optimal detection after antigen retrieval (AR; for example, Ki-67, bcl-2, ER). The transfer to a graded alcohol series results in an enhanced staining effect, reproduced by treating the sections with detergents, possibly because of a better access of the polymeric immunohistochemical detection system to tissue structures. A second round of masking occurs upon entering the clearing agent, mostly at the paraffin embedding step. This may depend on the non-freezable water removal. AR fully reverses the masking due both to the fixation time and the paraffin embedding. AR itself destroys some epitopes which do not survive routine processing. Processed frozen sections are a tool to investigate fixation and processing requirements for antigens in routine specimens.
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Affiliation(s)
- Carla Rossana Scalia
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC)
| | - Giovanna Boi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC)
| | - Maddalena Maria Bolognesi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC)
| | - Lorella Riva
- Azienda Socio Sanitaria Territoriale Monza, Monza, Italy (LR, BEL, GC)
| | - Marco Manzoni
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC)
| | - Linde DeSmedt
- Laboratory of Translational Cell and Tissue Research, University of Leuven, KUL, Leuven, Belgium (LD, FMB)
| | - Francesca Maria Bosisio
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC).,Laboratory of Translational Cell and Tissue Research, University of Leuven, KUL, Leuven, Belgium (LD, FMB)
| | - Susanna Ronchi
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC)
| | - Biagio Eugenio Leone
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC).,Azienda Socio Sanitaria Territoriale Monza, Monza, Italy (LR, BEL, GC)
| | - Giorgio Cattoretti
- Dipartimento di Medicina e Chirurgia, Universitá degli Studi di Milano-Bicocca, Monza, Italy (CRS, GB, MMB, MM, FMB, SR, BEL, GC).,Azienda Socio Sanitaria Territoriale Monza, Monza, Italy (LR, BEL, GC)
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