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Lim HJ, McWilliam HEG. Quantitative Measurement of Plasma Membrane Protein Internalisation and Recycling in Heterogenous Cellular Samples by Flow Cytometry. Bio Protoc 2024; 14:e4986. [PMID: 38737503 PMCID: PMC11082785 DOI: 10.21769/bioprotoc.4986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Plasma membrane proteins mediate important aspects of physiology, including nutrient acquisition, cell-cell interactions, and monitoring homeostasis. The trafficking of these proteins, involving internalisation from and/or recycling back to the cell surface, is often critical to their functions. These processes can vary among different proteins and cell types and states and are still being elucidated. Current strategies to measure surface protein internalisation and recycling are typically microscopy or biochemical assays; these are accurate but generally limited to analysing a homogenous cell population and are often low throughput. Here, we present flow cytometry-based methods involving probe-conjugated antibodies that enable quantification of internalisation or recycling rates at the single-cell level in complex samples. To measure internalisation, we detail an assay where the protein of interest is labelled with a specific antibody conjugated to a fluorescent oligonucleotide-labelled probe. To measure recycling, a specific antibody conjugated to a cleavable biotin group is employed. These probes permit the differentiation of molecules that have been internalised or recycled from those that have not. When combined with cell-specific marker panels, these methods allow the quantitative study of plasma membrane protein trafficking dynamics in a heterogenous cell mixture at the single-cell level. Key features • These assays allow sensitive quantification of internalised or recycled surface molecules using oligonucleotide or cleavable biotin-conjugated probes, respectively, and detected by flow cytometry. • They can be adapted to any membrane protein that transits via the cell surface and for which a specific purified antibody is available. • The dynamics of a cell surface protein can be measured in heterogenous cell populations simultaneously, including various cellular activation states. • The internalisation assay builds upon the method developed by Liu et al. [1,2] and extends its application to heterogenous human peripheral blood mononuclear cells. • These assays have been extensively used on suspension cells but have not been tested on adherent cells.
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Affiliation(s)
- Hui Jing Lim
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Hämälistö S, Del Valle Batalla F, Yuseff MI, Mattila PK. Endolysosomal vesicles at the center of B cell activation. J Cell Biol 2024; 223:e202307047. [PMID: 38305771 PMCID: PMC10837082 DOI: 10.1083/jcb.202307047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/22/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The endolysosomal system specializes in degrading cellular components and is crucial to maintaining homeostasis and adapting rapidly to metabolic and environmental cues. Cells of the immune system exploit this network to process antigens or promote cell death by secreting lysosome-related vesicles. In B lymphocytes, lysosomes are harnessed to facilitate the extraction of antigens and to promote their processing into peptides for presentation to T cells, critical steps to mount protective high-affinity antibody responses. Intriguingly, lysosomal vesicles are now considered important signaling units within cells and also display secretory functions by releasing their content to the extracellular space. In this review, we focus on how B cells use pathways involved in the intracellular trafficking, secretion, and function of endolysosomes to promote adaptive immune responses. A basic understanding of such mechanisms poses an interesting frontier for the development of therapeutic strategies in the context of cancer and autoimmune diseases.
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Affiliation(s)
- Saara Hämälistö
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
- Cancer Research Unit and FICAN West Cancer Centre Laboratory, Turku, Finland
| | - Felipe Del Valle Batalla
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Isabel Yuseff
- Laboratory of Immune Cell Biology, Department of Cellular and Molecular Biology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pieta K. Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
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Runsala M, Kuokkanen E, Uski E, Šuštar V, Balci MÖ, Rajala J, Paavola V, Mattila PK. The Small GTPase Rab7 Regulates Antigen Processing in B Cells in a Possible Interplay with Autophagy Machinery. Cells 2023; 12:2566. [PMID: 37947644 PMCID: PMC10649364 DOI: 10.3390/cells12212566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
In B cells, antigen processing and peptide-antigen (pAg) presentation is essential to ignite high-affinity antibody responses with the help of cognate T cells. B cells efficiently internalize and direct specific antigens for processing and loading onto MHCII. This critical step, which enables pAg presentation, occurs in MHCII compartments (MIICs) which possess the enzymatic machinery for pAg loading on MHCII. The intracellular transport systems that guide antigen and maintain this unique compartment remain enigmatic. Here, we probed the possible functional role of two known endosomal proteins, the Rab family small GTPases Rab7 and Rab9, that are both reported to colocalize with internalized antigen. As compared to Rab9, we found Rab7 to exhibit a higher overlap with antigen and MIIC components. Rab7 also showed a higher association with antigen degradation. The inhibition of Rab7 drastically decreased pAg presentation. Additionally, we detected the strong colocalization of perinuclearly clustered and presumably MIIC-associated antigen with autophagy protein LC3. When we pharmacologically inhibited autophagy, pAg presentation was inhibited. Together, our data promote Rab7 as an important regulator of antigen processing and, considering the previously reported functions of Rab7 in autophagy, this also raises the possibility of the involvement of autophagy-related machinery in this process.
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Affiliation(s)
- Marika Runsala
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Elina Kuokkanen
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - Eveliina Uski
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - Vid Šuštar
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - Meryem Özge Balci
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Johanna Rajala
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - Vilma Paavola
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - Pieta K. Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- InFLAMES Research Flagship, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
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Awoniyi LO, Cunha DM, Sarapulov AV, Hernández-Pérez S, Runsala M, Tejeda-González B, Šuštar V, Balci MÖ, Petrov P, Mattila PK. B cell receptor-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics. J Cell Sci 2023; 136:jcs261119. [PMID: 37417469 PMCID: PMC10445728 DOI: 10.1242/jcs.261119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
Successful B cell activation, which is critical for high-affinity antibody production, is controlled by the B cell antigen receptor (BCR). However, we still lack a comprehensive protein-level view of the very dynamic multi-branched cellular events triggered by antigen binding. Here, we employed APEX2 proximity biotinylation to study antigen-induced changes, 5-15 min after receptor activation, at the vicinity of the plasma membrane lipid rafts, wherein BCR enriches upon activation. The data reveals dynamics of signaling proteins, as well as various players linked to the subsequent processes, such as actin cytoskeleton remodeling and endocytosis. Interestingly, our differential expression analysis identified dynamic responses in various proteins previously not linked to early B cell activation. We demonstrate active SUMOylation at the sites of BCR activation in various conditions and report its functional role in BCR signaling through the AKT and ERK1/2 axes.
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Affiliation(s)
- Luqman O. Awoniyi
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Diogo M. Cunha
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Alexey V. Sarapulov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Sara Hernández-Pérez
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Marika Runsala
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Blanca Tejeda-González
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Vid Šuštar
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - M. Özge Balci
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Petar Petrov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Pieta K. Mattila
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
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Music A, Tejeda-González B, Cunha DM, Fischer von Mollard G, Hernández-Pérez S, Mattila PK. The SNARE protein Vti1b is recruited to the sites of BCR activation but is redundant for antigen internalisation, processing and presentation. Front Cell Dev Biol 2022; 10:987148. [PMID: 36111340 PMCID: PMC9468668 DOI: 10.3389/fcell.2022.987148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
In order to fulfil the special requirements of antigen-specific activation and communication with other immune cells, B lymphocytes require finely regulated endosomal vesicle trafficking. How the endosomal machinery is regulated in B cells remains largely unexplored. In our previous proximity proteomic screen, we identified the SNARE protein Vti1b as one of the strongest candidates getting accumulated to the sites of early BCR activation. In this report, we follow up on this finding and investigate the localisation and function of Vti1b in B cells. We found that GFP-fused Vti1b was concentrated at the Golgi complex, around the MTOC, as well as in the Rab7+ lysosomal vesicles in the cell periphery. Upon BCR activation with soluble antigen, Vti1b showed partial localization to the internalized antigen vesicles, especially in the periphery of the cell. Moreover, upon BCR activation using surface-bound antigen, Vti1b polarised to the immunological synapse, colocalising with the Golgi complex, and with lysosomes at actin foci. To test for a functional role of Vti1b in early B cell activation, we used primary B cells isolated from Vit1b-deficient mouse. However, we found no functional defects in BCR signalling, immunological synapse formation, or processing and presentation of the internalized antigen, suggesting that the loss of Vti1b in B cells could be compensated by its close homologue Vti1a or other SNAREs.
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Affiliation(s)
- Amna Music
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Blanca Tejeda-González
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Diogo M. Cunha
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | | | - Sara Hernández-Pérez
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- *Correspondence: Sara Hernández-Pérez, ; Pieta K. Mattila,
| | - Pieta K. Mattila
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- *Correspondence: Sara Hernández-Pérez, ; Pieta K. Mattila,
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