1
|
Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024; 23:2700-2722. [PMID: 38451675 PMCID: PMC11296931 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
Collapse
Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
2
|
Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
Collapse
Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
| |
Collapse
|
3
|
Dumigan A, Gonzalez RC, Morris B, Sá-Pessoa J. Visualisation of Host-Pathogen Communication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1406:19-39. [PMID: 37016109 DOI: 10.1007/978-3-031-26462-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The core of biomedical science is the use of laboratory techniques to support the diagnosis and treatment of disease in clinical settings. Despite tremendous advancement in our understanding of medicine in recent years, we are still far from having a complete understanding of human physiology in homeostasis, let alone the pathology of disease states. Indeed medical advances over the last two hundred years would not have been possible without the invention of and continuous development of visualisation techniques available to research scientists and clinicians. As we have all learned from the recent COVID pandemic, despite advances in modern medicine we still have much to learn regarding infection biology. Indeed antimicrobial resistant (AMR) bacteria are a global threat to human health, meaning research into bacterial pathogenesis is vital. In this chapter, we will briefly describe the nature of microbes and host immune responses before delving into some of the visualisation techniques utilised in the field of biomedical research with a focus on host-pathogen interactions. We will give a brief overview of commonly used techniques from gold standard staining methods, in situ hybridisation, microscopy, western blotting, microbial characterisation, to cutting-edge image flow cytometry and mass spectrometry. Specifically, we will focus on techniques utilised to visualise interactions between the host, our own bodies, and invading organisms including bacteria. We will touch on in vitro and ex vivo modelling methodology with examples utilised to delineate pathogenicity in disease. A better understanding of bacterial biology, immunology and how these fields interact (host-pathogen communications) in biomedical research is integral to developing novel therapeutic approaches which circumvent the need for antibiotics, an important issue as we enter a post-antibiotic era.
Collapse
Affiliation(s)
- Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
| | | | - Brenda Morris
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| |
Collapse
|
4
|
Sandström N, Carannante V, Olofsson K, Sandoz PA, Moussaud-Lamodière EL, Seashore-Ludlow B, Van Ooijen H, Verron Q, Frisk T, Takai M, Wiklund M, Östling P, Önfelt B. Miniaturized and multiplexed high-content screening of drug and immune sensitivity in a multichambered microwell chip. CELL REPORTS METHODS 2022; 2:100256. [PMID: 35880015 PMCID: PMC9308168 DOI: 10.1016/j.crmeth.2022.100256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 12/01/2022]
Abstract
Here, we present a methodology based on multiplexed fluorescence screening of two- or three-dimensional cell cultures in a newly designed multichambered microwell chip, allowing direct assessment of drug or immune cell cytotoxic efficacy. We establish a framework for cell culture, formation of tumor spheroids, fluorescence labeling, and imaging of fixed or live cells at various magnifications directly in the chip together with data analysis and interpretation. The methodology is demonstrated by drug cytotoxicity screening using ovarian and non-small cell lung cancer cells and by cellular cytotoxicity screening targeting tumor spheroids of renal carcinoma and ovarian carcinoma with natural killer cells from healthy donors. The miniaturized format allowing long-term cell culture, efficient screening, and high-quality imaging of small sample volumes makes this methodology promising for individualized cytotoxicity tests for precision medicine.
Collapse
Affiliation(s)
- Niklas Sandström
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Valentina Carannante
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| | - Karl Olofsson
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Patrick A. Sandoz
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | | | - Brinton Seashore-Ludlow
- Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| | - Hanna Van Ooijen
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Quentin Verron
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Thomas Frisk
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Madoka Takai
- Department of Bioengineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Martin Wiklund
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
| | - Päivi Östling
- Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 65 Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
| |
Collapse
|
5
|
Wen L, Marki A, Wang Z, Orecchioni M, Makings J, Billitti M, Wang E, Suthahar SSA, Kim K, Kiosses WB, Mikulski Z, Ley K. A humanized β 2 integrin knockin mouse reveals localized intra- and extravascular neutrophil integrin activation in vivo. Cell Rep 2022; 39:110876. [PMID: 35649374 PMCID: PMC10375464 DOI: 10.1016/j.celrep.2022.110876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
β2 integrins are leukocyte-specific adhesion molecules that are essential for leukocyte recruitment. The lack of tools for reporting β2 integrin activation in mice hindered the study of β2 integrin-related immune responses in vivo. Here, we generated a humanized β2 integrin knockin mouse strain by targeting the human β2 integrin coding sequence into the mouse Itgb2 locus to enable imaging of β2 integrin activation using the KIM127 (extension) and mAb24 (high-affinity) reporter antibodies. Using a CXCL1-induced acute inflammation model, we show the local dynamics of β2 integrin activation in arresting neutrophils in vivo in venules of the mouse cremaster muscle. Activated integrins are highly concentrated in a small area at the rear of arresting neutrophils in vivo. In a high-dose lipopolysaccharide model, we find that β2 integrins are activated in association with elevated neutrophil adhesion in lung and liver. Thus, these mice enable studies of β2 integrin activation in vivo.
Collapse
Affiliation(s)
- Lai Wen
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Alex Marki
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Zhihao Wang
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Marco Orecchioni
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Jeffrey Makings
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Monica Billitti
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Erpei Wang
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Sujit S A Suthahar
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - William B Kiosses
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Klaus Ley
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
6
|
Kratz J, Geisler C, Egner A. ISM-assisted tomographic STED microscopy. OPTICS EXPRESS 2022; 30:939-956. [PMID: 35209272 DOI: 10.1364/oe.445441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Stimulated emission depletion (STED) microscopy theoretically provides unlimited resolution. However, in practice the achievable resolution in biological samples is essentially limited by photobleaching. One method which overcomes this problem is tomographic STED (tomoSTED) microscopy. In tomoSTED microscopy, one-dimensional depletion patterns facing in different directions are successively applied in order to acquire a highly-resolved image in two dimensions. In this context, the number of addressed directions depends on the desired angular homogeneity of the point spread function or the optical transfer function and thus on the resolution increase as compared to diffraction-limited imaging. At a reasonable angular homogeneity the light dose and thus bleaching can be reduced, as compared to conventional STED microscopy. Here, we propose and demonstrate for the first time, to our knowledge, that the number of required depletion pattern orientations can be reduced by combining tomoSTED microscopy with the concept of image scanning microscopy (ISM). With our realization of an ISM-tomoSTED microscope, we show that approximately a factor of 2 lower number of orientations are required to achieve the same resolution and image quality as in tomoSTED microscopy.
Collapse
|
7
|
Hmeljak J, Agullo-Pascual E. Celebrating FocalPlane and microscopy in Disease Models & Mechanisms. Dis Model Mech 2021; 14:270975. [PMID: 34279567 DOI: 10.1242/dmm.049183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
8
|
Cai C, Sun H, Hu L, Fan Z. Visualization of integrin molecules by fluorescence imaging and techniques. ACTA ACUST UNITED AC 2021; 45:229-257. [PMID: 34219865 PMCID: PMC8249084 DOI: 10.32604/biocell.2021.014338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Integrin molecules are transmembrane αβ heterodimers involved in cell adhesion, trafficking, and signaling. Upon activation, integrins undergo dynamic conformational changes that regulate their affinity to ligands. The physiological functions and activation mechanisms of integrins have been heavily discussed in previous studies and reviews, but the fluorescence imaging techniques -which are powerful tools for biological studies- have not. Here we review the fluorescence labeling methods, imaging techniques, as well as Förster resonance energy transfer assays used to study integrin expression, localization, activation, and functions.
Collapse
Affiliation(s)
- Chen Cai
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
| | - Hao Sun
- Department of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Liang Hu
- Cardiovascular Institute of Zhengzhou University, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450051, China
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
| |
Collapse
|
9
|
Li M, Yu Y. Innate immune receptor clustering and its role in immune regulation. J Cell Sci 2021; 134:134/4/jcs249318. [PMID: 33597156 DOI: 10.1242/jcs.249318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The discovery of receptor clustering in the activation of adaptive immune cells has revolutionized our understanding of the physical basis of immune signal transduction. In contrast to the extensive studies of adaptive immune cells, particularly T cells, there is a lesser, but emerging, recognition that the formation of receptor clusters is also a key regulatory mechanism in host-pathogen interactions. Many kinds of innate immune receptors have been found to assemble into nano- or micro-sized domains on the surfaces of cells. The clusters formed between diverse categories of innate immune receptors function as a multi-component apparatus for pathogen detection and immune response regulation. Here, we highlight these pioneering efforts and the outstanding questions that remain to be answered regarding this largely under-explored research topic. We provide a critical analysis of the current literature on the clustering of innate immune receptors. Our emphasis is on studies that draw connections between the phenomenon of receptor clustering and its functional role in innate immune regulation.
Collapse
Affiliation(s)
- Miao Li
- Department of Chemistry, Indiana University, Bloomington, IN 47401, USA
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN 47401, USA
| |
Collapse
|
10
|
|
11
|
Wen L, Marki A, Roy P, McArdle S, Sun H, Fan Z, Gingras AR, Ginsberg MH, Ley K. Kindlin-3 recruitment to the plasma membrane precedes high-affinity β2-integrin and neutrophil arrest from rolling. Blood 2021; 137:29-38. [PMID: 32777822 PMCID: PMC7808012 DOI: 10.1182/blood.2019003446] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Integrin-mediated neutrophil adhesion starts by arrest from rolling. Activation of integrins involves conformational changes from an inactive, bent conformation to an extended conformation (E+) with high affinity for ligand binding (H+). The cytoplasmic protein kindlin-3 is necessary for leukocyte adhesion; mutations of kindlin-3 cause leukocyte adhesion deficiency type 3. Kindlin-3 binds the β2-integrin cytoplasmic tail at a site distinct from talin-1, but the molecular mechanism by which kindlin-3 activates β2-integrins is unknown. In this study, we measured the spatiotemporal dynamics of kindlin-3 and β2-integrin conformation changes during neutrophil and HL-60 cell rolling and arrest under flow. Using high-resolution quantitative dynamic footprinting microscopy and kindlin-3-fluorescent protein (FP) fusion proteins, we found that kindlin-3 was recruited to the plasma membrane in response to interleukin-8 (IL-8) before induction of the H+ β2-integrin conformation. Intravital imaging revealed that EGFP-kindlin-3-reconstituted, kindlin-3-knockout neutrophils arrest in vivo in response to CXCL1. EGFP-kindlin-3 in primary mouse neutrophils was also recruited to the plasma membrane before arrest. Upon arrest, we found small clusters of high-affinity β2-integrin molecules within large areas of membrane-proximal kindlin-3 FP. Deletion of kindlin-3 or its pleckstrin homology (PH) domain in neutrophil-like HL-60 cells completely abolished H+ β2-integrin induction. IL-8 also triggered recruitment of the isolated kindlin-3 PH domain to the plasma membrane before arrest. In summary, we showed that the kindlin-3 PH domain is necessary for recruitment to the plasma membrane, where full-length kindlin-3 is indispensable for the induction of high-affinity β2-integrin.
Collapse
Affiliation(s)
- Lai Wen
- Laboratory of Inflammation Biology and
| | | | - Payel Roy
- Laboratory of Inflammation Biology and
| | - Sara McArdle
- Microscopy Core Facility, La Jolla Institute for Immunology, La Jolla, CA
| | - Hao Sun
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Zhichao Fan
- Laboratory of Inflammation Biology and
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT; and
| | | | - Mark H Ginsberg
- Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Klaus Ley
- Laboratory of Inflammation Biology and
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
| |
Collapse
|