1
|
Lombard-Banek C, Pohl KI, Kwee EJ, Elliott JT, Schiel JE. A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies. J Proteome Res 2022; 21:1229-1239. [PMID: 35404046 PMCID: PMC9087334 DOI: 10.1021/acs.jproteome.1c00887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS)-based proteomic measurements are uniquely poised to impact the development of cell and gene therapies. With the adoption of rigorous instrumental performance qualifications (PQs), large-scale proteomics can move from a research to a manufacturing control tool. Especially suited, data-independent acquisition (DIA) approaches have distinctive qualities to extend multiattribute method (MAM) principles to characterize the proteome of cell therapies. Here, we describe the development of a DIA method for the sensitive identification and quantification of proteins on a Q-TOF instrument. Using the improved acquisition parameters, we defined a control strategy and highlighted some metrics to improve the reproducibility of SWATH acquisition-based proteomic measurements. Finally, we applied the method to analyze the proteome of Jurkat cells that here serves as a model for human T-cells. Raw and processed data were deposited in PRIDE (PXD029780).
Collapse
Affiliation(s)
- Camille Lombard-Banek
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Bioengineering Research, Rockville, Maryland 20850, United States
| | | | - Edward J. Kwee
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
| | - John T. Elliott
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
| | - John E. Schiel
- National
Institute of Standards and Technology, Material and Measurements Laboratory, Gaithersburg, Maryland 20899, United States
- Institute
for Bioscience and Bioengineering Research, Rockville, Maryland 20850, United States
| |
Collapse
|
2
|
Hadjitheodorou A, Bell GRR, Ellett F, Shastry S, Irimia D, Collins SR, Theriot JA. Directional reorientation of migrating neutrophils is limited by suppression of receptor input signaling at the cell rear through myosin II activity. Nat Commun 2021; 12:6619. [PMID: 34785640 PMCID: PMC8595366 DOI: 10.1038/s41467-021-26622-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 11/09/2022] Open
Abstract
To migrate efficiently to target locations, cells must integrate receptor inputs while maintaining polarity: a distinct front that leads and a rear that follows. Here we investigate what is necessary to overwrite pre-existing front-rear polarity in neutrophil-like HL60 cells migrating inside straight microfluidic channels. Using subcellular optogenetic receptor activation, we show that receptor inputs can reorient weakly polarized cells, but the rear of strongly polarized cells is refractory to new inputs. Transient stimulation reveals a multi-step repolarization process, confirming that cell rear sensitivity to receptor input is the primary determinant of large-scale directional reversal. We demonstrate that the RhoA/ROCK/myosin II pathway limits the ability of receptor inputs to signal to Cdc42 and reorient migrating neutrophils. We discover that by tuning the phosphorylation of myosin regulatory light chain we can modulate the activity and localization of myosin II and thus the amenability of the cell rear to 'listen' to receptor inputs and respond to directional reprogramming.
Collapse
Affiliation(s)
- Amalia Hadjitheodorou
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - George R R Bell
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Felix Ellett
- Department of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shashank Shastry
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Daniel Irimia
- Department of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sean R Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA.
| | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Abstract
Cell motility is required for diverse biological processes including development, homing of immune cells, wound healing, and cancer cell invasion. Motile neutrophils exhibit a polarized morphology characterized by the formation of leading-edge pseudopods and a highly contractile cell rear known as the uropod. Although it is known that perturbing uropod formation impairs neutrophil migration, the role of the uropod in cell polarization and motility remains incompletely understood. Here we discuss cell intrinsic mechanisms that regulate neutrophil polarization and motility, with a focus on the uropod, and examine how relationships among regulatory mechanisms change when cells change their direction of migration.
Collapse
|
4
|
A review of chemical gradient systems for cell analysis. Anal Chim Acta 2016; 907:7-17. [DOI: 10.1016/j.aca.2015.12.008] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/01/2015] [Accepted: 12/12/2015] [Indexed: 01/22/2023]
|
5
|
Miki Y, Oguri E, Hirano K, Beppu M. Macrophage recognition of cells with elevated calcium is mediated by carbohydrate chains of CD43. Cell Struct Funct 2013; 38:43-54. [PMID: 23400223 DOI: 10.1247/csf.12024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Macrophages remove deteriorating cells (those undergoing apoptosis and oxidation) via poly-N-acetyllactosaminyl chains on CD43 caps, a major cell-surface glycoprotein. Unusually high intracellular calcium levels are also deteriorating for cells and tissue. Here we artificially elevated calcium levels in cells and examined the mechanism by which this elevation was resolved by macrophages. Results showed that treatment with the calcium ionophore A23187 and ionomycin induces capping of CD43 on Jurkat cells, which are subsequently recognized and phagocytosed by macrophages, indicating that macrophages regard cells with elevated calcium as targets for removal. Further tests showed that A23187- and ionomycin-treated Jurkat cells did not induce apoptotic changes such as DNA fragmentation or phosphatidylserine expression, indicating that these cells were removed despite still being viable. Jurkat cells pretreated with anti-CD43 antibody or those with poly-N-acetyllactosaminyl chains containing oligosaccharides inhibited macrophage binding, indicating that macrophages recognize the poly-N-acetyllactosaminyl chains on CD43. Binding was also inhibited by treating macrophages with anti-nucleolin antibody, indicating that recognition occurs through nucleolin, a cell-surface receptor. Further, nucleolin-transfected HEK293 cells bound A23187-treated cells, and this binding was inhibited by in the presence of oligosaccharides. Taken together, these results show that elevated calcium levels induce CD43 capping, and macrophages remove the cells if their nucleolin receptors can bind to the poly-N-acetyllactosaminyl chains of capped CD43.
Collapse
Affiliation(s)
- Yuichi Miki
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
| | | | | | | |
Collapse
|
6
|
Auvynet C, Moreno S, Melchy E, Coronado-Martínez I, Montiel JL, Aguilar-Delfin I, Rosenstein Y. Galectin-1 promotes human neutrophil migration. Glycobiology 2012; 23:32-42. [PMID: 22942212 DOI: 10.1093/glycob/cws128] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An important step of innate immune response is the recruitment of polymorphonuclear leukocytes (PMN) to injured tissues through chemotactic molecules. Galectins, a family of endogenous lectins, participate in numerous functions such as lymphoid cell migration, homing, cell-cell and cell-matrix interactions. Particularly, galectin-3 (Gal-3) and -9 have been implicated in the modulation of acute and chronic inflammation by inducing the directional migration of monocytes/macrophages and eosinophils, whereas Gal-1 is considered to function as an anti-inflammatory molecule, capable of inhibiting the influx of PMN to the site of injury. In this study, we assessed the effect of Gal-1 on neutrophil recruitment, in the absence of additional inflammatory insults. Contrasting with its capacity to inhibit cell trafficking and modulate the release of mediators described in models of acute inflammation and autoimmunity, we evidenced that Gal-1 has the capacity to induce neutrophil migration both in vitro and in vivo. This effect is not mediated through a G-protein-coupled receptor but potentially through the sialoglycoprotein CD43, via carbohydrate binding and through the p38 mitogen-activated protein kinase pathway. These results suggest a novel biological function for CD43 on neutrophils and highlight that depending on the environment, Gal-1 can act either as chemoattractant or, as a molecule that negatively regulates migration under acute inflammatory conditions, underscoring the potential of Gal-1 as a target for innovative drug development.
Collapse
Affiliation(s)
- Constance Auvynet
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologia, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Col Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | | | | | | | | | | | | |
Collapse
|
7
|
Oguri E, Miki Y, Hirano K, Yamanaka M, Beppu M. Clearance of CD43-capped cells by macrophages: capping alone leads to phagocytosis. Biol Pharm Bull 2012; 35:551-8. [PMID: 22466560 DOI: 10.1248/bpb.35.551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Apoptotic cells must be recognized early for phagocytosis to ensure that their toxic contents do not damage neighboring cells. In some cases this is achieved via CD43-capped membrane glycoproteins, the sialylpolylactosaminyl chains of which serve as ligands for phagocytosis by macrophages. However, because many additional changes occur during apoptosis, determining exactly which events are responsible for signaling macrophages to initiate phagocytosis remains a challenge. Here, we examined one clearance mechanism in detail and determined that capping of CD43 alone is sufficient to initiate phagocytosis. We induced macrophage-mediated phagocytosis by using cytochalasin B to artificially cap CD43 on healthy (non-apoptotic) Jurkat cells. Additional experiments confirmed that sialylpolylactosaminyl chains formed through this capping method are a prerequisite for removal, and that nucleolin is the macrophage receptor responsible for their detection. These findings strongly suggest that capping of CD43 presents a sufficient signal for phagocytosis without any additional membrane changes.
Collapse
Affiliation(s)
- Emiri Oguri
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Japan
| | | | | | | | | |
Collapse
|
8
|
Szabady RL, Lokuta MA, Walters KB, Huttenlocher A, Welch RA. Modulation of neutrophil function by a secreted mucinase of Escherichia coli O157:H7. PLoS Pathog 2009; 5:e1000320. [PMID: 19247439 PMCID: PMC2642718 DOI: 10.1371/journal.ppat.1000320] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 01/30/2009] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli O157∶H7 is a human enteric pathogen that causes hemorrhagic colitis which can progress to hemolytic uremic syndrome, a severe kidney disease with immune involvement. During infection, E. coli O157∶H7 secretes StcE, a metalloprotease that promotes the formation of attaching and effacing lesions and inhibits the complement cascade via cleavage of mucin-type glycoproteins. We found that StcE cleaved the mucin-like, immune cell-restricted glycoproteins CD43 and CD45 on the neutrophil surface and altered neutrophil function. Treatment of human neutrophils with StcE led to increased respiratory burst production and increased cell adhesion. StcE-treated neutrophils exhibited an elongated morphology with defective rear detachment and impaired migration, suggesting that removal of the anti-adhesive capability of CD43 by StcE impairs rear release. Use of zebrafish embryos to model neutrophil migration revealed that StcE induced neutrophil retention in the fin after tissue wounding, suggesting that StcE modulates neutrophil-mediated inflammation in vivo. Neutrophils are crucial innate effectors of the antibacterial immune response and can contribute to severe complications caused by infection with E. coli O157∶H7. Our data suggest that the StcE mucinase can play an immunomodulatory role by directly altering neutrophil function during infection. StcE may contribute to inflammation and tissue destruction by mediating inappropriate neutrophil adhesion and activation. Enterohemorrhagic Escherichia coli (EHEC) poses a significant threat to the U.S. food supply, causing foodborne gastrointestinal disease in humans that can progress to hemolytic uremic syndrome (HUS), a potentially fatal kidney disease. Research suggests that EHEC strains are growing more virulent, resulting in a higher incidence of hospitalization and development of HUS from recent produce-associated outbreaks. Although immune dysregulation is a feature of HUS disease, the specific mechanisms contributing to altered immune function require investigation. Furthermore, the contribution of the immune response to early intestinal disease is not known. StcE is a secreted protease of EHEC that is expressed during infection and may contribute to virulence via cleavage of mucin-like glycoproteins. In this study, we define mucinase activity toward glycoproteins on the surface of human neutrophils and find that StcE alters neutrophil activity by interacting with these proteins. StcE affected crucial neutrophil functions including oxidative burst production and migration. The effects of StcE were both cleavage-dependent and cleavage-independent, providing insight into a novel mechanism for mediating neutrophil function via mucin interactions. Our study reports an immune-modulating role for a potential EHEC virulence factor and provides a possible explanation for altered neutrophil phenotypes observed during E. coli O157∶H7-induced disease.
Collapse
Affiliation(s)
- Rose L. Szabady
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mary A. Lokuta
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kevin B. Walters
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Rodney A. Welch
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
9
|
Khunkaewla P, Schiller HB, Paster W, Leksa V, Čermák L, Anděra L, Hořejší V, Stockinger H. LFA-1-mediated leukocyte adhesion regulated by interaction of CD43 with LFA-1 and CD147. Mol Immunol 2008; 45:1703-11. [DOI: 10.1016/j.molimm.2007.09.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 09/27/2007] [Indexed: 10/22/2022]
|
10
|
Abstract
Biomolecule gradients have been shown to play roles in a wide range of biological processes including development, inflammation, wound healing, and cancer metastasis. Elucidation of these phenomena requires the ability to expose cells to biomolecule gradients that are quantifiable, controllable, and mimic those that are present in vivo. Here we review the major biological phenomena in which biomolecule gradients are employed, traditional in vitro gradient-generating methods developed over the past 50 years, and new microfluidic devices for generating gradients. Microfluidic gradient generators offer greater levels of precision, quantitation, and spatiotemporal gradient control than traditional methods, and may greatly enhance our understanding of many biological phenomena. For each method, we outline the salient features, capabilities, and applications.
Collapse
Affiliation(s)
- Thomas M Keenan
- Department of Bioengineering, University of Washington, Washington 98195, USA
| | | |
Collapse
|
11
|
|
12
|
Sengupta K, Aranda-Espinoza H, Smith L, Janmey P, Hammer D. Spreading of neutrophils: from activation to migration. Biophys J 2006; 91:4638-48. [PMID: 17012330 PMCID: PMC1779913 DOI: 10.1529/biophysj.105.080382] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Neutrophils rely on rapid changes in morphology to ward off invaders. Time-resolved dynamics of spreading human neutrophils after activation by the chemoattractant fMLF (formyl methionyl leucyl phenylalanine) was observed by RICM (reflection interference contrast microscopy). An image-processing algorithm was developed to identify the changes in the overall cell shape and the zones of close contact with the substrate. We show that in the case of neutrophils, cell spreading immediately after exposure of fMLF is anisotropic and directional. The dependence of spreading area, A, of the cell as a function of time, t, shows several distinct regimes, each of which can be fitted as power laws (A ~ t(b)). The different spreading regimes correspond to distinct values of the exponent b and are related to the adhesion state of the cell. Treatment with cytochalasin-B eliminated the anisotropy in the spreading.
Collapse
Affiliation(s)
- Kheya Sengupta
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | |
Collapse
|