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Leijonhufvud C, Sanz-Ortega L, Schlums H, Gaballa A, Andersson A, Eriksson C, Segerberg F, Uhlin M, Bryceson YT, Carlsten M. KIR2DS1 and KIR2DL1-C245 Dominantly Repress NK Cell Degranulation Triggered by Monoclonal or Bispecific Antibodies, whereas Education by Uptuning Inhibitory Killer Ig-related Receptors Exerts No Advantage in Ab-dependent Cellular Cytotoxicity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:868-880. [PMID: 38240527 DOI: 10.4049/jimmunol.2300197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/30/2023] [Indexed: 02/22/2024]
Abstract
NK cell responsiveness to target cells is tuned by interactions between inhibitory NK cell receptors and their cognate HLA class I ligands in a process termed "NK cell education." Previous studies addressing the role for NK cell education in Ab-dependent cellular cytotoxicity (ADCC) show ambiguous results and do not encompass full educational resolution. In this study, we systematically characterized human NK cell CD16-triggered degranulation toward defined human tumor cell lines in the presence of either the mAb rituximab or a recently developed CD34xCD16 bispecific killer engager. Despite positive correlation between killer Ig-related receptor (KIR)-mediated education and CD16 expression, NK cells educated by one or even two inhibitory KIRs did not perform better in terms of ADCC than uneducated NK cells in either missing-self or KIR-ligand matched settings at saturating Ab concentrations. Instead, NKG2A+ NK cells consistently showed more potent ADCC in the missing-self context despite lower levels of CD16 expression. KIR2DS1+ NK cells demonstrated dampened ADCC in both the missing-self and KIR-ligand matched settings, even in the presence of its ligand HLA C2. The lower response by KIR2DS1+ NK cells was also observed when stimulated with a bispecific killer engager. Surprisingly, repression of ADCC was also observed by NKG2A+ NK cells coexpressing the inhibitory KIR2DL1-C245 receptor that confers weak education. In conclusion, our study suggests that NK cell education by inhibitory KIRs does not augment ADCC per se, whereas expression of KIR2DS1 and KIR2DL1-C245 dominantly represses ADCC. These insights add to the fundamental understanding of NK cells and may have implications for their therapeutic use.
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Affiliation(s)
- Caroline Leijonhufvud
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Laura Sanz-Ortega
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Heinrich Schlums
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ahmed Gaballa
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
| | - Agneta Andersson
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Caroline Eriksson
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Filip Segerberg
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Michael Uhlin
- Department of Clinical Science, Intervention and Technology, Karolinska Institute, Stockholm, Sweden
- Department of Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Yenan T Bryceson
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mattias Carlsten
- Department of Medicine, Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
- Center for Cell Therapy and Allogeneic Stem Cell Transplantation, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
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2
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Wu J, Stewart WCL, Jayaprakash C, Das J. BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells. NPJ Syst Biol Appl 2023; 9:46. [PMID: 37736766 PMCID: PMC10516955 DOI: 10.1038/s41540-023-00299-0] [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] [Received: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
Mechanistic models are commonly employed to describe signaling and gene regulatory kinetics in single cells and cell populations. Recent advances in single-cell technologies have produced multidimensional datasets where snapshots of copy numbers (or abundances) of a large number of proteins and mRNA are measured across time in single cells. The availability of such datasets presents an attractive scenario where mechanistic models are validated against experiments, and estimated model parameters enable quantitative predictions of signaling or gene regulatory kinetics. To empower the systems biology community to easily estimate parameters accurately from multidimensional single-cell data, we have merged a widely used rule-based modeling software package BioNetGen, which provides a user-friendly way to code for mechanistic models describing biochemical reactions, and the recently introduced CyGMM, that uses cell-to-cell differences to improve parameter estimation for such networks, into a single software package: BioNetGMMFit. BioNetGMMFit provides parameter estimates of the model, supplied by the user in the BioNetGen markup language (BNGL), which yield the best fit for the observed single-cell, time-stamped data of cellular components. Furthermore, for more precise estimates, our software generates confidence intervals around each model parameter. BioNetGMMFit is capable of fitting datasets of increasing cell population sizes for any mechanistic model specified in the BioNetGen markup language. By streamlining the process of developing mechanistic models for large single-cell datasets, BioNetGMMFit provides an easily-accessible modeling framework designed for scale and the broader biochemical signaling community.
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Affiliation(s)
- John Wu
- Department of Computer Science, The Ohio State University, 281 W Lane Ave, Columbus, OH, 43210, USA.
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
| | | | - Ciriyam Jayaprakash
- Department of Physics, The Ohio State University, 191 W Woodruff Ave, Columbus, OH, 43210, USA
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
- Departments of Pediatrics, Biomedical Informatics, Pelotonia Institute of Immuno-Oncology, College of Medicine, and Biophysics Program, The Ohio State University, 370 W 9th Ave, Columbus, OH, 43210, USA.
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3
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Hallisey M, Dennis J, Gabriel EP, Masciarelli A, Chen J, Abrecht C, Brainard M, Marcotte WM, Dong H, Hathaway E, Tarannum M, Vergara JA, Schork AN, Tyan K, Tarantino G, Liu D, Romee R, Rahma OE, Severgnini M, Hodi FS, Baginska J. Profiling of Natural Killer Interactions With Cancer Cells Using Mass Cytometry. J Transl Med 2023; 103:100174. [PMID: 37169083 DOI: 10.1016/j.labinv.2023.100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
We developed a comprehensive method for functional assessment of the changes in immune populations and killing activity of peripheral blood mononuclear cells after cocultures with cancer cells using mass cytometry. In this study, a 43-marker mass cytometry panel was applied to a coculture of immune cells from healthy donors' peripheral blood mononuclear cells with diverse cancer cell lines. DNA content combined with classical CD45 surface staining was used as gating parameters for cocultures of immune cells (CD45high/DNAlow) with hematological (CD45low/DNAhigh) and solid cancer cell lines (CD45neg/DNAhigh). This strategy allows for universal discrimination of cancer cells from immune populations without the need for a specific cancer cell marker and simultaneous assessment of phenotypical changes in both populations. The use of mass cytometry allows for simultaneous detection of changes in natural killer, natural killer T cell, and T cell phenotypes and degranulation of immune populations upon target recognition, analysis of target cells for cytotoxic protein granzyme B content, and cancer cell death. These findings have broad applicability in research and clinical settings with the aim to phenotype and assess functional changes following not only NK-cancer cell interactions but also the effect of those interactions on other immune populations.
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Affiliation(s)
- Margaret Hallisey
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jenna Dennis
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth P Gabriel
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alyssa Masciarelli
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jiajia Chen
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Charlotte Abrecht
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Martha Brainard
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William M Marcotte
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Han Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emma Hathaway
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mubin Tarannum
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Juliana A Vergara
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Abigail N Schork
- Longwood Medical Area CyTOF Core, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kevin Tyan
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Tarantino
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David Liu
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rizwan Romee
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Osama E Rahma
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Mariano Severgnini
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joanna Baginska
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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4
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Wethington D, Mukherjee S, Das J. McSNAC: A software to approximate first-order signaling networks from mass cytometry data. QUANTITATIVE BIOLOGY 2023; 11:59-71. [PMID: 37123637 PMCID: PMC10134772 DOI: 10.15302/j-qb-022-0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Background Mass cytometry (CyTOF) gives unprecedented opportunity to simultaneously measure up to 40 proteins in single cells, with a theoretical potential to reach 100 proteins. This high-dimensional single-cell information can be very useful in dissecting mechanisms of cellular activity. In particular, measuring abundances of signaling proteins like phospho-proteins can provide detailed information on the dynamics of single-cell signaling processes. However, computational analysis is required to reconstruct such networks with a mechanistic model. Methods We propose our Mass cytometry Signaling Network Analysis Code (McSNAC), a new software capable of reconstructing signaling networks and estimating their kinetic parameters from CyTOF data. McSNAC approximates signaling networks as a network of first-order reactions between proteins. This assumption often breaks down as signaling reactions can involve binding and unbinding, enzymatic reactions, and other nonlinear constructions. Furthermore, McSNAC may be limited to approximating indirect interactions between protein species, as cytometry experiments are only able to assay a small fraction of protein species involved in signaling. Results We carry out a series of in silico experiments here to show (1) McSNAC is capable of accurately estimating the ground-truth model in a scalable manner when given data originating from a first-order system; (2) McSNAC is capable of qualitatively predicting outcomes to perturbations of species abundances in simple second-order reaction models and in a complex in silico nonlinear signaling network in which some proteins are unmeasured. Conclusions These findings demonstrate that McSNAC can be a valuable screening tool for generating models of signaling networks from time-stamped CyTOF data.
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Affiliation(s)
- Darren Wethington
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sayak Mukherjee
- Battelle Memorial Institute, Columbus, Ohio 43201, United States
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio 43205, United States
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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5
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Improving NK cell function in multiple myeloma with NKTR-255, a novel polymer-conjugated human IL-15. Blood Adv 2023; 7:9-19. [PMID: 35882498 DOI: 10.1182/bloodadvances.2022007985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 01/18/2023] Open
Abstract
Multiple myeloma (MM) is characterized by an immunosuppressive microenvironment that enables tumor development. One of the mechanisms of immune evasion used by MM cells is the inhibition of natural killer (NK) cell effector functions; thus, the restoration of NK cell antitumor activity represents a key goal to increase tumor cell recognition, avoid tumor escape and potentially enhancing the effect of other drugs. In this study, we evaluated the ability of the investigational medicine NKTR-255, an IL-15 receptor agonist, to engage the IL-15 pathway and stimulate NK cells against MM cells. We observed that incubation with NKTR-255 was able to tilt the balance toward an activated phenotype in NK cells isolated from peripheral blood mononuclear cells of patients with MM, with increased expression of activating receptors on the surface of treated NK cells. This resulted in an enhanced degranulation, cytokine release, and anti-tumor cytotoxicity when the NK cells were exposed to both MM cell lines and primary MM cells. We further evaluated the in vivo effect of NKTR-255 in fully humanized immunocompetent mice subcutaneously engrafted with H929 MM cells. Compared with placebo, weekly injection of the mice with NKTR-255 increased the number of circulating NK cells in peripheral blood and delayed tumor growth. Finally, we observed that combination of NKTR-255 with the anti-CD38 antibody, daratumumab, was effective against MM cells in vitro and in vivo. Taken together, our data suggest a significant impact of NKTR-255 in inducing NK cell function against MM cells with important translational implications.
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6
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Grewal RK, Das J. Spatially resolved in silico modeling of NKG2D signaling kinetics suggests a key role of NKG2D and Vav1 Co-clustering in generating natural killer cell activation. PLoS Comput Biol 2022; 18:e1010114. [PMID: 35584138 PMCID: PMC9154193 DOI: 10.1371/journal.pcbi.1010114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/31/2022] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
Natural Killer (NK) cells provide key resistance against viral infections and tumors. A diverse set of activating and inhibitory NK cell receptors (NKRs) interact with cognate ligands presented by target host cells, where integration of dueling signals initiated by the ligand-NKR interactions determines NK cell activation or tolerance. Imaging experiments over decades have shown micron and sub-micron scale spatial clustering of activating and inhibitory NKRs. The mechanistic roles of these clusters in affecting downstream signaling and activation are often unclear. To this end, we developed a predictive in silico framework by combining spatially resolved mechanistic agent based modeling, published TIRF imaging data, and parameter estimation to determine mechanisms by which formation and spatial movements of activating NKG2D microclusters affect early time NKG2D signaling kinetics in a human cell line NKL. We show co-clustering of NKG2D and the guanosine nucleotide exchange factor Vav1 in NKG2D microclusters plays a dominant role over ligand (ULBP3) rebinding in increasing production of phospho-Vav1(pVav1), an activation marker of early NKG2D signaling. The in silico model successfully predicts several scenarios of inhibition of NKG2D signaling and time course of NKG2D spatial clustering over a short (~3 min) interval. Modeling shows the presence of a spatial positive feedback relating formation and centripetal movements of NKG2D microclusters, and pVav1 production offers flexibility towards suppression of activating signals by inhibitory KIR ligands organized in inhomogeneous spatial patterns (e.g., a ring). Our in silico framework marks a major improvement in developing spatiotemporal signaling models with quantitatively estimated model parameters using imaging data. Natural Killer cells are lymphocytes of our innate immunity and provide important resistance against viral infections and tumors. NK cells scan the local environment with diverse activating and inhibitory NK cell receptors (NKRs) and remain tolerized or lyse target cells expressing cognate ligands to NKRs. NKRs have been found to form micron sized clusters (or microclusters) as they interact with cognate ligands, and mechanisms regarding how the formation and movements of these microclusters influence NK cell signaling and activation, specifically related to activating NKRs, are often unclear. To this end, we develop a predictive spatially resolved early-time NK cell signaling model to study the interplay between membrane-proximal biochemical signaling events and the kinetics of microclusters of activating NKG2D and inhibitory KIR2DL2 receptors. We used published TIRF imaging data to validate our in silico models and estimate model parameters. Predictions from multiple in silico models are tested against a variety of data obtained from published imaging experiments and immunoassays. Our analysis suggests co-clustering of NKG2D and the guanosine nucleotide exchange factor Vav1 in the microclusters plays a major role in enhancing downstream activating signals. The developed framework can be extended to describe spatiotemporal signaling for other activating NKRs including CD16.
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Affiliation(s)
- Rajdeep Kaur Grewal
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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7
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Ben-Shmuel A, Sabag B, Puthenveetil A, Biber G, Levy M, Jubany T, Awwad F, Roy RK, Joseph N, Matalon O, Kivelevitz J, Barda-Saad M. Inhibition of SHP-1 activity by PKC-θ regulates NK cell activation threshold and cytotoxicity. eLife 2022; 11:73282. [PMID: 35258455 PMCID: PMC8903836 DOI: 10.7554/elife.73282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/23/2022] [Indexed: 12/26/2022] Open
Abstract
Natural killer (NK) cells play a crucial role in immunity, killing virally infected and cancerous cells. The balance of signals initiated upon engagement of activating and inhibitory NK receptors with cognate ligands determines killing or tolerance. Nevertheless, the molecular mechanisms regulating rapid NK cell discrimination between healthy and malignant cells in a heterogeneous tissue environment are incompletely understood. The SHP-1 tyrosine phosphatase is the central negative NK cell regulator that dephosphorylates key activating signaling proteins. Though the mechanism by which SHP-1 mediates NK cell inhibition has been partially elucidated, the pathways by which SHP-1 is itself regulated remain unclear. Here, we show that phosphorylation of SHP-1 in NK cells on the S591 residue by PKC-θ promotes the inhibited SHP-1 ‘folded’ state. Silencing PKC-θ maintains SHP-1 in the active conformation, reduces NK cell activation and cytotoxicity, and promotes tumor progression in vivo. This study reveals a molecular pathway that sustains the NK cell activation threshold through suppression of SHP-1 activity.
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Affiliation(s)
- Aviad Ben-Shmuel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Batel Sabag
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Abhishek Puthenveetil
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Guy Biber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Moria Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Tammir Jubany
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Fatima Awwad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Roshan Kumar Roy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noah Joseph
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omri Matalon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jessica Kivelevitz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Mira Barda-Saad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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8
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Wu Z, Park S, Lau CM, Zhong Y, Sheppard S, Sun JC, Das J, Altan-Bonnet G, Hsu KC. Dynamic variability in SHP-1 abundance determines natural killer cell responsiveness. Sci Signal 2021; 14:eabe5380. [PMID: 34752140 DOI: 10.1126/scisignal.abe5380] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Zeguang Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Soo Park
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yi Zhong
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sam Sheppard
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Pediatrics, Pelotonia Institute of ImmunoOncology, Wexner College of Medicine, Ohio State University, Columbus, OH 43210, USA.,Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Katharine C Hsu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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9
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Makaryan SZ, Finley SD. An optimal control approach for enhancing natural killer cells' secretion of cytolytic molecules. APL Bioeng 2020; 4:046107. [PMID: 33376936 PMCID: PMC7758091 DOI: 10.1063/5.0024726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/27/2020] [Indexed: 12/31/2022] Open
Abstract
Natural killer (NK) cells are immune effector cells that can detect and lyse cancer cells. However, NK cell exhaustion, a phenotype characterized by reduced secretion of cytolytic models upon serial stimulation, limits the NK cell's ability to lyse cells. In this work, we investigated in silico strategies that counteract the NK cell's reduced secretion of cytolytic molecules. To accomplish this goal, we constructed a mathematical model that describes the dynamics of the cytolytic molecules granzyme B (GZMB) and perforin-1 (PRF1) and calibrated the model predictions to published experimental data using a Bayesian parameter estimation approach. We applied an information-theoretic approach to perform a global sensitivity analysis, from which we found that the suppression of phosphatase activity maximizes the secretion of GZMB and PRF1. However, simply reducing the phosphatase activity is shown to deplete the cell's intracellular pools of GZMB and PRF1. Thus, we added a synthetic Notch (synNotch) signaling circuit to our baseline model as a method for controlling the secretion of GZMB and PRF1 by inhibiting phosphatase activity and increasing production of GZMB and PRF1. We found that the optimal synNotch system depends on the frequency of NK cell stimulation. For only a few rounds of stimulation, the model predicts that inhibition of phosphatase activity leads to more secreted GZMB and PRF1; however, for many rounds of stimulation, the model reveals that increasing production of the cytolytic molecules is the optimal strategy. In total, we developed a mathematical framework that provides actionable insight into engineering robust NK cells for clinical applications.
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Affiliation(s)
- Sahak Z Makaryan
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Stacey D Finley
- Department of Biomedical Engineering, Mork Family Department of Chemical Engineering and Materials Science, and Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
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10
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Makaryan SZ, Finley SD. Enhancing network activation in natural killer cells: predictions from in silico modeling. Integr Biol (Camb) 2020; 12:109-121. [PMID: 32409824 PMCID: PMC7480959 DOI: 10.1093/intbio/zyaa008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 01/08/2023]
Abstract
Natural killer (NK) cells are part of the innate immune system and are capable of killing diseased cells. As a result, NK cells are being used for adoptive cell therapies for cancer patients. The activation of NK cell stimulatory receptors leads to a cascade of intracellular phosphorylation reactions, which activates key signaling species that facilitate the secretion of cytolytic molecules required for cell killing. Strategies that maximize the activation of such intracellular species can increase the likelihood of NK cell killing upon contact with a cancer cell and thereby improve efficacy of NK cell-based therapies. However, due to the complexity of intracellular signaling, it is difficult to deduce a priori which strategies can enhance species activation. Therefore, we constructed a mechanistic model of the CD16, 2B4 and NKG2D signaling pathways in NK cells to simulate strategies that enhance signaling. The model predictions were fit to published data and validated with a separate dataset. Model simulations demonstrate strong network activation when the CD16 pathway is stimulated. The magnitude of species activation is most sensitive to the receptor's initial concentration and the rate at which the receptor is activated. Co-stimulation of CD16 and NKG2D in silico required fewer ligands to achieve half-maximal activation than other combinations, suggesting co-stimulating these pathways is most effective in activating the species. We applied the model to predict the effects of perturbing the signaling network and found two strategies that can potently enhance network activation. When the availability of ligands is low, it is more influential to engineer NK cell receptors that are resistant to proteolytic cleavage. In contrast, for high ligand concentrations, inhibiting phosphatase activity leads to sustained species activation. The work presented here establishes a framework for understanding the complex, nonlinear aspects of NK cell signaling and provides detailed strategies for enhancing NK cell activation.
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Affiliation(s)
- Sahak Z. Makaryan
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Stacey D. Finley
- Department of Biomedical Engineering, Mork Family Department of Chemical Engineering and Materials Science, and Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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11
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François P, Zilman A. Physical approaches to receptor sensing and ligand discrimination. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Das J, Lanier LL. Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute? J Leukoc Biol 2019; 105:1305-1317. [PMID: 31063614 DOI: 10.1002/jlb.6mr1218-505r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 12/31/2022] Open
Abstract
The use of mathematical and computational tools in investigating Natural Killer (NK) cell biology and in general the immune system has increased steadily in the last few decades. However, unlike the physical sciences, there is a persistent ambivalence, which however is increasingly diminishing, in the biology community toward appreciating the utility of quantitative tools in addressing questions of biological importance. We survey some of the recent developments in the application of quantitative approaches for investigating different problems in NK cell biology and evaluate opportunities and challenges of using quantitative methods in providing biological insights in NK cell biology.
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Affiliation(s)
- Jayajit Das
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Physics, The Ohio State University, Columbus, Ohio, USA.,Biophysics Program, The Ohio State University, Columbus, Ohio, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, California, USA
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13
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Mbiribindi B, Mukherjee S, Wellington D, Das J, Khakoo SI. Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes. Front Immunol 2019; 10:605. [PMID: 31024524 PMCID: PMC6460049 DOI: 10.3389/fimmu.2019.00605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
Natural Killer (NK) cell activation requires integration of inhibitory and activating signaling. Inhibitory signals are determined by members of the killer cell immunoglobulin-like receptor (KIR) family, which have major histocompatibility complex (MHC) class I ligands. Loss of this inhibitory signal leads to NK cell activation. Thus, down-regulation of MHC I during viral infection or cancer induces NK cell activation. However, NK cell activation in the presence of MHC-I has been demonstrated for HLA-C*0102 through changes in its peptide content: "peptide antagonism." Here we identify an antagonist peptide for HLA-C*0304 suggesting that peptide antagonism is a generalizable phenomenon and, using a combination of mathematical modeling, confocal imaging, and immune-assays, we quantitatively determine mechanisms that underlie peptide antagonism in inhibitory KIR2DL2/3 signaling. These data provide a mechanism for NK cell activation based on a reduction of inhibitory signaling in the presence of preserved levels of MHC class I.
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Affiliation(s)
- Berenice Mbiribindi
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sayak Mukherjee
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Dannielle Wellington
- Department of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Wexner College of Medicine, The Ohio State University, Columbus, OH, United States.,Biophysics Program, The Ohio State University, Columbus, OH, United States
| | - Salim I Khakoo
- Department of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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14
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Lee SJ, Choi JS, Bong SM, Hwang HJ, Lee J, Song HJ, Lee J, Kim JH, Koh JS, Lee BI. Crystal Structures of Spleen Tyrosine Kinase in Complex with Two Novel 4-Aminopyrido[4,3-d] Pyrimidine Derivative Inhibitors. Mol Cells 2018; 41:545-552. [PMID: 29890824 PMCID: PMC6030240 DOI: 10.14348/molcells.2018.2219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/01/2018] [Accepted: 04/06/2018] [Indexed: 11/27/2022] Open
Abstract
Spleen tyrosine kinase (SYK) is a cytosolic non-receptor protein tyrosine kinase. Because SYK mediates key receptor signaling pathways involving the B cell receptor and Fc receptors, SYK is an attractive target for autoimmune disease and cancer treatments. To date, representative oral SYK inhibitors, including fostamatinib (R406 or R788), entospletinib (GS-9973), cerdulatinib (PRT062070), and TAK-659, have been assessed in clinical trials. Here, we report the crystal structures of SYK in complex with two newly developed inhibitors possessing 4-aminopyrido[4,3-D]pyrimidine moieties (SKI-G-618 and SKI-O-85). One SYK inhibitor (SKI-G-618) exhibited moderate inhibitory activity against SYK, whereas the other inhibitor (SKI-O-85) exhibited a low inhibitory profile against SYK. Binding mode analysis indicates that a highly potent SYK inhibitor might be developed by modifying and optimizing the functional groups that interact with Leu377, Gly378, and Val385 in the G-loop and the nearby region in SYK. In agreement with our structural analysis, one of our SYK inhibitor (SKI-G-618) shows strong inhibitory activities on the β-hexosaminidase release and phosphorylation of SYK/Vav in RBL-2H3 cells. Taken together, our findings have important implications for the design of high affinity SYK inhibitors.
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Affiliation(s)
- Sang Jae Lee
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408,
Korea
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826,
Korea
| | | | - Seoung Min Bong
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408,
Korea
| | | | | | - Ho-Juhn Song
- Genosco, 767C Concord Ave, 2nd Floor, Cambridge, MA 02138,
USA
| | - Jaekyoo Lee
- Genosco, 767C Concord Ave, 2nd Floor, Cambridge, MA 02138,
USA
| | | | - Jong Sung Koh
- Genosco, 767C Concord Ave, 2nd Floor, Cambridge, MA 02138,
USA
| | - Byung Il Lee
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408,
Korea
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15
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Mukherjee S, Jensen H, Stewart W, Stewart D, Ray WC, Chen SY, Nolan GP, Lanier LL, Das J. In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells. Sci Signal 2017; 10:10/485/eaai9062. [PMID: 28655861 DOI: 10.1126/scisignal.aai9062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Natural killer (NK) cells perform immunosurveillance of virally infected and transformed cells, and their activation depends on the balance between signaling by inhibitory and activating receptors. Cytokine receptor signaling can synergize with activating receptor signaling to induce NK cell activation. We investigated the interplay between the signaling pathways stimulated by the cytokine interleukin-2 (IL-2) and the activating receptor NKG2D in immature (CD56bright) and mature (CD56dim) subsets of human primary NK cells using mass cytometry experiments and in silico modeling. Our analysis revealed that IL-2 changed the abundances of several key proteins, including NKG2D and the phosphatase CD45. Furthermore, we found differences in correlations between protein abundances, which were associated with the maturation state of the NK cells. The mass cytometry measurements also revealed that the signaling kinetics of key protein abundances induced by NKG2D stimulation depended on the maturation state and the pretreatment condition of the NK cells. Our in silico model, which described the multidimensional data with coupled first-order reactions, predicted that the increase in CD45 abundance was a major enhancer of NKG2D-mediated activation in IL-2-treated CD56bright NK cells but not in IL-2-treated CD56dim NK cells. This dependence on CD45 was verified by measurement of CD107a mobilization to the NK cell surface (a marker of activation). Our mathematical framework can be used to glean mechanisms underlying synergistic signaling pathways in other activated immune cells.
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Affiliation(s)
- Sayak Mukherjee
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Helle Jensen
- Department of Microbiology and Immunology and Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - William Stewart
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - David Stewart
- Department of Mathematics, University of Iowa, Iowa City, IA 52242, USA
| | - William C Ray
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.,Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Jayajit Das
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.,Biophysics Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
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16
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Alhajjat AM, Strong BS, Lee AE, Turner LE, Wadhwani RK, Ortaldo JR, Heusel JW, Shaaban AF. Prenatal Allospecific NK Cell Tolerance Hinges on Instructive Allorecognition through the Activating Receptor during Development. THE JOURNAL OF IMMUNOLOGY 2015; 195:1506-16. [PMID: 26136432 DOI: 10.4049/jimmunol.1500463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/11/2015] [Indexed: 12/24/2022]
Abstract
Little is known about how the prenatal interaction between NK cells and alloantigens shapes the developing NK cell repertoire toward tolerance or immunity. Specifically, the effect on NK cell education arising from developmental corecognition of alloantigens by activating and inhibitory receptors with shared specificity is uncharacterized. Using a murine prenatal transplantation model, we examined the manner in which this seemingly conflicting input affects NK cell licensing and repertoire formation in mixed hematopoietic chimeras. We found that prenatal NK cell tolerance arose from the elimination of phenotypically hostile NK cells that express an allospecific activating receptor without coexpressing any allospecific inhibitory receptors. Importantly, the checkpoint for the system appeared to occur centrally within the bone marrow during the final stage of NK cell maturation and hinged on the instructive recognition of allogeneic ligand by the activating receptor rather than through the inhibitory receptor as classically proposed. Residual nondeleted hostile NK cells expressing only the activating receptor exhibited an immature, anergic phenotype, but retained the capacity to upregulate inhibitory receptor expression in peripheral sites. However, the potential for this adaptive change to occur was lost in developmentally mature chimeras. Collectively, these findings illuminate the intrinsic process in which developmental allorecognition through the activating receptor regulates the emergence of durable NK cell tolerance and establishes a new paradigm to fundamentally guide future investigations of prenatal NK cell-allospecific education.
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Affiliation(s)
- Amir M Alhajjat
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Beverly S Strong
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Amanda E Lee
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Lucas E Turner
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Ram K Wadhwani
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - John R Ortaldo
- Experimental Therapeutics Section, National Cancer Institute, Frederick, MD 21702
| | - Jonathan W Heusel
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110; and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110
| | - Aimen F Shaaban
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45229;
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17
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Bicknell BA, Dayan P, Goodhill GJ. The limits of chemosensation vary across dimensions. Nat Commun 2015; 6:7468. [PMID: 26088726 PMCID: PMC4557358 DOI: 10.1038/ncomms8468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/13/2015] [Indexed: 01/20/2023] Open
Abstract
Many biological processes rely on the ability of cells to measure local ligand concentration. However, such measurements are constrained by noise arising from diffusion and the stochastic nature of receptor–ligand interactions. It is thus critical to understand how accurately, in principle, concentration measurements can be made. Previous theoretical work has mostly investigated this in 3D under the simplifying assumption of an unbounded domain of diffusion, but many biological problems involve 2D concentration measurement in bounded domains, for which diffusion behaves quite differently. Here we present a theory of the precision of chemosensation that covers bounded domains of any dimensionality. We find that the quality of chemosensation in lower dimensions is controlled by domain size, suggesting a general principle applicable to many biological systems. Applying the theory to biological problems in 2D shows that diffusion-limited signalling is an efficient mechanism on time scales consistent with behaviour. Theoretical studies on chemosensation often invoke a model of three dimensional unbounded diffusion, but many biological problems involve two-dimensional diffusion in a bounded domain. Here Bicknell et al. present a model for chemosensation that covers bounded domains of any dimension, and apply it to biological problems in two dimensions.
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Affiliation(s)
- Brendan A Bicknell
- 1] Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia [2] School of Mathematics and Physics, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Dayan
- Gatsby Computational Neuroscience Unit, University College London, London WC1N 3AR, UK
| | - Geoffrey J Goodhill
- 1] Queensland Brain Institute, The University of Queensland, St Lucia, Queensland 4072, Australia [2] School of Mathematics and Physics, The University of Queensland, St Lucia, Queensland 4072, Australia
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18
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Prinz PU, Mendler AN, Brech D, Masouris I, Oberneder R, Noessner E. NK-cell dysfunction in human renal carcinoma reveals diacylglycerol kinase as key regulator and target for therapeutic intervention. Int J Cancer 2014; 135:1832-41. [DOI: 10.1002/ijc.28837] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Petra U. Prinz
- Helmholtz Zentrum München; Germany Research Center for Environmental Health; Institute of Molecular Immunology, Munich Germany
| | - Anna N. Mendler
- Helmholtz Zentrum München; Germany Research Center for Environmental Health; Institute of Molecular Immunology, Munich Germany
| | - Dorothee Brech
- Helmholtz Zentrum München; Germany Research Center for Environmental Health; Institute of Molecular Immunology, Munich Germany
| | - Ilias Masouris
- Helmholtz Zentrum München; Germany Research Center for Environmental Health; Institute of Molecular Immunology, Munich Germany
| | | | - Elfriede Noessner
- Helmholtz Zentrum München; Germany Research Center for Environmental Health; Institute of Molecular Immunology, Munich Germany
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19
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Long EO, Kim HS, Liu D, Peterson ME, Rajagopalan S. Controlling natural killer cell responses: integration of signals for activation and inhibition. Annu Rev Immunol 2013; 31:227-58. [PMID: 23516982 PMCID: PMC3868343 DOI: 10.1146/annurev-immunol-020711-075005] [Citation(s) in RCA: 877] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding how signals are integrated to control natural killer (NK) cell responsiveness in the absence of antigen-specific receptors has been a challenge, but recent work has revealed some underlying principles that govern NK cell responses. NK cells use an array of innate receptors to sense their environment and respond to alterations caused by infections, cellular stress, and transformation. No single activation receptor dominates; instead, synergistic signals from combinations of receptors are integrated to activate natural cytotoxicity and cytokine production. Inhibitory receptors for major histocompatibility complex class I (MHC-I) have a critical role in controlling NK cell responses and, paradoxically, in maintaining NK cells in a state of responsiveness to subsequent activation events, a process referred to as licensing. MHC-I-specific inhibitory receptors both block activation signals and trigger signals to phosphorylate and inactivate the small adaptor Crk. These different facets of inhibitory signaling are incorporated into a revocable license model for the reversible tuning of NK cell responsiveness.
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Affiliation(s)
- Eric O. Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Hun Sik Kim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
- Department of Medicine, Graduate School, University of Ulsan, Seoul 138-736, Korea;
| | - Dongfang Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
- Center for Human Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030;
| | - Mary E. Peterson
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Sumati Rajagopalan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
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20
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Watzl C, Sternberg-Simon M, Urlaub D, Mehr R. Understanding natural killer cell regulation by mathematical approaches. Front Immunol 2012; 3:359. [PMID: 23264774 PMCID: PMC3525018 DOI: 10.3389/fimmu.2012.00359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/10/2012] [Indexed: 11/13/2022] Open
Abstract
The activity of natural killer (NK) cells is regulated by various processes including education/licensing, priming, integration of positive and negative signals through an array of activating and inhibitory receptors, and the development of memory-like functionality. These processes are often very complex due to the large number of different receptors and signaling pathways involved. Understanding these complex mechanisms is therefore a challenge, but is critical for understanding NK cell regulation. Mathematical approaches can facilitate the analysis and understanding of complex systems. Therefore, they may be instrumental for studies in NK cell biology. Here we provide a review of the different mathematical approaches to the analysis of NK cell signal integration, activation, proliferation, and the acquisition of inhibitory receptors. These studies show how mathematical methods can aid the analysis of NK cell regulation.
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Affiliation(s)
- Carsten Watzl
- IfADo - Leibniz Institute for Occupational Research Dortmund, Germany
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21
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Brodin P, Lakshmikanth T, Kärre K, Höglund P. Skewing of the NK Cell Repertoire by MHC Class I via Quantitatively Controlled Enrichment and Contraction of Specific Ly49 Subsets. THE JOURNAL OF IMMUNOLOGY 2012; 188:2218-26. [DOI: 10.4049/jimmunol.1102801] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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