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Edgar L, Thompson AJ, Vartabedian VF, Kikuchi C, Woehl JL, Teijaro JR, Paulson JC. Sialic Acid Ligands of CD28 Suppress Costimulation of T Cells. ACS Cent Sci 2021; 7:1508-1515. [PMID: 34584952 PMCID: PMC8461770 DOI: 10.1021/acscentsci.1c00525] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 05/07/2023]
Abstract
Effector T cells comprise the cellular arm of the adaptive immune system and are essential for mounting immune responses against pathogens and cancer. To reach effector status, costimulation through CD28 is required. Here, we report that sialic acid-containing glycans on the surface of both T cells and APCs are alternative ligands of CD28 that compete with binding to its well-documented activatory ligand CD80 on the APC, resulting in attenuated costimulation. Removal of sialic acids enhances antigen-mediated activation of naïve T cells and also increases the revival of effector T cells made hypofunctional or exhausted via chronic viral infection. This occurs through a mechanism that is synergistic with antibody blockade of the inhibitory PD-1 axis. These results reveal a previously unrecognized role of sialic acid ligands in attenuation of CD28-mediated costimulation of T cells.
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Affiliation(s)
- Landon
J. Edgar
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Andrew J. Thompson
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Vincent F. Vartabedian
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Chika Kikuchi
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Jordan L. Woehl
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
| | - John R. Teijaro
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
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2
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Woehl JL, Kitamura S, Dillon N, Han Z, Edgar LJ, Nizet V, Wolan DW. An Irreversible Inhibitor to Probe the Role of Streptococcus pyogenes Cysteine Protease SpeB in Evasion of Host Complement Defenses. ACS Chem Biol 2020; 15:2060-2069. [PMID: 32662975 DOI: 10.1021/acschembio.0c00191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the CA class of cysteine proteases have multifaceted roles in physiology and virulence for many bacteria. Streptococcal pyrogenic exotoxin B (SpeB) is secreted by Streptococcus pyogenes and implicated in the pathogenesis of the bacterium through degradation of key human immune effector proteins. Here, we developed and characterized a clickable inhibitor, 2S-alkyne, based on X-ray crystallographic analysis and structure-activity relationships. Our SpeB probe showed irreversible enzyme inhibition in biochemical assays and labeled endogenous SpeB in cultured S. pyogenes supernatants. Importantly, application of 2S-alkyne decreased S. pyogenes survival in the presence of human neutrophils and supports the role of SpeB-mediated proteolysis as a mechanism to limit complement-mediated host defense. We posit that our SpeB inhibitor will be a useful chemical tool to regulate, label, and quantitate secreted cysteine proteases with SpeB-like activity in complex biological samples and a lead candidate for new therapeutics designed to sensitize S. pyogenes to host immune clearance.
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3
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Yao Y, Kadam RU, Lee CCD, Woehl JL, Wu NC, Zhu X, Kitamura S, Wilson IA, Wolan DW. An influenza A hemagglutinin small-molecule fusion inhibitor identified by a new high-throughput fluorescence polarization screen. Proc Natl Acad Sci U S A 2020; 117:18431-18438. [PMID: 32690700 PMCID: PMC7414093 DOI: 10.1073/pnas.2006893117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Influenza hemagglutinin (HA) glycoprotein is the primary surface antigen targeted by the host immune response and a focus for development of novel vaccines, broadly neutralizing antibodies (bnAbs), and therapeutics. HA enables viral entry into host cells via receptor binding and membrane fusion and is a validated target for drug discovery. However, to date, only a very few bona fide small molecules have been reported against the HA. To identity new antiviral lead candidates against the highly conserved fusion machinery in the HA stem, we synthesized a fluorescence-polarization probe based on a recently described neutralizing cyclic peptide P7 derived from the complementarity-determining region loops of human bnAbs FI6v3 and CR9114 against the HA stem. We then designed a robust binding assay compatible with high-throughput screening to identify molecules with low micromolar to nanomolar affinity to influenza A group 1 HAs. Our simple, low-cost, and efficient in vitro assay was used to screen H1/Puerto Rico/8/1934 (H1/PR8) HA trimer against ∼72,000 compounds. The crystal structure of H1/PR8 HA in complex with our best hit compound F0045(S) confirmed that it binds to pockets in the HA stem similar to bnAbs FI6v3 and CR9114, cyclic peptide P7, and small-molecule inhibitor JNJ4796. F0045 is enantioselective against a panel of group 1 HAs and F0045(S) exhibits in vitro neutralization activity against multiple H1N1 and H5N1 strains. Our assay, compound characterization, and small-molecule candidate should further stimulate the discovery and development of new compounds with unique chemical scaffolds and enhanced influenza antiviral capabilities.
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MESH Headings
- Antiviral Agents/chemistry
- Antiviral Agents/pharmacology
- Drug Evaluation, Preclinical/methods
- Fluorescence Polarization/methods
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H5N1 Subtype/drug effects
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/metabolism
- Influenza, Human/virology
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/pharmacology
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Affiliation(s)
- Yao Yao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Chang-Chun David Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jordan L Woehl
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Seiya Kitamura
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037;
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037;
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
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Kitamura S, Zheng Q, Woehl JL, Solania A, Chen E, Dillon N, Hull MV, Kotaniguchi M, Cappiello JR, Kitamura S, Nizet V, Sharpless KB, Wolan DW. Sulfur(VI) Fluoride Exchange (SuFEx)-Enabled High-Throughput Medicinal Chemistry. J Am Chem Soc 2020; 142:10899-10904. [PMID: 32479075 DOI: 10.1021/jacs.9b13652] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Optimization of small-molecule probes or drugs is a synthetically lengthy, challenging, and resource-intensive process. Lack of automation and reliance on skilled medicinal chemists is cumbersome in both academic and industrial settings. Here, we demonstrate a high-throughput hit-to-lead process based on the biocompatible sulfur(VI) fluoride exchange (SuFEx) click chemistry. A high-throughput screening hit benzyl (cyanomethyl)carbamate (Ki = 8 μM) against a bacterial cysteine protease SpeB was modified with a SuFExable iminosulfur oxydifluoride [RN═S(O)F2] motif, rapidly diversified into 460 analogs in overnight reactions, and the products were directly screened to yield drug-like inhibitors with 480-fold higher potency (Ki = 18 nM). We showed that the improved molecule is active in a bacteria-host coculture. Since this SuFEx linkage reaction succeeds on picomole scale for direct screening, we anticipate our methodology can accelerate the development of robust biological probes and drug candidates.
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Affiliation(s)
| | | | | | | | | | | | | | - Miyako Kotaniguchi
- Laboratory of Advanced Food Process Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Nakaku, Sakai, Osaka 599-8570, Japan
| | | | - Shinichi Kitamura
- Laboratory of Advanced Food Process Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Nakaku, Sakai, Osaka 599-8570, Japan
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Stapels DAC, Woehl JL, Milder FJ, Tromp AT, van Batenburg AA, de Graaf WC, Broll SC, White NM, Rooijakkers SHM, Geisbrecht BV. Evidence for multiple modes of neutrophil serine protease recognition by the EAP family of Staphylococcal innate immune evasion proteins. Protein Sci 2017; 27:509-522. [PMID: 29114958 DOI: 10.1002/pro.3342] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022]
Abstract
Neutrophils contain high levels of chymotrypsin-like serine proteases (NSPs) within their azurophilic granules that have a multitude of functions within the immune system. In response, the pathogen Staphylococcus aureus has evolved three potent inhibitors (Eap, EapH1, and EapH2) that protect the bacterium as well as several of its secreted virulence factors from the degradative action of NSPs. We previously showed that these so-called EAP domain proteins represent a novel class of NSP inhibitors characterized by a non-covalent inhibitory mechanism and a distinct target specificity profile. Based upon high levels of structural homology amongst the EAP proteins and the NSPs, as well as supporting biochemical data, we predicted that the inhibited complex would be similar for all EAP/NSP pairs. However, we present here evidence that EapH1 and EapH2 bind the canonical NSP, Neutrophil Elastase (NE), in distinct orientations. We discovered that alteration of EapH1 residues at the EapH1/NE interface caused a dramatic loss of affinity and inhibition of NE, while mutation of equivalent positions in EapH2 had no effect on NE binding or inhibition. Surprisingly, mutation of residues in an altogether different region of EapH2 severely impacted both the NE binding and inhibitory properties of EapH2. Even though EapH1 and EapH2 bind and inhibit NE and a second NSP, Cathepsin G, equally well, neither of these proteins interacts with the structurally related, but non-proteolytic granule protein, azurocidin. These studies expand our understanding of EAP/NSP interactions and suggest that members of this immune evasion protein family are capable of diverse target recognition modes.
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Affiliation(s)
- Daphne A C Stapels
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Fin J Milder
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Angelino T Tromp
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Aernoud A van Batenburg
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Wilco C de Graaf
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Samuel C Broll
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Natalie M White
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Suzan H M Rooijakkers
- Department of Medical Microbiology, University Medical Center Utrecht, 3584, CX Utrecht, The Netherlands
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
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Woehl JL, Ramyar KX, Katz BB, Walker JK, Geisbrecht BV. The structural basis for inhibition of the classical and lectin complement pathways by S. aureus extracellular adherence protein. Protein Sci 2017; 26:1595-1608. [PMID: 28512867 DOI: 10.1002/pro.3195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 01/07/2023]
Abstract
The extracellular adherence protein (Eap) plays a crucial role in pathogenesis and survival of Staphylococcus aureus by inhibiting the classical and lectin pathways of complement. We have previously shown that Eap binds with nanomolar affinity to complement C4b and disrupts the initial interaction between C4b and C2, thereby inhibiting formation of the classical and lectin pathway C3 pro-convertase. Although an underlying mechanism has been identified, the structural basis for Eap binding to C4b is poorly understood. Here, we show that Eap domains 3 and 4 each contain a low-affinity, but saturable binding site for C4b. Taking advantage of the high lysine content of Eap, we used a zero-length crosslinking approach to map the Eap binding site to both the α'- and γ-chains of C4b. We also probed the C4b/Eap interface through a chemical footprinting approach involving lysine modification, proteolytic digestion, and mass spectrometry. This identified seven lysines in Eap that undergo changes in solvent exposure upon C4b binding. We found that simultaneous mutation of these lysines to either alanine or glutamate diminished C4b binding and complement inhibition by Eap. Together, our results provide insight into Eap recognition of C4b, and suggest that the repeating domains that comprise Eap are capable of multiple ligand-binding modes.
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Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Benjamin B Katz
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - John K Walker
- Department of Pharmacology and Physiology, St. Louis University School of Medicine, St. Louis, Missouri, 63104
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
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7
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Woehl JL, Takahashi D, Herrera AI, Geisbrecht BV, Prakash O. (1)H, (15)N, and (13)C resonance assignments of Staphylococcus aureus extracellular adherence protein domain 4. Biomol NMR Assign 2016; 10:301-5. [PMID: 27372920 PMCID: PMC5503465 DOI: 10.1007/s12104-016-9688-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/22/2016] [Indexed: 05/25/2023]
Abstract
The pathogenic bacterium Staphylococcus aureus has evolved to actively evade many aspects of the human innate immune system by expressing a series of secreted inhibitory proteins. Among these, the extracellular adherence protein (Eap) has been shown to inhibit the classical and lectin pathways of the complement system. By binding to complement component C4b, Eap is able to inhibit formation of the CP/LP C3 pro-convertase. Secreted full-length, mature Eap consists of four ~98 residue domains, all of which adopt a similar beta-grasp fold, and are connected through a short linker region. Through multiple biochemical approaches, it has been determined that the third and fourth domains of Eap are responsible for C4b binding. Here we report the backbone and side-chain resonance assignments of the 11.3 kDa fourth domain of Eap. The assignment data has been deposited in the BMRB database under the accession number 26726.
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Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Daisuke Takahashi
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Alvaro I Herrera
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS, 66506, USA.
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Woehl JL, Stapels DAC, Garcia BL, Ramyar KX, Keightley A, Ruyken M, Syriga M, Sfyroera G, Weber AB, Zolkiewski M, Ricklin D, Lambris JD, Rooijakkers SHM, Geisbrecht BV. The extracellular adherence protein from Staphylococcus aureus inhibits the classical and lectin pathways of complement by blocking formation of the C3 proconvertase. J Immunol 2014; 193:6161-6171. [PMID: 25381436 DOI: 10.4049/jimmunol.1401600] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The pathogenic bacterium Staphylococcus aureus actively evades many aspects of human innate immunity by expressing a series of small inhibitory proteins. A number of these proteins inhibit the complement system, which labels bacteria for phagocytosis and generates inflammatory chemoattractants. Although the majority of staphylococcal complement inhibitors act on the alternative pathway to block the amplification loop, only a few proteins act on the initial recognition cascades that constitute the classical pathway (CP) and lectin pathway (LP). We screened a collection of recombinant, secreted staphylococcal proteins to determine whether S. aureus produces other molecules that inhibit the CP and/or LP. Using this approach, we identified the extracellular adherence protein (Eap) as a potent, specific inhibitor of both the CP and LP. We found that Eap blocked CP/LP-dependent activation of C3, but not C4, and that Eap likewise inhibited deposition of C3b on the surface of S. aureus cells. In turn, this significantly diminished the extent of S. aureus opsonophagocytosis and killing by neutrophils. This combination of functional properties suggested that Eap acts specifically at the level of the CP/LP C3 convertase (C4b2a). Indeed, we demonstrated a direct, nanomolar-affinity interaction of Eap with C4b. Eap binding to C4b inhibited binding of both full-length C2 and its C2b fragment, which indicated that Eap disrupts formation of the CP/LP C3 proconvertase (C4b2). As a whole, our results demonstrate that S. aureus inhibits two initiation routes of complement by expression of the Eap protein, and thereby define a novel mechanism of immune evasion.
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Affiliation(s)
- Jordan L Woehl
- Department of Biochemistry & Molecular Biophysics; Kansas State University, Manhattan, KS, USA
| | - Daphne A C Stapels
- Medical Microbiology; University Medical Center Utrecht, Utrecht, The Netherlands
| | - Brandon L Garcia
- School of Biological Sciences; University of Missouri-Kansas City, Kansas City, MO, USA
| | - Kasra X Ramyar
- Department of Biochemistry & Molecular Biophysics; Kansas State University, Manhattan, KS, USA
| | - Andrew Keightley
- School of Biological Sciences; University of Missouri-Kansas City, Kansas City, MO, USA
| | - Maartje Ruyken
- Medical Microbiology; University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maria Syriga
- Department of Pathology & Laboratory Medicine; University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia Sfyroera
- Department of Pathology & Laboratory Medicine; University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander B Weber
- School of Biological Sciences; University of Missouri-Kansas City, Kansas City, MO, USA
| | - Michal Zolkiewski
- Department of Biochemistry & Molecular Biophysics; Kansas State University, Manhattan, KS, USA
| | - Daniel Ricklin
- Department of Pathology & Laboratory Medicine; University of Pennsylvania, Philadelphia, PA, USA
| | - John D Lambris
- Department of Pathology & Laboratory Medicine; University of Pennsylvania, Philadelphia, PA, USA
| | | | - Brian V Geisbrecht
- School of Biological Sciences; University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Biochemistry & Molecular Biophysics; Kansas State University, Manhattan, KS, USA
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