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Ashkarran AA, Gharibi H, Modaresi SM, Sayadi M, Jafari M, Lin Z, Ritz D, Kakhniashvili D, Sun L, Landry MP, Saei AA, Mahmoudi M. Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.582595. [PMID: 38496642 PMCID: PMC10942461 DOI: 10.1101/2024.03.06.582595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients, into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 μg/ml phosphatidylcholine could singularly increase the number of unique proteins within the protein corona (897 proteins). This specific concentration of phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing concentration dynamic range of plasma proteome and boosting LC-MS/MS sensitivity for detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in plasma. This significant achievement is made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in proteomic depth of the plasma sample. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics.
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Affiliation(s)
- Ali Akbar Ashkarran
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Maryam Sayadi
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Maryam Jafari
- Division of ENT Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Zijin Lin
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| | - Danilo Ritz
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - David Kakhniashvili
- Proteomics and Metabolomics Core Facility, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, United States
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Neuroscience, University of California, Berkeley, Berkeley, CA, 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94063, USA
| | - Amir Ata Saei
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17165, Sweden
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
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Mladěnka P, Macáková K, Kujovská Krčmová L, Javorská L, Mrštná K, Carazo A, Protti M, Remião F, Nováková L. Vitamin K - sources, physiological role, kinetics, deficiency, detection, therapeutic use, and toxicity. Nutr Rev 2021; 80:677-698. [PMID: 34472618 PMCID: PMC8907489 DOI: 10.1093/nutrit/nuab061] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Vitamin K is traditionally connected with blood coagulation, since it is needed for the posttranslational modification of 7 proteins involved in this cascade. However, it is also involved in the maturation of another 11 or 12 proteins that play different roles, encompassing in particular the modulation of the calcification of connective tissues. Since this process is physiologically needed in bones, but is pathological in arteries, a great deal of research has been devoted to finding a possible link between vitamin K and the prevention of osteoporosis and cardiovascular diseases. Unfortunately, the current knowledge does not allow us to make a decisive conclusion about such a link. One possible explanation for this is the diversity of the biological activity of vitamin K, which is not a single compound but a general term covering natural plant and animal forms of vitamin K (K1 and K2) as well as their synthetic congeners (K3 and K4). Vitamin K1 (phylloquinone) is found in several vegetables. Menaquinones (MK4–MK13, a series of compounds known as vitamin K2) are mostly of a bacterial origin and are introduced into the human diet mainly through fermented cheeses. Current knowledge about the kinetics of different forms of vitamin K, their detection, and their toxicity are discussed in this review.
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Affiliation(s)
- Přemysl Mladěnka
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic. K. Macáková is with the Department of Pharmacognosy, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republicv
| | - Kateřina Macáková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Lenka Kujovská Krčmová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic.,Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Lenka Javorská
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Kristýna Mrštná
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic.,Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Alejandro Carazo
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic. K. Macáková is with the Department of Pharmacognosy, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republicv
| | - Michele Protti
- M. Protti is with the Research Group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Fernando Remião
- F. Remião is with the UCIBIO-REQUIMTE, Laboratory of Toxicology, The Biological Sciences Department, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, Porto, Portugal
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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Chellam Gayathri S, Gupta S, Suresh A, Senapati S, Sengupta T. Effect of variations in the conserved residues E371 and S359 on the structural dynamics of protein Z dependent protease inhibitor (ZPI): a molecular dynamic simulation study. J Biomol Struct Dyn 2021; 40:6405-6414. [PMID: 33554754 DOI: 10.1080/07391102.2021.1883114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein Z (PZ) dependent protease inhibitor (ZPI) is a natural anticoagulant inhibiting blood coagulation proteases fXa and fXIa. Despite being a member of the serpin superfamily, it possesses unique structural features such as activation by PZ, regulating its inhibitory function. In order to understand the Reactive Centre Loop (RCL) dynamics of ZPI, which is absolutely critical for its activity, we performed Molecular Dynamics (MD) simulation on ZPI and its E371 and S359 variants located at important conserved functional sites. Unexpectedly, the RCL of E371 variants, (E371K, E371R, and E371Q), were shown to be very stable due to compensatory interactions at the proximal end of RCL. Interestingly, RCL flexibility was shown to be enhanced in the double mutant K318E-E371K due to the repulsive effect of increased negative charge on top of the breach region. Principal component analysis (PCA) coupled with residue wise interaction network analysis(RIN) revealed correlated motion between the RCL and the PZ binding regions in the WT. However, a loss of regulation in correlated motion between RCL and PZ binding hotspot Tyr240 in the double mutant was also observed. Additionally, the S359F and S359I mutations resulted in increased RCL flexibility owing to the disruption of stabilizing hydrogen bonding interaction at the distal end of strand S5A. Thus, the current study proposes that the overall stabilizing interactions of S5A is a major regulator of proper loop movement of ZPI for its activity. The results would be beneficial to engineer activity compromised ZPI as a prophylactic agent for the treatment of hemophilia.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Suchetana Gupta
- BJM School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Aravind Suresh
- Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Chennai, India
| | - Sanjib Senapati
- BJM School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Tanusree Sengupta
- Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Chennai, India
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Phosphatidylserine and phosphatidylethanolamine regulate the structure and function of FVIIa and its interaction with soluble tissue factor. Biosci Rep 2021; 41:227639. [PMID: 33479740 PMCID: PMC7859323 DOI: 10.1042/bsr20204077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/04/2022] Open
Abstract
Cell membranes have important functions in many steps of the blood coagulation cascade, including the activation of factor X (FX) by the factor VIIa (FVIIa)-tissue factor (TF) complex (extrinsic Xase). FVIIa shares structural similarity with factor IXa (FIXa) and FXa. FIXa and FXa are regulated by binding to phosphatidylserine (PS)-containing membranes via their γ-carboxyglutamic acid-rich domain (Gla) and epidermal growth-factor (EGF) domains. Although FVIIa also has a Gla-rich region, its affinity for PS-containing membranes is much lower compared with that of FIXa and FXa. Research suggests that a more common endothelial cell lipid, phosphatidylethanolamine (PE), might augment the contribution of PS in FVIIa membrane-binding and proteolytic activity. We used soluble forms of PS and PE (1,2-dicaproyl-sn-glycero-3-phospho-l-serine (C6PS), 1,2-dicaproyl-sn-glycero-3-phospho-ethanolamine (C6PE)) to test the hypothesis that the two lipids bind to FVIIa jointly to promote FVIIa membrane binding and proteolytic activity. By equilibrium dialysis and tryptophan fluorescence, we found two sites on FVIIa that bound equally to C6PE and C6PS with Kd of ∼ 150–160 μM, however, deletion of Gla domain reduced the binding affinity. Binding of lipids occurred with greater affinity (Kd∼70–80 μM) when monitored by FVIIa proteolytic activity. Global fitting of all datasets indicated independent binding of two molecules of each lipid. The proteolytic activity of FVIIa increased by ∼50–100-fold in the presence of soluble TF (sTF) plus C6PS/C6PE. However, the proteolytic activity of Gla-deleted FVIIa in the presence of sTF was reduced drastically, suggesting the importance of Gla domain to maintain full proteolytic activity.
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Lee HR, Lee GY, You DG, Kim HK, Yoo YD. Hepatitis C Virus p7 Induces Membrane Permeabilization by Interacting with Phosphatidylserine. Int J Mol Sci 2020; 21:ijms21030897. [PMID: 32019133 PMCID: PMC7037181 DOI: 10.3390/ijms21030897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus (HCV) p7 is known to be a nonselective cation channel for HCV maturation. Because the interaction of HCV proteins with host lipids in the endoplasmic reticulum membrane is crucial for the budding process, the identification of p7–lipid interactions could be important for understanding the HCV life cycle. Here, we report that p7 interacts with phosphatidylserine (PS) to induce membrane permeabilization. The interaction of p7 with PS was not inhibited by Gd3+ ions, which have been known to interact with negatively charged lipids, but channel activity and p7-induced mitochondrial depolarization were inhibited by Gd3+ ions. From the present results, we suggest that the p7–PS interaction plays an essential role in regulating its ion channel function and could be a potential molecular target for anti-HCV therapy.
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Affiliation(s)
- Hye-Ra Lee
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul 02841, Korea; (H.-R.L.); (G.Y.L.)
- Department of Biosystems and Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Gi Young Lee
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul 02841, Korea; (H.-R.L.); (G.Y.L.)
| | - Deok-Gyun You
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul 02841, Korea; (H.-R.L.); (G.Y.L.)
| | - Hong Kyu Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Young Do Yoo
- Laboratory of Molecular Cell Biology, Graduate School of Medicine, Korea University College of Medicine, Korea University, Seoul 02841, Korea; (H.-R.L.); (G.Y.L.)
- Correspondence:
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Huang X, Swanson R, Kroh HK, Bock PE. Protein Z-dependent protease inhibitor (ZPI) is a physiologically significant inhibitor of prothrombinase function. J Biol Chem 2019; 294:7644-7657. [PMID: 30918026 DOI: 10.1074/jbc.ra118.006787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/11/2019] [Indexed: 01/26/2023] Open
Abstract
Current thought holds that factor Xa (FXa) bound in the prothrombinase complex is resistant to regulation by protein protease inhibitors during prothrombin activation. Here we provide evidence that, contrary to this view, the FXa-specific serpin inhibitor, protein Z-dependent protease inhibitor (ZPI), complexed with its cofactor, protein Z (PZ), functions as a physiologically significant inhibitor of prothrombinase-bound FXa during prothrombin activation. Kinetics studies showed that the rapid rate of inhibition of FXa by the ZPI-PZ complex on procoagulant membrane vesicles (ka (app) ∼107 m-1 s-1) was decreased ∼10-fold when FXa was bound to FVa in prothrombinase and a further ∼3-4-fold when plasma levels of S195A prothrombin were present (ka (app) 2 × 105 m-1 s-1). Nevertheless, the ZPI-PZ complex produced a major inhibition of thrombin generation during prothrombinase-catalyzed activation of prothrombin under physiologically relevant conditions. The importance of ZPI-PZ complex anticoagulant regulation of FXa both before and after incorporation into prothrombinase was supported by thrombin generation assays in plasma. These showed enhanced thrombin generation when the inhibitor was neutralized with a PZ-specific antibody and decreased thrombin generation when exogenous ZPI-PZ complex was added whether prothrombin was activated directly by FXa or through extrinsic or intrinsic pathway activators. Moreover, the PZ antibody enhanced thrombin generation both in the absence and presence of activated protein C (APC) anticoagulant activity. Taken together, these results suggest an important anticoagulant role for the ZPI-PZ complex in regulating both free FXa generated in the initiation phase of coagulation as well as prothrombinase-bound FXa in the propagation phase that complement prothrombinase regulation by APC.
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Affiliation(s)
- Xin Huang
- From the Department of Periodontics, University of Illinois at Chicago, Chicago, Illinois 60612 and
| | - Richard Swanson
- From the Department of Periodontics, University of Illinois at Chicago, Chicago, Illinois 60612 and
| | - Heather K Kroh
- the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Paul E Bock
- the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
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Leskova GF. Phospholipid-Dependent Mechanisms of Platelet Dysfunction in Rabbits with Hemorrhagic Shock. Bull Exp Biol Med 2018; 165:731-733. [PMID: 30353341 DOI: 10.1007/s10517-018-4253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Indexed: 10/28/2022]
Abstract
The time course of phospholipid composition of platelet plasma membranes at the peak of hemorrhagic shock were studied in rabbit experiments. The results indicate the key role of impairment of the structure of platelet membrane phospholipid bilayer in the pathogenesis of shockogenic thrombocytopathy.
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Affiliation(s)
- G F Leskova
- Research Institute of Pathology and Pathophysiology, Moscow, Russia.
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Kerr D, Tietjen GT, Gong Z, Tajkhorshid E, Adams EJ, Lee KYC. Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2126-2133. [PMID: 29920237 DOI: 10.1016/j.bbamem.2018.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/17/2022]
Abstract
There is a diverse class of peripheral membrane-binding proteins that specifically bind phosphatidylserine (PS), a lipid that signals apoptosis or cell fusion depending on the membrane context of its presentation. PS-receptors are specialized for particular PS-presenting pathways, indicating that they might be sensitive to the membrane context. In this review, we describe a combination of thermodynamic, structural, and computational techniques that can be used to investigate the mechanisms underlying this sensitivity. As an example, we focus on three PS-receptors of the T-cell Immunoglobulin and Mucin containing (TIM) protein family, which we have previously shown to differ in their sensitivity to PS surface density.
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Affiliation(s)
- Daniel Kerr
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America
| | - Gregory T Tietjen
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America
| | - Zhiliang Gong
- Department of Chemistry, The University of Chicago, Chicago, IL, United States of America
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology and Committee on Immunology, The University of Chicago, Chicago, IL, United States of America
| | - Ka Yee C Lee
- Program in Biophysical Sciences, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America; Department of Chemistry, The University of Chicago, Chicago, IL, United States of America; James Franck Institute, The University of Chicago, Chicago, IL, United States of America.
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Deguchi H, Elias DJ, Griffin JH. Minor Plasma Lipids Modulate Clotting Factor Activities and May Affect Thrombosis Risk. Res Pract Thromb Haemost 2017; 1:93-102. [PMID: 29082360 PMCID: PMC5658053 DOI: 10.1002/rth2.12017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Essentials Circulating blood contains hundreds of lipids, many of which might influence blood coagulation. Recent discoveries about circulating lipids that can affect blood coagulation are reviewed. Minor abundance plasma lipids can modulate thrombin generation via direct effects on factor Xa. Variations in minor abundance plasma lipids can influence thrombin generation and thrombosis risk.
Abstract Different minor abundance plasma lipids significantly influence thrombin generation in vitro and significant differences in such lipids are linked to risk for venous thrombosis. Some plasma sphingolipids including glucosylceramide, lyso‐sulfatide and sphingosine have anticoagulant properties whereas, conversely, some plasma phospholipid derivatives, including certain lyso‐phospholipids and ethanolamides, have procoagulant properties. Plasma metabolite profiling of venous thrombosis patients showed association of venous thrombosis with decreased plasma long‐chain acylcarntines, leading to discovery of their anticoagulant activity as inhibitors of factor Xa. Inhibition of factor Xa by acylcarnitines does not require the protein's Gla‐domain, emphasizing an expanded framework for the paradigm for lipid‐clotting factor interactions. Overall, whether by genetics or environment, alterations in the dynamics of lipid metabolism linked to an altered lipidome may contribute to regulation of blood coagulation because imbalances between physiologic procoagulant and anticoagulant lipids may contribute to excessive thrombin generation that augments risk for thrombosis.
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Affiliation(s)
- Hiroshi Deguchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Darlene J Elias
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Scripps Clinic and Scripps Green Hospital, La Jolla, CA, USA
| | - John H Griffin
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
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