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Sawetaji, Aggarwal KK. A Protease from Moringa oleifera Lam. Exhibits In-vitro Blood Clot Solubilization and Fibrin Hydrolysis. Protein J 2024; 43:923-934. [PMID: 39068632 DOI: 10.1007/s10930-024-10222-z] [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] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
Thrombosis is the formation of abnormal blood clots in the blood vessels that obstruct blood flow and lead to thrombosis. Current treatments for thrombosis are associated with serious side effects. Therefore there is a need for alternative natural therapy. A fibrinolytic protease was isolated from fresh leaves of Moringa oleifera Lam. and characterized for its potential to solubilize blood clots and hydrolyse fibrin under in-vitro conditions. The isolated protease showed a single protein band on native-PAGE. It showed optimum fibrinolytic activity at pH 8.0, 37 oC with 50 µg protein. The fibrinolytic activity of isolated protease was also confirmed by fibrin zymography. Km and Vmax of isolated protease were determined by the Lineweaver Burk plot. The isolated protease could solubilize 96.41% of blood clots by 96 h under in-vitro conditions. In-vitro fibrin hydrolysis and blood clot solubilization activities shown by an isolated protease from leaves of Moringa oleifera Lam. suggest its fibrinolytic potential to dissolve blood clots. Being a natural molecule and from a dietary plant it can be explored as an alternative natural therapy against thrombosis.
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Affiliation(s)
- Sawetaji
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16-C Dwarka, New Delhi, 110078, India
| | - Kamal Krishan Aggarwal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16-C Dwarka, New Delhi, 110078, India.
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2
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Ohashi Y, Protack CD, Aoyagi Y, Gonzalez L, Thaxton C, Zhang W, Kano M, Bai H, Yatsula B, Alves R, Hoshina K, Schneider EB, Long X, Perry RJ, Dardik A. Heterogeneous gene expression during early arteriovenous fistula remodeling suggests that downregulation of metabolism predicts adaptive venous remodeling. Sci Rep 2024; 14:13287. [PMID: 38858395 PMCID: PMC11164895 DOI: 10.1038/s41598-024-64075-8] [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: 10/10/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Clinical outcomes of arteriovenous fistulae (AVF) for hemodialysis remain inadequate since biological mechanisms of AVF maturation and failure are still poorly understood. Aortocaval fistula creation (AVF group) or a sham operation (sham group) was performed in C57BL/6 mice. Venous limbs were collected on postoperative day 7 and total RNA was extracted for high throughput RNA sequencing and bioinformatic analysis. Genes in metabolic pathways were significantly downregulated in the AVF, whereas significant sex differences were not detected. Since gene expression patterns among the AVF group were heterogenous, the AVF group was divided into a 'normal' AVF (nAVF) group and an 'outliers' (OUT) group. The gene expression patterns of the nAVF and OUT groups were consistent with previously published data showing venous adaptive remodeling, whereas enrichment analyses showed significant upregulation of metabolism, inflammation and coagulation in the OUT group compared to the nAVF group, suggesting the heterogeneity during venous remodeling reflects early gene expression changes that may correlate with AVF maturation or failure. Early detection of these processes may be a translational strategy to predict fistula failure and reduce patient morbidity.
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Affiliation(s)
- Yuichi Ohashi
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
- Division of Vascular Surgery, Department of Surgery, The University of Tokyo, Tokyo, Japan
| | - Clinton D Protack
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Yukihiko Aoyagi
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Luis Gonzalez
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Carly Thaxton
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Weichang Zhang
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Masaki Kano
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
- Department of Cardiovascular Surgery, Tokyo Medical University, Tokyo, Japan
| | - Hualong Bai
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Bogdan Yatsula
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Rafael Alves
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Katsuyuki Hoshina
- Division of Vascular Surgery, Department of Surgery, The University of Tokyo, Tokyo, Japan
| | - Eric B Schneider
- Department of Surgery, Center for Health Services and Outcomes Research, Yale School of Medicine, New Haven, CT, USA
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Rachel J Perry
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Alan Dardik
- Vascular Biology and Therapeutics Program, Yale School of Medicine, New Haven, CT, USA.
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA.
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA.
- Surgical Service, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA.
- Yale School of Medicine, 10 Amistad Street, Room 437, PO Box 208089, New Haven, CT, 06520-8089, USA.
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Balogh G, Bereczky Z. Molecular Mechanisms of the Impaired Heparin Pentasaccharide Interactions in 10 Antithrombin Heparin Binding Site Mutants Revealed by Enhanced Sampling Molecular Dynamics. Biomolecules 2024; 14:657. [PMID: 38927061 PMCID: PMC11201378 DOI: 10.3390/biom14060657] [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: 04/17/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Antithrombin (AT) is a critical regulator of the coagulation cascade by inhibiting multiple coagulation factors including thrombin and FXa. Binding of heparinoids to this serpin enhances the inhibition considerably. Mutations located in the heparin binding site of AT result in thrombophilia in affected individuals. Our aim was to study 10 antithrombin mutations known to affect their heparin binding in a heparin pentasaccharide bound state using two molecular dynamics (MD) based methods providing enhanced sampling, GaMD and LiGaMD2. The latter provides an additional boost to the ligand and the most important binding site residues. From our GaMD simulations we were able to identify four variants (three affecting amino acid Arg47 and one affecting Lys114) that have a particularly large effect on binding. The additional acceleration provided by LiGaMD2 allowed us to study the consequences of several other mutants including those affecting Arg13 and Arg129. We were able to identify several conformational types by cluster analysis. Analysis of the simulation trajectories revealed the causes of the impaired pentasaccharide binding including pentasaccharide subunit conformational changes and altered allosteric pathways in the AT protein. Our results provide insights into the effects of AT mutations interfering with heparin binding at an atomic level and can facilitate the design or interpretation of in vitro experiments.
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Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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Vankwani S, Mirza MR, Awan FR, Zafar M, Nawrocki A, Wasim M, Khan HN, Ayesha H, Larsen MR, Choudhary MI. Label free quantitative proteomic profiling of serum samples of intellectually disabled young patients revealed dysregulation of complement coagulation and cholesterol cascade systems. Metab Brain Dis 2024; 39:855-869. [PMID: 38733546 DOI: 10.1007/s11011-024-01351-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Intellectual disability is a heterogeneous disorder, diagnosed using intelligence quotient (IQ) score criteria. Currently, no specific clinical test is available to diagnose the disease and its subgroups due to inadequate understanding of the pathophysiology. Therefore, current study was designed to explore the molecular mechanisms involved in disease perturbation, and to identify potential biomarkers for disease diagnosis and prognosis. A total of 250 participants were enrolled in this study, including 200 intellectually disabled (ID) subjects from the subgroups (mild, moderate, and severe) with age and gender matched healthy controls (n = 50). Initially, IQ testing score and biochemical profile of each subject was generated, followed by label-free quantitative proteomics of subgroups of IQ and healthy control group through nano-LC/MS- mass spectrometry. A total of 310 proteins were identified, among them198 proteins were common among all groups. Statistical analysis (ANOVA) of the subgroups of ID showed 142 differentially expressed proteins, in comparison to healthy control group. From these, 120 proteins were found to be common among all subgroups. The remaining 22 proteins were categorized as exclusive proteins found only in disease subgroups. Furthermore, the hierarchical cluster analysis (HCL) of common significant proteins was also performed, followed by PANTHER protein classification and GO functional enrichment analysis. Results provides that the datasets of differentially expressed proteins, belong to the categories of immune / defense proteins, transfer carrier proteins, apolipoproteins, complement proteins, protease inhibitors, hemoglobin proteins etc., they are known to involvein immune system, and complement and coagulation pathway cascade and cholesterol metabolism pathway. Exclusively expressed 22 proteins were found to be disease stage specific and strong PPI network specifically those that have significant role in platelets activation and degranulation, such as Filamin A (FLNA). Furthermore, to validate the mass spectrometric findings, four highly significant proteins (APOA4, SAP, FLNA, and SERPING) were quantified by ELISA in all the study subjects. AUROC analysis showed a significant association of APOA4 (0.830), FLNA (0.958), SAP (0.754) and SERPING (0.600) with the disease. Apolipoprotein A4 (APOA4) has a significant role in cholesterol transport, and in modulation of glucose and lipid metabolism in the CNS. Similarly, FLNA has a crucial role in the nervous system, especially in the functioning of synaptic network. Therefore, both APOA4, and FLNA proteins represent good potential for candidate biomarkers for the diagnosis and prognosis of the intellectual disability. Overall, serum proteome of ID patients provides valuable information of proteins/pathways that are altered during ID progression.
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Affiliation(s)
- Soma Vankwani
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Munazza Raza Mirza
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Fazli Rabbi Awan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box. 577, Faisalabad, Pakistan.
| | - Muneeza Zafar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box. 577, Faisalabad, Pakistan
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Muhammad Wasim
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box. 577, Faisalabad, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Haq Nawaz Khan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box. 577, Faisalabad, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Hina Ayesha
- Department of Pediatrics, Punjab Medical College, Allied & DHQ Hospitals, Faisalabad Medical University, Faisalabad, Pakistan
| | - Martin Rossel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Muhammad Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
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Siddiqui U, Khan AB, Ahmad T, Rehman AA, Jairajpuri MA. A common protein C inhibitor exosite partially controls the heparin induced activation and inhibition of serine proteases. Int J Biol Macromol 2024; 266:131065. [PMID: 38521329 DOI: 10.1016/j.ijbiomac.2024.131065] [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: 01/06/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and irreversibly inhibits the proteases like APC (activating protein C), thrombin (FIIa) and factor Xa (FXa). Previous studies on antithrombin (ATIII) had identified Tyr253 and Glu255 as functional exosites that interact and aid in the inhibition of factor IXa and FXa. Presence of exosite in PCI is not known, however a sequence comparison with the PCI from different vertebrate species and ATIII identified Glu239 to be absolutely conserved. PCI residues analogous to ATIII exosite residues were mutated to R238A and E239A. Purified variant PCI in the presence of heparin (10 μg/ml) showed a 2-4 fold decrease in the rate of inhibition of the proteases. However, the stoichiometry of inhibition of FIIa, APC, and FXa by native PCI, R238A and E239A variants were found to be close to 1.0, which also indicated the formation of stable complexes based on SDS-PAGE and western blot analysis with thrombin and APC. Our findings revealed the possible presence of an exosite in PCI that influences the protease inhibition rates.
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Affiliation(s)
- Urfi Siddiqui
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abdul Burhan Khan
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tahif Ahmad
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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Sinegre T, Abergel A, Lecompte T, Lebreton A. Prothrombin conversion and thrombin decay in patients with cirrhosis-role of prothrombin and antithrombin deficiencies. J Thromb Haemost 2024; 22:1347-1357. [PMID: 38309434 DOI: 10.1016/j.jtha.2024.01.016] [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: 09/19/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Thrombin generation (TG) in the presence of thrombomodulin (TG-TM) in the plasma of patients with cirrhosis (PWC) is tilted toward a hypercoagulable phenotype. Low protein C and elevated factor VIII levels play a role, but other determinants, such as the prothrombin/antithrombin pair, must also be studied. OBJECTIVES The objectives were (i) to quantitatively assess the subprocesses (prothrombin conversion and thrombin decay) and (ii) to understand the underlying mechanism by studying TG dynamics after prothrombin and antithrombin plasma level correction in PWC. METHODS We studied TG-TM in plasma samples of 36 healthy controls (HCs) and 41 PWC with prothrombin and antithrombin levels of <70% and after their correction. We initiated coagulation with an intermediate picomolar concentration of tissue factor. We determined the overall thrombin potential, prothrombin conversion, and thrombin decay. RESULTS TG-TM was increased in PWC compared with HC due to impaired thrombin inhibition. Indeed, thrombin decay capacity (min-1) decreased from 0.37 (0.35-0.40) in HC to 0.33 (0.30-0.37) in the Child-Turcotte-Pugh A (CTP-A; P = .09), 0.27 (0.26-0.30) in the CTP-B (P < .001), and 0.20 (0.19-0.20) in the CTP-C (P < .001) group. Concomitant correction of prothrombin and antithrombin increased endogenous thrombin potential with prothrombin conversion surpassing thrombin decay. By contrast, when we corrected only antithrombin, TG-TM was normalized and even consistent with a hypocoagulable phenotype in the CTP-C group. CONCLUSION Our results highlight that in PWC, hypercoagulability (evidenced in the presence of TM) is due to impaired thrombin decay, whereas low prothrombin levels do not translate into decreased prothrombin conversion, likely due to altered TM-activated protein C negative feedback.
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Affiliation(s)
- Thomas Sinegre
- Service Hématologie biologique, CHU Clermont Ferrand, Clermont-Ferrand, France.
| | - Armand Abergel
- Service de Médecine Digestive et Hépato-biliaire, CHU, Clermont Ferrand, France; UMR 6602 CNRS-Sigma-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas Lecompte
- Université de Lorraine, Faculté de médecine de Nancy, Nancy, France
| | - Aurélien Lebreton
- Service Hématologie biologique, CHU Clermont Ferrand, Clermont-Ferrand, France; Université Clermont Auvergne, INRAE, UMR 1019 Unité de Nutrition Humaine, Clermont-Ferrand, France. https://twitter.com/aurelebre
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7
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Zhao X, Zhao J, Wang J, Liao C, Guan Q, Han Q. Immune protection of three serine protease inhibitors vaccine in mice against Rhipicephalus sanguineus. Sci Rep 2024; 14:7703. [PMID: 38565937 PMCID: PMC10987660 DOI: 10.1038/s41598-024-58303-4] [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: 08/30/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Bioactive molecules in tick saliva are considered to be key to successful feeding and further the transmission of tick-borne pathogens. Problems such as pathogen transmission and animal weight loss result in tick infestation can cause tremendous economic losses to the livestock industry. Therefore, the development of a universal tick vaccine is urgently needed. In this paper, three serine protease inhibitor (serpin) proteins RMS-3, L7LRK7 and L7LTU1 were analyzed with bioinformatics methods. Subsequently the proteins were expressed and purified, and inoculated into Kunming mice for immune protection analysis. The amino acid sequence similarities between RMS-3, L7LRK7 and L7LTU1 were up to 90% in Rhipicephalus sanguineus. The recombinant RMS-3 + L7LRK7 + L7LTU1 showed anticoagulant reaction function and could inhibit the activity of CD4+ lymphocytes, when inoculated into Kunming mice. Additionally, After the immunized mice were challenged with Rhipicephalus sanguineus, the percentage of larvae and nymphs that were fully engorged dropped to 40.87% (P < 0.05) and 87.68% (P > 0.05) in the RmS-3 + L7LRK7 immune group, 49.57% (P < 0.01) and 52.06% (P < 0.05) in the RmS-3 + L7LTU1 group, and 45.22% (P < 0.05) and 60.28% (P < 0.05) in the RmS-3 + L7LRK7 + L7LTU1 immune group, in comparison with the control group. These data indicate that RmS-3 + L7LRK7 + L7LTU1 has good immune protection and has the potential to be developed into a vaccine against the larvae and nymphs of R. sanguineus.
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Affiliation(s)
- Xiaoya Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China
| | - Jianguo Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China
| | - Jinhua Wang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China
| | - Qingfeng Guan
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China.
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China.
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou, 570228, Hainan, China.
- One Health Institute, Hainan University, Haikou, 570228, Hainan, China.
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Kang J, Jayaraman A, Antaki JF, Kirby B. Shear Histories Alter Local Shear Effects on Thrombus Nucleation and Growth. Ann Biomed Eng 2024; 52:1039-1050. [PMID: 38319505 DOI: 10.1007/s10439-023-03439-z] [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: 09/06/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024]
Abstract
Our goal was to determine the impact of physiological and pathological shear histories on platelet nucleation and thrombus growth at various local shear rates. We designed and characterized a microfluidic device capable of subjecting platelets to shear histories reaching as high as 6700 s- 1 in a single passage. Time-lapse videos of platelets and thrombi are captured using fluorescence microscopy. Thrombi are tracked, and the degree of thrombosis is evaluated through surface coverage, platelet nucleation maps, and ensemble-averaged aggregate areas and intensities. Surface coverage rates were the lowest when platelets deposited at high shear rates following a pathological shear history and were highest at low shear rates following a pathological shear history. Early aggregate area growth rates were significantly larger for thrombi developing at high shear following physiological shear history than at high shear following a pathological shear history. Aggregate vertical growth was restricted when depositing at low shear following a pathological shear history. In contrast, thrombi grew faster vertically following physiological shear histories. These results show that physiological shear histories pose thrombotic risks via volumetric growth, and pathological shear histories drastically promote nucleation. These findings may inform region-based geometries for biomedical devices and refine thrombosis simulations.
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Affiliation(s)
- Junhyuk Kang
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
| | - Anjana Jayaraman
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - James F Antaki
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Brian Kirby
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill-Cornell Medicine, New York, NY, USA
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Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI. Macromolecular crowding in human tenocyte and skin fibroblast cultures: A comparative analysis. Mater Today Bio 2024; 25:100977. [PMID: 38322661 PMCID: PMC10846491 DOI: 10.1016/j.mtbio.2024.100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Although human tenocytes and dermal fibroblasts have shown promise in tendon engineering, no tissue engineered medicine has been developed due to the prolonged ex vivo time required to develop an implantable device. Considering that macromolecular crowding has the potential to substantially accelerate the development of functional tissue facsimiles, herein we compared human tenocyte and dermal fibroblast behaviour under standard and macromolecular crowding conditions to inform future studies in tendon engineering. Basic cell function analysis made apparent the innocuousness of macromolecular crowding for both cell types. Gene expression analysis of the without macromolecular crowding groups revealed expression of tendon related molecules in human dermal fibroblasts and tenocytes. Protein electrophoresis and immunocytochemistry analyses showed significantly increased and similar deposition of collagen fibres by macromolecular crowding in the two cell types. Proteomics analysis demonstrated great similarities between human tenocyte and dermal fibroblast cultures, as well as the induction of haemostatic, anti-microbial and tissue-protective proteins by macromolecular crowding in both cell populations. Collectively, these data rationalise the use of either human dermal fibroblasts or tenocytes in combination with macromolecular crowding in tendon engineering.
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Affiliation(s)
- Adrian Djalali-Cuevas
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikhail Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jack Kelly
- Galway University Hospital, Galway, Ireland
| | - Manus Biggs
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I. Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
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10
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Vervuurt M, Schrader JM, de Kort AM, Kersten I, Wessels HJCT, Klijn CJM, Schreuder FHBM, Kuiperij HB, Gloerich J, Van Nostrand WE, Verbeek MM. Cerebrospinal fluid shotgun proteomics identifies distinct proteomic patterns in cerebral amyloid angiopathy rodent models and human patients. Acta Neuropathol Commun 2024; 12:6. [PMID: 38191511 PMCID: PMC10775534 DOI: 10.1186/s40478-023-01698-4] [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: 10/13/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Abstract
Cerebral amyloid angiopathy (CAA) is a form of small vessel disease characterised by the progressive deposition of amyloid β protein in the cerebral vasculature, inducing symptoms including cognitive impairment and cerebral haemorrhages. Due to their accessibility and homogeneous disease phenotypes, animal models are advantageous platforms to study diseases like CAA. Untargeted proteomics studies of CAA rat models (e.g. rTg-DI) and CAA patients provide opportunities for the identification of novel biomarkers of CAA. We performed untargeted, data-independent acquisition proteomic shotgun analyses on the cerebrospinal fluid of rTg-DI rats and wild-type (WT) littermates. Rodents were analysed at 3 months (n = 6/10), 6 months (n = 8/8), and 12 months (n = 10/10) for rTg-DI and WT respectively. For humans, proteomic analyses were performed on CSF of sporadic CAA patients (sCAA) and control participants (n = 39/28). We show recurring patterns of differentially expressed (mostly increased) proteins in the rTg-DI rats compared to wild type rats, especially of proteases of the cathepsin protein family (CTSB, CTSD, CTSS), and their main inhibitor (CST3). In sCAA patients, decreased levels of synaptic proteins (e.g. including VGF, NPTX1, NRXN2) and several members of the granin family (SCG1, SCG2, SCG3, SCG5) compared to controls were discovered. Additionally, several serine protease inhibitors of the SERPIN protein family (including SERPINA3, SERPINC1 and SERPING1) were differentially expressed compared to controls. Fifteen proteins were significantly altered in both rTg-DI rats and sCAA patients, including (amongst others) SCG5 and SERPING1. These results identify specific groups of proteins likely involved in, or affected by, pathophysiological processes involved in CAA pathology such as protease and synapse function of rTg-DI rat models and sCAA patients, and may serve as candidate biomarkers for sCAA.
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Affiliation(s)
- Marc Vervuurt
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joseph M Schrader
- Department of Biomedical and Pharmaceutical Sciences, George & Anne Institute for Neuroscience, University of Rhode Island, Kingston, RI, USA
| | - Anna M de Kort
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Iris Kersten
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Hans J C T Wessels
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Catharina J M Klijn
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Floris H B M Schreuder
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - H Bea Kuiperij
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jolein Gloerich
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - William E Van Nostrand
- Department of Biomedical and Pharmaceutical Sciences, George & Anne Institute for Neuroscience, University of Rhode Island, Kingston, RI, USA
| | - Marcel M Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, 830 TML, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Human Genetics, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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11
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Phan P, Deshwal A, McMahon TA, Slikas M, Andrews E, Becker B, Kumar TKS. A Review of Rattlesnake Venoms. Toxins (Basel) 2023; 16:2. [PMID: 38276526 PMCID: PMC10818703 DOI: 10.3390/toxins16010002] [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: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Venom components are invaluable in biomedical research owing to their specificity and potency. Many of these components exist in two genera of rattlesnakes, Crotalus and Sistrurus, with high toxicity and proteolytic activity variation. This review focuses on venom components within rattlesnakes, and offers a comparison and itemized list of factors dictating venom composition, as well as presenting their known characteristics, activities, and significant applications in biosciences. There are 64 families and subfamilies of proteins present in Crotalus and Sistrurus venom. Snake venom serine proteases (SVSP), snake venom metalloproteases (SVMP), and phospholipases A2 (PLA2) are the standard components in Crotalus and Sistrurus venom. Through this review, we highlight gaps in the knowledge of rattlesnake venom; there needs to be more information on the venom composition of three Crotalus species and one Sistrurus subspecies. We discuss the activity and importance of both major and minor components in biomedical research and drug development.
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Affiliation(s)
- Phuc Phan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Anant Deshwal
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Tyler Anthony McMahon
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Matthew Slikas
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Elodie Andrews
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Brian Becker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
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12
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Li Z, Qi Z, Wang X, Lu L, Wang H, He Z, Chen Z, Shao Y, Tu J, Song X. Avian pathogenic Escherichia coli infection causes infiltration of heterophilic granulocytes of chick tracheal by the complement and coagulation cascades pathway. BMC Vet Res 2023; 19:262. [PMID: 38066606 PMCID: PMC10704733 DOI: 10.1186/s12917-023-03838-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Avian pathogenic Escherichia coli (APEC) causes tracheal damage and heterophilic granulocytic infiltration and inflammation in infected chicks. In this study, we infected chick tracheal tissue with strain AE17 and produced pathological sections with proteomic sequencing. We compared the results of pathological sections from the APEC-infected group with those from the PBS control group; the pathological sections from the experimental group showed hemorrhage, fibrinization, and infiltration of heterophilic granulocytes in the tracheal tissue. In order to explore the effect on proteomics on inflammation and to further search for the caus. RESULTS The tandem mass tag-based (TMT) sequencing analysis showed 224 upregulated and 140 downregulated proteins after infection with the AE17 strain. Based on the results of KEGG in Complement and coagulation cascades, differential protein expression in the Protein export pathway was upregulated. CONCLUSIONS With these results, we found that chemokines produced by the Complement and coagulation cascades pathway may cause infiltration of heterophilic granulocytes involved in inflammation, as well as antimicrobial factors produced by the complement system to fight the infection together.These results suggest that APEC causes the infiltration of heterophilic granulocytes through the involvement of the complement system with serine protease inhibitors.
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Affiliation(s)
- Ziqi Li
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Zhao Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Xiaoru Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Liting Lu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Haiyang Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Zhenjie He
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Zhe Chen
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Ying Shao
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Jian Tu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Xiangjun Song
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China.
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China.
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui, 230036, PR China.
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Bencosme-Cuevas E, Kim TK, Nguyen TT, Berry J, Li J, Adams LG, Smith LA, Batool SA, Swale DR, Kaufmann SHE, Jones-Hall Y, Mulenga A. Ixodes scapularis nymph saliva protein blocks host inflammation and complement-mediated killing of Lyme disease agent, Borrelia burgdorferi. Front Cell Infect Microbiol 2023; 13:1253670. [PMID: 37965264 PMCID: PMC10641286 DOI: 10.3389/fcimb.2023.1253670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/14/2023] [Indexed: 11/16/2023] Open
Abstract
Tick serine protease inhibitors (serpins) play crucial roles in tick feeding and pathogen transmission. We demonstrate that Ixodes scapularis (Ixs) nymph tick saliva serpin (S) 41 (IxsS41), secreted by Borrelia burgdorferi (Bb)-infected ticks at high abundance, is involved in regulating tick evasion of host innate immunity and promoting host colonization by Bb. Recombinant (r) proteins were expressed in Pichia pastoris, and substrate hydrolysis assays were used to determine. Ex vivo (complement and hemostasis function related) and in vivo (paw edema and effect on Bb colonization of C3H/HeN mice organs) assays were conducted to validate function. We demonstrate that rIxsS41 inhibits chymase and cathepsin G, pro-inflammatory proteases that are released by mast cells and neutrophils, the first immune cells at the tick feeding site. Importantly, stoichiometry of inhibition analysis revealed that 2.2 and 2.8 molecules of rIxsS41 are needed to 100% inhibit 1 molecule of chymase and cathepsin G, respectively, suggesting that findings here are likely events at the tick feeding site. Furthermore, chymase-mediated paw edema, induced by the mast cell degranulator, compound 48/80 (C48/80), was blocked by rIxsS41. Likewise, rIxsS41 reduced membrane attack complex (MAC) deposition via the alternative and lectin complement activation pathways and dose-dependently protected Bb from complement killing. Additionally, co-inoculating C3H/HeN mice with Bb together with rIxsS41 or with a mixture (rIxsS41 and C48/80). Findings in this study suggest that IxsS41 markedly contributes to tick feeding and host colonization by Bb. Therefore, we conclude that IxsS41 is a potential candidate for an anti-tick vaccine to prevent transmission of the Lyme disease agent.
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Affiliation(s)
- Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Tae Kwon Kim
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Thu-Thuy Nguyen
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Jacquie Berry
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Jianrong Li
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Leslie Garry Adams
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | | | | | - Daniel R. Swale
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Stefan H. E. Kaufmann
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
- Hagler Institute for Advanced Study, Texas A&M University, College Station, TX, United States
- Max Planck Institute for Infection Biology, Berlin, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Yava Jones-Hall
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Albert Mulenga
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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14
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Varkoly K, Beladi R, Hamada M, McFadden G, Irving J, Lucas AR. Viral SERPINS-A Family of Highly Potent Immune-Modulating Therapeutic Proteins. Biomolecules 2023; 13:1393. [PMID: 37759793 PMCID: PMC10526531 DOI: 10.3390/biom13091393] [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: 06/28/2023] [Revised: 08/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Serine protease inhibitors, SERPINS, are a highly conserved family of proteins that regulate serine proteases in the central coagulation and immune pathways, representing 2-10% of circulating proteins in the blood. Serine proteases form cascades of sequentially activated enzymes that direct thrombosis (clot formation) and thrombolysis (clot dissolution), complement activation in immune responses and also programmed cell death (apoptosis). Virus-derived serpins have co-evolved with mammalian proteases and serpins, developing into highly effective inhibitors of mammalian proteolytic pathways. Through interacting with extracellular and intracellular serine and cysteine proteases, viral serpins provide a new class of highly active virus-derived coagulation-, immune-, and apoptosis-modulating drug candidates. Viral serpins have unique characteristics: (1) function at micrograms per kilogram doses; (2) selectivity in targeting sites of protease activation; (3) minimal side effects at active concentrations; and (4) the demonstrated capacity to be modified, or fine-tuned, for altered protease targeting. To date, the virus-derived serpin class of biologics has proven effective in a wide range of animal models and in one clinical trial in patients with unstable coronary disease. Here, we outline the known viral serpins and review prior studies with viral serpins, considering their potential for application as new sources for immune-, coagulation-, and apoptosis-modulating therapeutics.
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Affiliation(s)
- Kyle Varkoly
- Department of Internal Medicine, McLaren Macomb Hospital, Michigan State University College of Human Medicine, 1000 Harrington St., Mt Clemens, MI 48043, USA;
| | - Roxana Beladi
- Department of Neurological Surgery, Ascension Providence Hospital, Michigan State University College of Human Medicine, 16001 W Nine Mile Rd., Southfield, MI 48075, USA;
| | - Mostafa Hamada
- College of Medicine, Kansas City University, 1750 Independence Ave, Kansas City, MO 64106, USA;
- Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E Tyler St., Tempe, AZ 85287, USA;
| | - Grant McFadden
- Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E Tyler St., Tempe, AZ 85287, USA;
| | - James Irving
- UCL Respiratory and the Institute of Structural and Molecular Biology, University College London, 5 University Street, London WC1E 6JF, UK
| | - Alexandra R. Lucas
- Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E Tyler St., Tempe, AZ 85287, USA;
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, 727 E Tyler St., Tempe, AZ 85287, USA
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15
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Devadasan MJ, Ramesha KP, Ramesh P, Kootimole CN, Jeyakumar S, Ashwitha A, Ammankallu S, Rai AB, Kumaresan A, Vedamurthy VG, Raju R, Das DN, Kataktalware MA, Prasad TSK. Exploring molecular dynamic indicators associated with reproductive performance of Bos indicus cattle in blood plasma samples through data-independent acquisition mass spectrometry. J Proteomics 2023; 285:104950. [PMID: 37321300 DOI: 10.1016/j.jprot.2023.104950] [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: 02/24/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023]
Abstract
Improving reproductive performance of cattle is of paramount importance for sustainable dairy farming. Poor reproduction performance (RP) hinders the genetic improvement of important Bos indicus cattle breeds. It is well known that incorporation of molecular information along with conventional breeding method is far better than use of conventional method alone for the genetic improvement of reproductive performance traits in cattle. Therefore, the present study sought to investigate the plasma proteome of the Deoni cows in cyclical (n = 6) and pregnant (n = 6) reproductive phases with varying reproductive performance (high and low). High-throughput data independent acquisition (DIA) based proteomics was performed to understand corresponding proteome. We identified a total of 430 plasma proteins. Among cyclic cows, twenty proteins were differentially regulated in low RP as compared to high RP. BARD1 and AFP proteins were observed upregulated in cyclical cows whose upregulation reported to affect reproductive performance in cattle. Among the pregnant cows, thirty-five proteins were differentially regulated, including the downregulation of FGL2 and ZNFX1 that modulates the maternal immune response mechanism which is required for successful implantation of the embryo. Also, proteins such as AHSG, CLU and SERPINA6 were upregulated in the pregnant cows whose upregulation reported to reduced reproductive performance. The results of this study will be helpful in establishing a framework for future research on the aspect of improving reproductive performance in Bos indicus cattle breeds. SIGNIFICANCE: The Indian subcontinent is the center of domestication for Bos indicus cattle breeds and they are known for their disease resistance, heat tolerance, ability to survive in low input regime and harsh climatic conditions. In recent times, population of many important Bos indicus breeds including Deoni cattle is declining due to various factors, especially due to reproductive performance. Traditional breeding methods are not sufficient enough to understand and improve the reproductive performance traits in important Bos indicus cattle breeds. Proteomics approach is a promising technology to understand the complex biological factors which leads to poor reproductive performance in cattle. The present study utilized DIA based LC- MS/MS analysis to identify the plasma proteins associated with reproductive performance in cyclical and pregnant cows. This study if improved further, can be used to develop potential protein markers associated with reproductive performance which is useful for the selection and genetic improvement of important Bos indicus breeds.
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Affiliation(s)
- M Joel Devadasan
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - Kerekoppa P Ramesha
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India.
| | - Poornima Ramesh
- Centre for System Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Chinmaya Narayana Kootimole
- Centre for System Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Sakthivel Jeyakumar
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - A Ashwitha
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - Shruthi Ammankallu
- Centre for System Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Akhila Balakrishna Rai
- Centre for System Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Arumugam Kumaresan
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - Veerappa G Vedamurthy
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - Rajesh Raju
- Centre for System Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - D N Das
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
| | - Mukund A Kataktalware
- Southern Regional Station, ICAR- National Dairy Research Institute, Banglore 560030, India
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16
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Valenzuela-Leon PC, Campos Chagas A, Martin-Martin I, Williams AE, Berger M, Shrivastava G, Paige AS, Kotsyfakis M, Tirloni L, Calvo E. Guianensin, a Simulium guianense salivary protein, has broad anti-hemostatic and anti-inflammatory properties. Front Immunol 2023; 14:1163367. [PMID: 37469515 PMCID: PMC10353047 DOI: 10.3389/fimmu.2023.1163367] [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] [Received: 02/10/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023] Open
Abstract
Background Salivary glands from blood-feeding arthropods secrete several molecules that inhibit mammalian hemostasis and facilitate blood feeding and pathogen transmission. The salivary functions from Simulium guianense, the main vector of Onchocerciasis in South America, remain largely understudied. Here, we have characterized a salivary protease inhibitor (Guianensin) from the blackfly Simulium guianense. Materials and methods A combination of bioinformatic and biophysical analyses, recombinant protein production, in vitro and in vivo experiments were utilized to characterize the molecula mechanism of action of Guianensin. Kinetics of Guianensin interaction with proteases involved in vertebrate inflammation and coagulation were carried out by surface plasmon resonance and isothermal titration calorimetry. Plasma recalcification and coagulometry and tail bleeding assays were performed to understand the role of Guianensin in coagulation. Results Guianensin was identified in the sialotranscriptome of adult S. guianense flies and belongs to the Kunitz domain of protease inhibitors. It targets various serine proteases involved in hemostasis and inflammation. Binding to these enzymes is highly specific to the catalytic site and is not detectable for their zymogens, the catalytic site-blocked human coagulation factor Xa (FXa), or thrombin. Accordingly, Guianensin significantly increased both PT (Prothrombin time) and aPTT (Activated partial thromboplastin time) in human plasma and consequently increased blood clotting time ex vivo. Guianensin also inhibited prothrombinase activity on endothelial cells. We show that Guianensin acts as a potent anti-inflammatory molecule on FXa-induced paw edema formation in mice. Conclusion The information generated by this work highlights the biological functionality of Guianensin as an antithrombotic and anti-inflammatory protein that may play significant roles in blood feeding and pathogen transmission.
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Affiliation(s)
| | - Andrezza Campos Chagas
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
| | - Adeline E. Williams
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
| | - Markus Berger
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT, United States
| | - Gaurav Shrivastava
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
| | - Andrew S. Paige
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
| | - Michalis Kotsyfakis
- Laboratory of Genomics and Proteomics of Disease Vectors, Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Lucas Tirloni
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT, United States
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institutes of Health, Bethesda, MD, United States
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17
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Rosenfeld MA, Yurina LV, Vasilyeva AD. Antioxidant role of methionine-containing intra- and extracellular proteins. Biophys Rev 2023; 15:367-383. [PMID: 37396452 PMCID: PMC10310685 DOI: 10.1007/s12551-023-01056-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/24/2023] [Indexed: 07/04/2023] Open
Abstract
Significant evidence suggests that reversible oxidation of methionine residues provides a mechanism capable of scavenging reactive species, thus creating a cycle with catalytic efficiency to counteract or mitigate deleterious effects of ROS on other functionally important amino acid residues. Because of the absence of MSRs in the blood plasma, oxidation of methionines in extracellular proteins is effectively irreversible and, therefore, the ability of methionines to serve as interceptors of oxidant molecules without impairment of the structure and function of plasma proteins is still debatable. This review presents data on the oxidative modification of both intracellular and extracellular proteins that differ drastically in their spatial structures and functions indicating that the proteins contain antioxidant methionines/the oxidation of which does not affect (or has a minor effect) on their functional properties. The functional consequences of methionine oxidation in proteins have been mainly identified from studies in vitro and, to a very limited extent, in vivo. Hence, much of the functioning of plasma proteins constantly subjected to oxidative stress remains unclear and requires further research to understand the evolutionary role of methionine oxidation in proteins for the maintenance of homeostasis and risk factors affecting the development of ROS-related pathologies. Data presented in this review contribute to increased evidence of antioxidant role of surface-exposed methionines and can be useful for understanding a possible mechanism that supports or impairs structure-function relationships of proteins subjected to oxidative stress.
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Affiliation(s)
- Mark A. Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Lyubov V. Yurina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - Alexandra D. Vasilyeva
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
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18
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Bano S, Khan AB, Fatima S, Rashid Q, Prakash A, Gupta N, Ahmad I, Ansari S, Lynn AM, Abid M, Jairajpuri MA. Mannose 2, 3, 4, 5, 6- O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential. J Biomol Struct Dyn 2023; 41:3717-3727. [PMID: 35343865 DOI: 10.1080/07391102.2022.2053749] [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: 09/22/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
Thromboembolic diseases are a major cause of mortality in human and the currently available anticoagulants are associated with various drawbacks, therefore the search for anticoagulants that have better safety profile is highly desirable. Compounds that are part of the dietary routine can be modified to possibly increase their anticoagulant potential. We show mannose 2,3,4,5,6-O-pentasulfate (MPS) as a synthetically modified form of mannose that has appreciable anticoagulation properties. An in silico study identified that mannose in sulfated form can bind effectively to the heparin-binding site of antithrombin (ATIII) and heparin cofactor II (HCII). Mannose was sulfated using a simple sulfation strategy-involving triethylamine-sulfur trioxide adduct. HCII and ATIII were purified from human plasma and the binding analysis using fluorometer and isothermal calorimetry showed that MPS binds at a unique site. A thrombin inhibition analysis using the chromogenic substrate showed that MPS partially enhances the activity of HCII. Further an assessment of in vitro blood coagulation assays using human plasma showed that the activated partial thromboplastin time (APTT) and prothrombin time (PT) were prolonged in the presence of MPS. A molecular dynamics simulation analysis of the HCII-MPS complex showed fluctuations in a N-terminal loop and the cofactor binding site of HCII. The results indicate that MPS is a promising lead due to its effect on the in vitro coagulation rate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shadabi Bano
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Abdul Burhan Khan
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Sana Fatima
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Qudsia Rashid
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neha Gupta
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Irshad Ahmad
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Shoyab Ansari
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Abid
- Medicinal Chemistry Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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19
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Coronel-Meneses D, Sánchez-Trasviña C, Ratera I, Mayolo-Deloisa K. Strategies for surface coatings of implantable cardiac medical devices. Front Bioeng Biotechnol 2023; 11:1173260. [PMID: 37256118 PMCID: PMC10225971 DOI: 10.3389/fbioe.2023.1173260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Cardiac medical devices (CMDs) are required when the patient's cardiac capacity or activity is compromised. To guarantee its correct functionality, the building materials in the development of CMDs must focus on several fundamental properties such as strength, stiffness, rigidity, corrosion resistance, etc. The challenge is more significant because CMDs are generally built with at least one metallic and one polymeric part. However, not only the properties of the materials need to be taken into consideration. The biocompatibility of the materials represents one of the major causes of the success of CMDs in the short and long term. Otherwise, the material will lead to several problems of hemocompatibility (e.g., protein adsorption, platelet aggregation, thrombus formation, bacterial infection, and finally, the rejection of the CMDs). To enhance the hemocompatibility of selected materials, surface modification represents a suitable solution. The surface modification involves the attachment of chemical compounds or bioactive compounds to the surface of the material. These coatings interact with the blood and avoid hemocompatibility and infection issues. This work reviews two main topics: 1) the materials employed in developing CMDs and their key characteristics, and 2) the surface modifications reported in the literature, clinical trials, and those that have reached the market. With the aim of providing to the research community, considerations regarding the choice of materials for CMDs, together with the advantages and disadvantages of the surface modifications and the limitations of the studies performed.
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Affiliation(s)
- David Coronel-Meneses
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Calef Sánchez-Trasviña
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Imma Ratera
- Institute of Materials Science of Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Instituto de Salud Carlos IIIBellaterra, Spain
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
- Institute of Materials Science of Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra, Spain
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20
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Balogh G, Bereczky Z. The Interaction of Factor Xa and IXa with Non-Activated Antithrombin in Michaelis Complex: Insights from Enhanced-Sampling Molecular Dynamics Simulations. Biomolecules 2023; 13:biom13050795. [PMID: 37238665 DOI: 10.3390/biom13050795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/28/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The interaction between coagulation factors Xa and IXa and the activated state of their inhibitor, antithrombin (AT),have been investigated using X-ray diffraction studies. However, only mutagenesis data are available for non-activated AT. Our aim was to propose a model based on docking and advanced-sampling molecular dynamics simulations that can reveal the conformational behavior of the systems when AT is not binding a pentasaccharide. We built the initial structure for non-activated AT-FXa and AT-FIXa complexes using HADDOCK 2.4. The conformational behavior was studied using Gaussian accelerated molecular dynamics simulations. In addition to the docked complexes, two systems based on the X-ray structures were also simulated, with and without the ligand. The simulations revealed large variability in conformation for both factors. In the docking-based complex of AT-FIXa, conformations with stable Arg150-AT interactions can exist for longer time periods but the system also has a higher tendency for reaching states with very limited interaction with the "exosite" of AT. By comparing simulations with or without the pentasaccharide, we were able to gain insights into the effects of conformational activation on the Michaelis complexes. RMSF analysis and correlation calculations for the alpha-carbon atoms revealed important details of the allosteric mechanisms. Our simulations provide atomistic models for better understanding the conformational activation mechanism of AT against its target factors.
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Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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21
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Li L, Song X, Chen G, Zhang Z, Zheng B, Zhang Q, Wang S, Xie L. Plasma exosomal protein PLG and SERPINA1 in colorectal cancer diagnosis and coagulation abnormalities. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04776-1. [PMID: 37093347 DOI: 10.1007/s00432-023-04776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023]
Abstract
PURPOSE Early diagnosis of colorectal cancer (CRC) is critical to patient prognosis; however, there is lack of non-invasive biomarkers that are extremely sensitive and specific for early screening and diagnosis. Exosomes are a novel tool applied to the diagnosis and treatment of cancer. Changes in plasma exosomal proteins have a certain relationship with the development of various diseases including tumors. Here, we aimed to find exosomal biomarkers for early diagnosis of CRC. METHODS Exosomes obtained by ultracentrifugation from CRC patients and healthy donors were characterized by transmission electron microscopy (TEM), qNano and western blotting. Proteomic and functional enrichment analyses confirmed differences in the specific expression of exosomal proteins in plasma between CRC patients and healthy donors. Western blotting with enzyme-linked immunosorbent assay (ELISA) was used to verify the difference proteins. Statistical methods were used to analyze the relationship between protein levels and CRC. RESULTS The expression levels of serpin peptidase inhibitor clade A member 1 (SERPINA1) and fibrinogen (PLG) in CRC patients were significantly higher than those in healthy groups. Receptor operating characteristic (ROC) curves analysis was superior to CEA and CA19-9 for the diagnosis of colorectal cancer and early-stage colorectal cancer. The two were related to TNM staging and coagulation, and the difference was statistically significant. CONCLUSION The results of this study have potential value in advancing the clinical diagnosis of colorectal cancer.
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Affiliation(s)
- Lei Li
- School of Medical Laboratory, Weifang Medical University, Weifang, China
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Xingguo Song
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Guanxuan Chen
- Department of Intensive Care Unit, Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Zhe Zhang
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Baibing Zheng
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Qianru Zhang
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Shiwen Wang
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China
| | - Li Xie
- Shandong Cancer Hospital and Institute, Shandong Academy of Medical Sciences, Shandong First Medical University, 440 Ji-Yan Road, Jinan, 250117, Shandong Province, People's Republic of China.
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22
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Dzobo K, Dandara C. The Extracellular Matrix: Its Composition, Function, Remodeling, and Role in Tumorigenesis. Biomimetics (Basel) 2023; 8:146. [PMID: 37092398 PMCID: PMC10123695 DOI: 10.3390/biomimetics8020146] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
The extracellular matrix (ECM) is a ubiquitous member of the body and is key to the maintenance of tissue and organ integrity. Initially thought to be a bystander in many cellular processes, the extracellular matrix has been shown to have diverse components that regulate and activate many cellular processes and ultimately influence cell phenotype. Importantly, the ECM's composition, architecture, and stiffness/elasticity influence cellular phenotypes. Under normal conditions and during development, the synthesized ECM constantly undergoes degradation and remodeling processes via the action of matrix proteases that maintain tissue homeostasis. In many pathological conditions including fibrosis and cancer, ECM synthesis, remodeling, and degradation is dysregulated, causing its integrity to be altered. Both physical and chemical cues from the ECM are sensed via receptors including integrins and play key roles in driving cellular proliferation and differentiation and in the progression of various diseases such as cancers. Advances in 'omics' technologies have seen an increase in studies focusing on bidirectional cell-matrix interactions, and here, we highlight the emerging knowledge on the role played by the ECM during normal development and in pathological conditions. This review summarizes current ECM-targeted therapies that can modify ECM tumors to overcome drug resistance and better cancer treatment.
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Affiliation(s)
- Kevin Dzobo
- Medical Research Council, SA Wound Healing Unit, Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
| | - Collet Dandara
- Division of Human Genetics and Institute of Infectious Disease and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
- The South African Medical Research Council-UCT Platform for Pharmacogenomics Research and Translation, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa
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23
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Humphreys SJ, Whyte CS, Mutch NJ. "Super" SERPINs-A stabilizing force against fibrinolysis in thromboinflammatory conditions. Front Cardiovasc Med 2023; 10:1146833. [PMID: 37153474 PMCID: PMC10155837 DOI: 10.3389/fcvm.2023.1146833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
The superfamily of serine protease inhibitors (SERPINs) are a class of inhibitors that utilise a dynamic conformational change to trap and inhibit their target enzymes. Their powerful nature lends itself well to regulation of complex physiological enzymatic cascades, such as the haemostatic, inflammatory and complement pathways. The SERPINs α2-antiplasmin, plasminogen-activator inhibitor-1, plasminogen-activator inhibitor-2, protease nexin-1, and C1-inhibitor play crucial inhibitory roles in regulation of the fibrinolytic system and inflammation. Elevated levels of these SERPINs are associated with increased risk of thrombotic complications, obesity, type 2 diabetes, and hypertension. Conversely, deficiencies of these SERPINs have been linked to hyperfibrinolysis with bleeding and angioedema. In recent years SERPINs have been implicated in the modulation of the immune response and various thromboinflammatory conditions, such as sepsis and COVID-19. Here, we highlight the current understanding of the physiological role of SERPINs in haemostasis and inflammatory disease progression, with emphasis on the fibrinolytic pathway, and how this becomes dysregulated during disease. Finally, we consider the role of these SERPINs as potential biomarkers of disease progression and therapeutic targets for thromboinflammatory diseases.
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24
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Pavan M, Bassani D, Sturlese M, Moro S. Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations. NAR Genom Bioinform 2022; 4:lqac088. [PMID: 36458023 PMCID: PMC9706429 DOI: 10.1093/nargab/lqac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/20/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins to control the genome expression and several biological processes. Due to its characteristic structural features, this polymer can mold itself into different three-dimensional structures able to recognize target biomolecules with high affinity and specificity, thereby attracting the interest of drug developers and medicinal chemists. One successful example of the exploitation of RNA's structural and functional peculiarities is represented by aptamers, a class of therapeutic and diagnostic tools that can recognize and tightly bind several pharmaceutically relevant targets, ranging from small molecules to proteins, making use of the available structural and conformational freedom to maximize the complementarity with their interacting counterparts. In this scientific work, we present the first application of Supervised Molecular Dynamics (SuMD), an enhanced sampling Molecular Dynamics-based method for the study of receptor-ligand association processes in the nanoseconds timescale, to the study of recognition pathways between RNA aptamers and proteins, elucidating the main advantages and limitations of the technique while discussing its possible role in the rational design of RNA-based therapeutics.
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Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- To whom correspondence should be addressed. Tel: +39 0498275704; Fax: +39 0498275366;
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Alsayejh B, Kietsiriroje N, Almutairi M, Simmons K, Pechlivani N, Ponnambalam S, Ajjan RA. Plasmin Inhibitor in Health and Diabetes: Role of the Protein as a Therapeutic Target. TH OPEN 2022; 6:e396-e407. [PMID: 36452200 PMCID: PMC9674435 DOI: 10.1055/a-1957-6817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
The vascular obstructive thrombus is composed of a mesh of fibrin fibers with blood cells trapped in these networks. Enhanced fibrin clot formation and/or suppression of fibrinolysis are associated with an increased risk of vascular occlusive events. Inhibitors of coagulation factors and activators of plasminogen have been clinically used to limit fibrin network formation and enhance lysis. While these agents are effective at reducing vascular occlusion, they carry a significant risk of bleeding complications. Fibrin clot lysis, essential for normal hemostasis, is controlled by several factors including the incorporation of antifibrinolytic proteins into the clot. Plasmin inhibitor (PI), a key antifibrinolytic protein, is cross-linked into fibrin networks with higher concentrations of PI documented in fibrin clots and plasma from high vascular risk individuals. This review is focused on exploring PI as a target for the prevention and treatment of vascular occlusive disease. We first discuss the relationship between the PI structure and antifibrinolytic activity, followed by describing the function of the protein in normal physiology and its role in pathological vascular thrombosis. Subsequently, we describe in detail the potential use of PI as a therapeutic target, including the array of methods employed for the modulation of protein activity. Effective and safe inhibition of PI may prove to be an alternative and specific way to reduce vascular thrombotic events while keeping bleeding risk to a minimum. Key Points Plasmin inhibitor (PI) is a key protein that inhibits fibrinolysis and stabilizes the fibrin network.This review is focused on discussing mechanistic pathways for PI action, role of the molecule in disease states, and potential use as a therapeutic target.
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Affiliation(s)
- Basmah Alsayejh
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
- Ministry of Education, Riyadh, Kingdom of Saudi Arabia
| | - Noppadol Kietsiriroje
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
- Endocrinology and Metabolism Unit, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Mansour Almutairi
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
- General Directorate of Medical Services, Ministry of Interior, Kingdom of Saudi Arabia
| | - Katie Simmons
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
| | - Nikoletta Pechlivani
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
| | - Sreenivasan Ponnambalam
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Ramzi A. Ajjan
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, Leeds, United Kingdom
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Identification of substrates of MBL Associated Serine Protease-1 (MASP-1) from human plasma using N-terminomics strategy. Mol Immunol 2022; 151:114-125. [PMID: 36126499 DOI: 10.1016/j.molimm.2022.09.001] [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: 04/13/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022]
Abstract
MBL Associated Serine Protease-1 (MASP-1) is an abundant enzyme of the lectin complement pathway. MASP-1 cleaves numerous substrates like MASP-2, MASP-3, C2, C3i, fibrinogen, FXIII and prothrombin. It has thrombin-like specificity and can cleave thrombin substrates. Owing to its high concentration and relaxed substrate specificity, MASP-1 has substrates outside the complement system and can influence other proteolytic cascades and physiological processes. The unidentified substrates may assist us to ascertain the role(s) of MASP-1. In this study, we used a high-throughput N-terminomics method to identify substrates of MASP-1 from human plasma. We have identified 35 putative substrates of MASP-1. Among the identified proteins, alpha 2-antiplasmin, alpha-1-acid glycoprotein, antithrombin III, and siglec-6 were demonstrated to be cleaved by MASP-1. We have discussed the physiological relevance of cleavage of these substrates by MASP-1. The expression of Siglec-6 and MASP-1 has been reported in the B cells. Alpha-1-acid glycoprotein cleavage by MASP-1 may occur in the acute phase as it is known to be an inhibitor of platelet aggregation, whereas MASP-1 triggers platelet aggregation. The cleavage alpha2 antiplasmin by MASP-1 implies that MASP-1 may be promoting plasmin-mediated fibrinolysis. Our study supports that MASP-1 may be implicated in thrombosis as well as thrombolysis.
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27
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Li Y, Chen L, Huang R, Li Y, Yang C, Gui B, Li Y, Liao L, Zhu Z, Wang Y. Grass carp SERPINA1 inhibits GCRV infection through degrading CF2. Front Immunol 2022; 13:969517. [PMID: 36159797 PMCID: PMC9494734 DOI: 10.3389/fimmu.2022.969517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022] Open
Abstract
SERPINA1, a member of the serine protease inhibitor family, plays a role in viral infection and inflammation by regulating the activities of serine and cysteine proteases. To date, there have been no reports on the immune function of SERPINA1 in fishes. In this study, we first cloned the serpina1 gene of grass carp (Ctenopharyngodon idellus) and found that it could respond rapidly to the infection of Grass carp reovirus (GCRV), and overexpression of serpina1 could enhance the antiviral response of CIK cells. A polyclonal antibody of SERPINA1 was prepared, and the protein interacting with SERPINA1 was screened by CoIP/MS in grass carp hepatopancreas tissue. It was found that SERPINA1 interacted with coagulation factor 2 (CF2) and could degrade it in a dose-dependent manner. In addition, overexpression of cf2 contributed to the infection of GCRV in CIK cells, whereas co-expression of serpina1 and cf2 in grass carp reduced the copy number of GCRV in cells. The results showed that grass carp SERPINA1 could inhibit GCRV infection by degrading CF2. This study proposes that SERPINA1 can inhibit viral infection through interaction with the coagulation factor, providing new insights into the molecular mechanism of SERPINA1’s antiviral function.
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Affiliation(s)
- Yangyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Rong Huang,
| | - Yangyu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Bin Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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Liu Y, Song L, Zheng N, Shi J, Wu H, Yang X, Xue N, Chen X, Li Y, Sun C, Chen C, Tang L, Ni X, Wang Y, Shi Y, Guo J, Wang G, Zhang Z, Qin J. A urinary proteomic landscape of COVID-19 progression identifies signaling pathways and therapeutic options. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1866-1880. [PMID: 35290573 PMCID: PMC8922985 DOI: 10.1007/s11427-021-2070-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/24/2022] [Indexed: 02/06/2023]
Abstract
Signaling pathway alterations in COVID-19 of living humans as well as therapeutic targets of the host proteins are not clear. We analyzed 317 urine proteomes, including 86 COVID-19, 55 pneumonia and 176 healthy controls, and identified specific RNA virus detector protein DDX58/RIG-I only in COVID-19 samples. Comparison of the COVID-19 urinary proteomes with controls revealed major pathway alterations in immunity, metabolism and protein localization. Biomarkers that may stratify severe symptoms from moderate ones suggested that macrophage induced inflammation and thrombolysis may play a critical role in worsening the disease. Hyper activation of the TCA cycle is evident and a macrophage enriched enzyme CLYBL is up regulated in COVID-19 patients. As CLYBL converts the immune modulatory TCA cycle metabolite itaconate through the citramalyl-CoA intermediate to acetyl-CoA, an increase in CLYBL may lead to the depletion of itaconate, limiting its anti-inflammatory function. These observations suggest that supplementation of itaconate and inhibition of CLYBL are possible therapeutic options for treating COVID-19, opening an avenue of modulating host defense as a means of combating SARS-CoV-2 viruses.
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Affiliation(s)
- Yuntao Liu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, 510120, China
| | - Lan Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jinwen Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Hongxing Wu
- Beijing Pineal Health Management Co. Ltd, Beijing, 102206, China
| | - Xing Yang
- Beijing Pineal Health Management Co. Ltd, Beijing, 102206, China
| | - Nianci Xue
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xing Chen
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, China
| | - Yimin Li
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.,Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China
| | - Changqing Sun
- Joint Center for Translational Medicine, Tianjin Medical University Baodi Clinical College, Tianjin, 301800, China
| | - Cha Chen
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Lijuan Tang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Xiaotian Ni
- Beijing Pineal Health Management Co. Ltd, Beijing, 102206, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yaling Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, China.
| | - Jianwen Guo
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China. .,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, 510120, China.
| | - Guangshun Wang
- Joint Center for Translational Medicine, Tianjin Medical University Baodi Clinical College, Tianjin, 301800, China.
| | - Zhongde Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China. .,Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, 510120, China.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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Venom Variation of Neonate and Adult Chinese Cobras in Captivity Concerning Their Foraging Strategies. Toxins (Basel) 2022; 14:toxins14090598. [PMID: 36136536 PMCID: PMC9501182 DOI: 10.3390/toxins14090598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
The venom and transcriptome profile of the captive Chinese cobra (Naja atra) is not characterized until now. Here, LC-MS/MS and illumine technology were used to unveil the venom and trascriptome of neonates and adults N. atra specimens. In captive Chinese cobra, 98 co-existing transcripts for venom-related proteins was contained. A total of 127 proteins belong to 21 protein families were found in the profile of venom. The main components of snake venom were three finger toxins (3-FTx), snake venom metalloproteinase (SVMP), cysteine-rich secretory protein (CRISP), cobra venom factor (CVF), and phosphodiesterase (PDE). During the ontogenesis of captive Chinese cobra, the rearrangement of snake venom composition occurred and with obscure gender difference. CVF, 3-FTx, PDE, phospholipase A2 (PLA2) in adults were more abundant than neonates, while SVMP and CRISP in the neonates was richer than the adults. Ontogenetic changes in the proteome of Chinese cobra venom reveals different strategies for handling prey. The levels of different types of toxin families were dramatically altered in the wild and captive specimens. Therefore, we speculate that the captive process could reshape the snake venom composition vigorously. The clear comprehension of the composition of Chinese cobra venom facilitates the understanding of the mechanism of snakebite intoxication and guides the preparation and administration of traditional antivenom and next-generation drugs for snakebite.
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30
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Church FC. Suggestions on leading an academic research laboratory group. Open Life Sci 2022; 17:599-609. [PMID: 35800075 PMCID: PMC9202531 DOI: 10.1515/biol-2022-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 03/25/2022] [Indexed: 11/15/2022] Open
Abstract
This commentary is about running an academic research laboratory group, including some reflections, memories, and tips on effectively managing such a group of scientists focused on one’s research. The author’s academic career has spanned from 1982 to 2022, including postdoctoral research associate through the rank of professor with tenure. Currently, the author is in the final year of 3 years of phased retirement. One must be willing to work hard at running a research laboratory. Also, stay focused on funding the laboratory tasks and publishing one’s work. Recruit the best people possible with advice from the collective laboratory group. Laboratory group members felt more like they were a part of a collective family than simply employees; however, what works best for the researcher is what matters. Several other points to discuss will include managing university roles, recruiting laboratory personnel, getting recognition, dealing with intellectual property rights, and publishing work. In closing, there are many more positives than negatives to leading a research laboratory group. Finally, one cannot replace the unforgettable memories and the legacy of a research laboratory group.
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Affiliation(s)
- Frank C. Church
- Department of Pathology and Laboratory Medicine, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
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31
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Abbas MN, Chlastáková A, Jmel MA, Iliaki-Giannakoudaki E, Chmelař J, Kotsyfakis M. Serpins in Tick Physiology and Tick-Host Interaction. Front Cell Infect Microbiol 2022; 12:892770. [PMID: 35711658 PMCID: PMC9195624 DOI: 10.3389/fcimb.2022.892770] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Tick saliva has been extensively studied in the context of tick-host interactions because it is involved in host homeostasis modulation and microbial pathogen transmission to the host. Accumulated knowledge about the tick saliva composition at the molecular level has revealed that serine protease inhibitors play a key role in the tick-host interaction. Serpins are one highly expressed group of protease inhibitors in tick salivary glands, their expression can be induced during tick blood-feeding, and they have many biological functions at the tick-host interface. Indeed, tick serpins have an important role in inhibiting host hemostatic processes and in the modulation of the innate and adaptive immune responses of their vertebrate hosts. Tick serpins have also been studied as potential candidates for therapeutic use and vaccine development. In this review, we critically summarize the current state of knowledge about the biological role of tick serpins in shaping tick-host interactions with emphasis on the mechanisms by which they modulate host immunity. Their potential use in drug and vaccine development is also discussed.
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Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Adéla Chlastáková
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
- Laboratory of Molecular Biology of Ticks, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Mohamed Amine Jmel
- Laboratory of Genomics and Proteomics of Disease Vectors, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | | | - Jindřich Chmelař
- Department of Medical Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
- *Correspondence: Jindřich Chmelař, ; Michail Kotsyfakis,
| | - Michail Kotsyfakis
- Laboratory of Genomics and Proteomics of Disease Vectors, Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- *Correspondence: Jindřich Chmelař, ; Michail Kotsyfakis,
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32
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Grover SP, Mackman N. Anticoagulant SERPINs: Endogenous Regulators of Hemostasis and Thrombosis. Front Cardiovasc Med 2022; 9:878199. [PMID: 35592395 PMCID: PMC9110684 DOI: 10.3389/fcvm.2022.878199] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 12/17/2022] Open
Abstract
Appropriate activation of coagulation requires a balance between procoagulant and anticoagulant proteins in blood. Loss in this balance leads to hemorrhage and thrombosis. A number of endogenous anticoagulant proteins, such as antithrombin and heparin cofactor II, are members of the serine protease inhibitor (SERPIN) family. These SERPIN anticoagulants function by forming irreversible inhibitory complexes with target coagulation proteases. Mutations in SERPIN family members, such as antithrombin, can cause hereditary thrombophilias. In addition, low plasma levels of SERPINs have been associated with an increased risk of thrombosis. Here, we review the biological activities of the different anticoagulant SERPINs. We further consider the clinical consequences of SERPIN deficiencies and insights gained from preclinical disease models. Finally, we discuss the potential utility of engineered SERPINs as novel therapies for the treatment of thrombotic pathologies.
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33
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Bianchini E, Auditeau C, Borgel D. How can the design of therapeutic SERPINs be improved? J Thromb Haemost 2022; 20:1037-1039. [PMID: 35174614 DOI: 10.1111/jth.15667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Elsa Bianchini
- UMR-S1176, INSERM, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Claire Auditeau
- UMR-S1176, INSERM, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Service d'Hématologie Biologique, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Delphine Borgel
- UMR-S1176, INSERM, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Service d'Hématologie Biologique, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
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34
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Wu T, Tang LV, Hu Y. Venous Thromboembolism in Kidney Diseases and Genetic Predisposition. KIDNEY DISEASES (BASEL, SWITZERLAND) 2022; 8:181-189. [PMID: 35702706 PMCID: PMC9149476 DOI: 10.1159/000523777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Many renal diseases have been associated with profound clinical effects on thrombosis. To our knowledge, patients with nephrotic syndrome (NS) and chronic kidney disease (CKD) display an elevated risk of vein thrombosis, which is among the common causes of mortality in patients with renal diseases. In addition, venous thrombosis, as a complication, has also been reported in a variety of other renal diseases such as glomerulonephritis without the NS, hypertensive nephropathy, and polycystic kidney disease. With the increasing incidence of kidney diseases and the deeper understanding of the disease, clinicians are becoming more and more aware of the complications of thrombus formation in kidney disease. SUMMARY We reviewed recent publications of vein thrombosis in kidney diseases, including primary and secondary glomerular diseases, CKD, hereditary kidney disease, renal transplantation, and hemodialysis-induced, catheter-related thrombus, focusing mainly on the main clinical manifestations, possible mechanisms, related risk factors as well as hereditary influencing factors. KEY MESSAGES Vein thrombosis is a complicated complication of a wide spectrum of kidney diseases due to different possible underlying mechanisms.
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35
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Linge CP, Jern A, Tydén H, Gullstrand B, Yan H, Welinder C, Kahn R, Jönssen A, Semple JW, Bengtsson AA. Enrichment of complement, immunoglobulins and autoantibody targets in the proteome of platelets from patients with Systemic Lupus Erythematosus (SLE). Thromb Haemost 2022; 122:1486-1501. [PMID: 35419777 PMCID: PMC9420555 DOI: 10.1055/a-1825-2915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background
Systemic lupus erythematosus (SLE) is a complex disease characterized by autoimmunity toward apoptotic cells, excessive amounts of circulating immune complexes, and complement activation. A decreased platelet size has been observed in SLE and their nonhemostatic functions may play an active role in the disease. The main objective of this study was to find clues that could explain their decreased size and functional role, analyzing the entire platelet proteome.
Methods
Platelets were isolated from 23 patients with SLE. The five individuals with the highest and lowest average platelet forward scatter were selected for further analysis. Platelet protein content was analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) and compared with platelets from five healthy controls. Data are available via ProteomeXchange with identifier PXD031202.
Results
Out of 2,572 proteins identified, 396 had significantly different levels (ANOVA
q
-value ≤ 0.01). Forty proteins, including immunoglobulin-, complement- and phosphatidylserine-binding proteins had higher abundance in platelets from SLE patients, largely independent of size (fold difference of ≥1.5 and a
t
-test
p
-value of ≤0.05 as cut-off). Functional characterization revealed increased degranulation and skewed hemostatic balance in platelets from SLE patients. In the SLE proteome, immunoglobulin proteins were negatively correlated to serum complement C3 and C4 and the highest relative levels were detected in platelets of normal size.
Conclusion
Platelets from SLE patients shared a specific protein profile, including immunoglobulins, complement proteins, and autoantigens, largely independent of the platelet size and in agreement with an integrated role for platelets in SLE.
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Affiliation(s)
- Carl Petrus Linge
- Department of Clinical Sciences Lund, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Andreas Jern
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Helena Tydén
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Birgitta Gullstrand
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - Hong Yan
- BioMS, Swedish National Infrastructure for Biological Mass Spectrometry, Lund, Sweden
| | - Charlotte Welinder
- Department of Clinical Sciences Lund, Lund University Department of Oncology and Pathology, Lund, Sweden
| | - Robin Kahn
- Wallenberg Center for Molecular Medicin, Lund University Faculty of Medicine, Lund, Sweden.,Paediatrics, Lund University Faculty of Medicine, Lund, Sweden
| | - Andreas Jönssen
- Department of Clinical Sciences Lund, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
| | - John W Semple
- Transfusion Medicine, Lunds Universitet, Lund, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences, Lund University Section for Molecular Skeletal Biology and Rheumatology, Lund, Sweden
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36
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Guimarães JR, Coêlho MDC, de Oliveira NFP. Contribution of DNA methylation to the pathogenesis of Sjögren's syndrome: A review. Autoimmunity 2022; 55:215-222. [DOI: 10.1080/08916934.2022.2062593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juliana Ramalho Guimarães
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Marina de Castro Coêlho
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
| | - Naila Francis Paulo de Oliveira
- Graduate Program in Dentistry, Centre of Health Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
- Molecular Biology Department, Centre of Exact and Natural Sciences, Federal University of Paraíba – UFPB, João Pessoa, PB, Brazil
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37
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Abbas T, Chaturvedi G, Prakrithi P, Pathak AK, Kutum R, Dakle P, Narang A, Manchanda V, Patil R, Aggarwal D, Girase B, Srivastava A, Kapoor M, Gupta I, Pandey R, Juvekar S, Dash D, Mukerji M, Prasher B. Whole Exome Sequencing in Healthy Individuals of Extreme Constitution Types Reveals Differential Disease Risk: A Novel Approach towards Predictive Medicine. J Pers Med 2022; 12:jpm12030489. [PMID: 35330488 PMCID: PMC8952204 DOI: 10.3390/jpm12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Precision medicine aims to move from traditional reactive medicine to a system where risk groups can be identified before the disease occurs. However, phenotypic heterogeneity amongst the diseased and healthy poses a major challenge for identification markers for risk stratification and early actionable interventions. In Ayurveda, individuals are phenotypically stratified into seven constitution types based on multisystem phenotypes termed “Prakriti”. It enables the prediction of health and disease trajectories and the selection of health interventions. We hypothesize that exome sequencing in healthy individuals of phenotypically homogeneous Prakriti types might enable the identification of functional variations associated with the constitution types. Exomes of 144 healthy Prakriti stratified individuals and controls from two genetically homogeneous cohorts (north and western India) revealed differential risk for diseases/traits like metabolic disorders, liver diseases, and body and hematological measurements amongst healthy individuals. These SNPs differ significantly from the Indo-European background control as well. Amongst these we highlight novel SNPs rs304447 (IFIT5) and rs941590 (SERPINA10) that could explain differential trajectories for immune response, bleeding or thrombosis. Our method demonstrates the requirement of a relatively smaller sample size for a well powered study. This study highlights the potential of integrating a unique phenotyping approach for the identification of predictive markers and the at-risk population amongst the healthy.
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Affiliation(s)
- Tahseen Abbas
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Gaura Chaturvedi
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - P. Prakrithi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Ankit Kumar Pathak
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Rintu Kutum
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Pushkar Dakle
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Ankita Narang
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
| | - Vijeta Manchanda
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Dhiraj Aggarwal
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Bhushan Girase
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Ankita Srivastava
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA;
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India;
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Debasis Dash
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Jodhpur 342037, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Correspondence: (D.D.); (M.M.); (B.P.)
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38
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Platelet Proteomics to Understand the Pathophysiology of Immune Thrombocytopenia: Studies in Mouse Models. Blood Adv 2022; 6:3529-3534. [PMID: 35298626 PMCID: PMC9198918 DOI: 10.1182/bloodadvances.2021006438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/08/2022] [Indexed: 12/03/2022] Open
Abstract
The platelet proteome distinguishes platelets from 2 different preclinical ITP mouse models and may be of use in profiling human disease. The platelet proteomes suggest a slow turnover of platelets in chronic ITP and basal degranulation in acute ITP due to hyporesponsiveness.
Immune thrombocytopenia (ITP) is an autoimmune disease characterized by enhanced platelet clearance and defective platelet production. Diagnosis by exclusion and trial-and-error treatment strategies is common practice, and despite the advancement in treatment options, many patients remain refractory. Although the existence of different pathophysiological entities is acknowledged, we are still far from stratifying and understanding ITP. To investigate, we sought to dissect the platelet proteome dynamics in so-called passive and active preclinical ITP mouse models, with which we propose to phenocopy respectively acute/newly diagnosed and persistent/chronic stages of ITP in humans. We obtained the platelet proteome at the thrombocytopenic stage and after platelet count recovery (reached naturally or by IVIg-treatment, depending on the model). Although most of the proteomic alterations were common to both ITP models, there were model-specific protein dynamics that accompanied and explained alterations in platelet aggregation responses, as measured in the passive ITP model. The expression dynamics observed in Syk may explain, extrapolated to humans and pending validation, the increased bleeding tendency of patients with ITP when treated with fostamatinib as third or later– as opposed to second line of treatment. We propose that the platelet proteome may give diagnostic and prognostic insights into ITP and that such studies should be pursued in humans.
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Inherited antithrombin deficiency in pregnancy. THROMBOSIS UPDATE 2022. [DOI: 10.1016/j.tru.2021.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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rDromaserpin: A Novel Anti-Hemostatic Serpin, from the Salivary Glands of the Hard Tick Hyalomma dromedarii. Toxins (Basel) 2021; 13:toxins13120913. [PMID: 34941750 PMCID: PMC8703697 DOI: 10.3390/toxins13120913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 01/17/2023] Open
Abstract
Hemostatic disorders are caused either by platelet-related dysfunctions, defective blood coagulation, or by a combination of both, leading to an increased susceptibility to cardiovascular diseases (CVD) and other related illnesses. The unique specificity of anticoagulants from hematophagous arthropods, such as ticks, suggests that tick saliva holds great promise for discovering new treatments for these life-threatening diseases. In this study, we combined in silico and in vitro analyses to characterize the first recombinant serpin, herein called Dromaserpin, from the sialotranscriptome of the Hyalomma dromedarii tick. Our in silico data described Dromaserpin as a secreted protein of ~43 kDa with high similarities to previously characterized inhibitory serpins. The recombinant protein (rDromaserpin) was obtained as a well-structured monomer, which was tested using global blood coagulation and platelet aggregation assays. With this approach, we confirmed rDromaserpin anticoagulant activity as it significantly delayed plasma clotting in activated partial thromboplastin time and thrombin time assays. The profiling of proteolytic activity shows its capacity to inhibit thrombin in the micromolar range (0.2 to 1 μM) and in the presence of heparin this inhibition was clearly increased. It was also able to inhibit Kallikrein, FXIa and slightly FXIIa, with no significant effect on other factors. In addition, the rDromaserpin inhibited thrombin-induced platelet aggregation. Taken together, our data suggest that rDromaserpin deserves to be further investigated as a potential candidate for developing therapeutic compounds targeting disorders related to blood clotting and/or platelet aggregation.
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Gillis-Germitsch N, Kockmann T, Asmis LM, Tritten L, Schnyder M. The Angiostrongylus vasorum Excretory/Secretory and Surface Proteome Contains Putative Modulators of the Host Coagulation. Front Cell Infect Microbiol 2021; 11:753320. [PMID: 34796127 PMCID: PMC8593241 DOI: 10.3389/fcimb.2021.753320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023] Open
Abstract
Angiostrongylus vasorum is a cardiopulmonary nematode of canids and is, among others, associated with bleeding disorders in dogs. The pathogenesis of such coagulopathies remains unclear. A deep proteomic characterization of sex specific A. vasorum excretory/secretory proteins (ESP) and of cuticular surface proteins was performed, and the effect of ESP on host coagulation and fibrinolysis was evaluated in vitro. Proteins were quantified by liquid chromatography coupled to mass spectrometry and functionally characterized through gene ontology and pathway enrichment analysis. In total, 1069 ESP (944 from female and 959 from male specimens) and 1195 surface proteins (705 and 1135, respectively) were identified. Among these were putative modulators of host coagulation, e.g., von Willebrand factor type D domain protein orthologues as well as several proteases, including serine type proteases, protease inhibitors and proteasome subunits. The effect of ESP on dog coagulation and fibrinolysis was evaluated on canine endothelial cells and by rotational thromboelastometry (ROTEM). After stimulation with ESP, tissue factor and serpin E1 transcript expression increased. ROTEM revealed minimal interaction of ESP with dog blood and ESP did not influence the onset of fibrinolysis, leading to the conclusion that Angiostrongylus vasorum ESP and surface proteins are not solely responsible for bleeding in dogs and that the interaction with the host's vascular hemostasis is limited. It is likely that coagulopathies in A. vasorum infected dogs are the result of a multifactorial response of the host to this parasitic infection.
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Affiliation(s)
- Nina Gillis-Germitsch
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tobias Kockmann
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology Zurich (ETH Zurich), University of Zurich, Zurich, Switzerland
| | - Lars M Asmis
- Center for Perioperative Thrombosis and Hemostasis, Zurich, Switzerland
| | - Lucienne Tritten
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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A curcumin analog CA-5f inhibits urokinase-type plasminogen activator and invasive phenotype of triple-negative breast cancer cells. Toxicol Res 2021; 38:19-26. [PMID: 35070937 PMCID: PMC8748588 DOI: 10.1007/s43188-021-00112-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive types of breast cancer with poor outcomes. Patients with TNBC cannot benefit from targeted therapies such as Tamoxifen and Herceptin. The aim of the present study was to seek a preventive or therapeutic agent with a potential inhibitory effect on aggressive progression of TNBC. Anticancer effect of a natural compound curcumin have been demonstrated, however, development of more effective curcumin analogs with better bioavailability is needed. We investigated if a curcumin analog CA-5f could inhibit the invasive phenotype of TNBC cell lines in the present study. Treatment with CA-5f inhibited the viability of MDA‑MB‑231 and Hs578T TNBC cells, possible by inducing apoptosis. The invasive phenotypes of these cells were inhibited by CA-5f in a concentration-dependent manner. Protein expression of urokinase-type plasminogen activator (uPA), a serine protease known to degrade the extracellular matrix and lead to invasion, was markedly decreased by CA-5f in Hs578T cells. However, mRNA level of uPA was not altered by CA-5f, implicating that the effect of CA-5f was not through transcriptional regulation. Of note, CA-5f upregulated plasminogen activator inhibitor type (PAI)-1, which is known to inhibit uPA by interacting with urokinase-type plasminogen receptor, in TNBC cells. Taken together, these results demonstrated that CA-5f significantly inhibited the invasive phenotype of TNBC cells, possibly by decreasing the protein level of uPA through upregulating PAI-1. Our results may provide useful information on developing CA-5f as a potential therapeutic agent against malignant progression of TNBC.
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Delrue L, Vanderheyden M, Beles M, Paolisso P, Di Gioia G, Dierckx R, Verstreken S, Goethals M, Heggermont W, Bartunek J. Circulating SERPINA3 improves prognostic stratification in patients with a de novo or worsened heart failure. ESC Heart Fail 2021; 8:4780-4790. [PMID: 34725968 PMCID: PMC8712810 DOI: 10.1002/ehf2.13659] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/18/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
Aims We investigated the prognostic relevance of serpin peptidase inhibitor, clade A member 3 (SERPINA3) in patients admitted with a de novo or worsened heart failure (HF). Methods and results In the first stage, 83 HF‐related left ventricular (LV) transcripts were examined in patients with congestive cardiomyopathy (CCMP, n = 44) who died within 5 years and compared with age‐matched and haemodynamically matched CCMP survivors (n = 39) and controls with normal LV function (n = 17). Among 14 differentially expressed transcripts, myocardial gene and circulating SERPINA3 levels were up‐regulated in non‐survivors vs. survivors (2.40 ± 3.66 vs. 0.36 ± 0.22 units, P < 0.01 and 334.7 ± 138.7 vs. 228.2 ± 83.1 μg/mL, P < 0.01, respectively). While no significant transmyocardial gradient was detected, cytokine stimulation of human endothelial cells induced SERPINA3 secretion. In an independent validation cohort with a de novo or worsened HF (n = 387), circulating SERPINA3 levels > 316 μg/mL were associated with increased all‐cause mortality {hazard ratio [HR] [95% confidence interval (CI)]: 2.4 [1.5–3.9], P = 0.0002} and its composite with unplanned cardiovascular readmission [HR (95% CI): 2.0 (1.2–3.3), P = 0.004]. Patients with elevated SERPINA3 levels and elevated either N‐terminal pro brain natriuretic peptide or ST2 showed worse freedom from both endpoints. In a multivariate analysis, including established clinical risk factors, SERPINA3 remained independent predictor of all‐cause mortality together with age, gender, ST2, glomerular filtration, and pulmonary capillary wedge pressure. Conclusion In patients with a de novo or worsened HF, increased SERPINA3 levels > 316 μg/mL are associated with increased mortality or unplanned cardiac readmission. Elevated SERPINA3 levels on top of established clinical predictors appear to identify a subgroup of HF patients at higher mortality risk. Prospective studies should further validate its value in prognostic stratification of HF.
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Affiliation(s)
- Leen Delrue
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Marc Vanderheyden
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Monika Beles
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Pasquale Paolisso
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium.,Department of Advanced Biomedical Sciences, University of Naples Frederico II, Naples, Italy
| | - Giuseppe Di Gioia
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium.,Department of Advanced Biomedical Sciences, University of Naples Frederico II, Naples, Italy
| | - Riet Dierckx
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Sofie Verstreken
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Marc Goethals
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Ward Heggermont
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
| | - Jozef Bartunek
- Cardiovascular Center, OLV Hospital, Moorselbaan 164, Aalst, 9300, Belgium
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Ianevski A, Yao R, Lysvand H, Grødeland G, Legrand N, Oksenych V, Zusinaite E, Tenson T, Bjørås M, Kainov DE. Nafamostat-Interferon-α Combination Suppresses SARS-CoV-2 Infection In Vitro and In Vivo by Cooperatively Targeting Host TMPRSS2. Viruses 2021; 13:1768. [PMID: 34578348 PMCID: PMC8473362 DOI: 10.3390/v13091768] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 and its vaccine/immune-escaping variants continue to pose a serious threat to public health due to a paucity of effective, rapidly deployable, and widely available treatments. Here, we address these challenges by combining Pegasys (IFNα) and nafamostat to effectively suppress SARS-CoV-2 infection in cell culture and hamsters. Our results indicate that Serpin E1 is an important mediator of the antiviral activity of IFNα and that both Serpin E1 and nafamostat can target the same cellular factor TMPRSS2, which plays a critical role in viral replication. The low doses of the drugs in combination may have several clinical advantages, including fewer adverse events and improved patient outcome. Thus, our study may provide a proactive solution for the ongoing pandemic and potential future coronavirus outbreaks, which is still urgently required in many parts of the world.
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Affiliation(s)
- Aleksandr Ianevski
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Rouan Yao
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Hilde Lysvand
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Gunnveig Grødeland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway;
- Institute of Clinical Medicine (KlinMed), University of Oslo, 0318 Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Nicolas Legrand
- Oncodesign, 25 Avenue du Québec, 91140 Villebon Sur Yvette, France;
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
| | - Denis E. Kainov
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7028 Trondheim, Norway; (R.Y.); (H.L.); (V.O.); (M.B.)
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia; (E.Z.); (T.T.)
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, 00014 Helsinki, Finland
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Quantitative Proteomic Analysis of Plasma after Remote Ischemic Conditioning in a Rhesus Monkey Ischemic Stroke Model. Biomolecules 2021; 11:biom11081164. [PMID: 34439830 PMCID: PMC8393806 DOI: 10.3390/biom11081164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022] Open
Abstract
Background: Animal and clinical studies have shown that remote ischemic conditioning (RIC) has protective effects for cerebral vascular diseases, with induced humoral factor changes in the peripheral blood. However, many findings are heterogeneous, perhaps due to differences in the RIC intervention schemes, enrolled populations, and sample times. This study aimed to examine the RIC-induced changes in the plasma proteome using rhesus monkey models of strokes. Methods: Two adult rhesus monkeys with autologous blood clot-induced middle cerebral artery (MCA) occlusion underwent RIC interventions twice a week for five consecutive weeks. Each RIC treatment included five cycles of five minutes of ischemia alternating with five minutes of reperfusion of the forearm. The blood samples were taken from the median cubital vein of the monkeys at baseline and immediately after each week’s RIC stimulus. The plasma samples were isolated for a proteomic analysis using mass spectrometry (MS). Results: Several proteins related to lipid metabolism (Apolipoprotein A-II and Apolipoprotein C-II), coagulation (Fibrinogen alpha chain and serpin), immunoinflammatory responses (complement C3 and C1), and endovascular hemostasis (basement membrane-specific heparan sulfate proteoglycan) were significantly modulated after the RIC intervention. Many of these induced changes, such as in the lipid metabolism regulation and anticoagulation responses, starting as early as two weeks following the RIC intervention. The complementary activation and protection of the endovascular cells occurred more than three weeks postintervention. Conclusions: Multiple protective effects were induced by RIC and involved lipid metabolism regulation (anti-atherogenesis), anticoagulation (antithrombosis), complement activation, and endovascular homeostasis (anti-inflammation). In conclusion, this study indicates that RIC results in significant modulations of the plasma proteome. It also provides ideas for future research and screening targets.
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Sullivan KD, Galbraith MD, Kinning KT, Bartsch KW, Levinsky NC, Araya P, Smith KP, Granrath RE, Shaw JR, Baxter RM, Jordan KR, Russell SA, Dzieciatkowska ME, Reisz JA, Gamboni F, Cendali FI, Ghosh T, Monte AA, Bennett TD, Miller MG, Hsieh EWY, D'Alessandro A, Hansen KC, Espinosa JM. The COVIDome Explorer researcher portal. Cell Rep 2021; 36:109527. [PMID: 34348131 PMCID: PMC8316015 DOI: 10.1016/j.celrep.2021.109527] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/30/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. To expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients, including matched analysis of the whole-blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate herein the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
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Affiliation(s)
- Kelly Daniel Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Matthew Dominic Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kohl Thomas Kinning
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kyle William Bartsch
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nik Caldwell Levinsky
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Paula Araya
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Keith Patrick Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ross Erich Granrath
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jessica Rose Shaw
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ryan Michael Baxter
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kimberly Rae Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Seth Aaron Russell
- Data Science to Patient Value, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Monika Ewa Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julie Ann Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Francesca Isabelle Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Andrew Albert Monte
- Department of Emergency Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tellen Demeke Bennett
- Department of Pediatrics, Sections of Informatics and Data Science and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael George Miller
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elena Wen-Yuan Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, Division of Allergy/Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kirk Charles Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin Maximiliano Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Niksirat H, Siino V, Steinbach C, Levander F. High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins. J Proteome Res 2021; 20:4075-4088. [PMID: 34185526 DOI: 10.1021/acs.jproteome.1c00387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the molecular basis of sexual dimorphism in the cardiovascular system may contribute to the improvement of the outcome in biological, pharmacological, and toxicological studies as well as on the development of sex-based drugs and therapeutic approaches. Label-free protein quantification using high-resolution mass spectrometry was applied to detect sex-based proteome differences in the heart of zebrafish Danio rerio. Out of almost 3000 unique identified proteins in the heart, 79 showed significant abundance differences between male and female fish. The functional differences were mapped using enrichment analyses. Our results suggest that a large amount of materials needed for reproduction (e.g., sugars, lipids, proteins, etc.) may impose extra pressure on blood, vessels, and heart on their way toward the ovaries. In the present study, the female's heart shows a clear sexual dimorphism by changing abundance levels of numerous proteins, which could be a way to safely overcome material-induced elevated pressures. These proteins belong to the immune system, oxidative stress response, drug metabolization, detoxification, energy, metabolism, and so on. In conclusion, we showed that sex can induce dimorphism at the molecular level in nonsexual organs such as heart and must be considered as an important factor in cardiovascular research. Data are available via ProteomeXchange with identifier PXD023506.
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Affiliation(s)
- Hamid Niksirat
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Vodňany, 370 05 České Budějovice, Czech Republic
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund 223 87, Sweden
| | - Christoph Steinbach
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Vodňany, 370 05 České Budějovice, Czech Republic
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund 223 87, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund 223 87, Sweden
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Galbraith MD, Kinning KT, Sullivan KD, Baxter R, Araya P, Jordan KR, Russell S, Smith KP, Granrath RE, Shaw JR, Dzieciatkowska M, Ghosh T, Monte AA, D'Alessandro A, Hansen KC, Benett TD, Hsieh EWY, Espinosa JM. Seroconversion stages COVID19 into distinct pathophysiological states. eLife 2021; 10:e65508. [PMID: 33724185 PMCID: PMC7963480 DOI: 10.7554/elife.65508] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
COVID19 is a heterogeneous medical condition involving diverse underlying pathophysiological processes including hyperinflammation, endothelial damage, thrombotic microangiopathy, and end-organ damage. Limited knowledge about the molecular mechanisms driving these processes and lack of staging biomarkers hamper the ability to stratify patients for targeted therapeutics. We report here the results of a cross-sectional multi-omics analysis of hospitalized COVID19 patients revealing that seroconversion status associates with distinct underlying pathophysiological states. Low antibody titers associate with hyperactive T cells and NK cells, high levels of IFN alpha, gamma and lambda ligands, markers of systemic complement activation, and depletion of lymphocytes, neutrophils, and platelets. Upon seroconversion, all of these processes are attenuated, observing instead increases in B cell subsets, emergency hematopoiesis, increased D-dimer, and hypoalbuminemia. We propose that seroconversion status could potentially be used as a biosignature to stratify patients for therapeutic intervention and to inform analysis of clinical trial results in heterogenous patient populations.
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Affiliation(s)
- Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pharmacology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kohl T Kinning
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, Division of Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ryan Baxter
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Paula Araya
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kimberly R Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Seth Russell
- Data Science to Patient Value, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Keith P Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Ross E Granrath
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Jessica R Shaw
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public HealthAuroraUnited States
| | - Andrew A Monte
- Department of Emergency Medicine, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Tellen D Benett
- Department of Pediatrics, Sections of Informatics and Data Science and Critical Care Medicine, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Elena WY Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, Division of Allergy/Immunology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pharmacology, University of Colorado Anschutz Medical CampusAuroraUnited States
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49
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Sullivan KD, Galbraith MD, Kinning KT, Bartsch K, Levinsky N, Araya P, Smith KP, Granrath RE, Shaw JR, Baxter R, Jordan KR, Russell S, Dzieciatkowska M, Reisz JA, Gamboni F, Cendali F, Ghosh T, Monte AA, Bennett TD, Miller MG, Hsieh EW, D’Alessandro A, Hansen KC, Espinosa JM. The COVIDome Explorer Researcher Portal. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.04.21252945. [PMID: 33758879 PMCID: PMC7987038 DOI: 10.1101/2021.03.04.21252945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
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Affiliation(s)
- Kelly D. Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D. Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kohl T. Kinning
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kyle Bartsch
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nik Levinsky
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paula Araya
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Keith P. Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ross E. Granrath
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica R. Shaw
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ryan Baxter
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kimberly R. Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Seth Russell
- Data Science to Patient Value, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Andrew A. Monte
- Department of Emergency Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tellen D. Bennett
- Department of Pediatrics, Sections of Informatics and Data Science and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael G. Miller
- Information Services, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Elena W.Y. Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, Division of Allergy/Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joaquin M. Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Correspondence to:
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50
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Kim TK, Tirloni L, Bencosme-Cuevas E, Kim TH, Diedrich JK, Yates JR, Mulenga A. Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs. BMC Genomics 2021; 22:152. [PMID: 33663385 PMCID: PMC7930271 DOI: 10.1186/s12864-021-07429-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lyme disease (LD) caused by Borrelia burgdorferi is the most prevalent tick-borne disease. There is evidence that vaccines based on tick proteins that promote tick transmission of B. burgdorferi could prevent LD. As Ixodes scapularis nymph tick bites are responsible for most LD cases, this study sought to identify nymph tick saliva proteins associated with B. burgdorferi transmission using LC-MS/MS. Tick saliva was collected using a non-invasive method of stimulating ticks (uninfected and infected: unfed, and every 12 h during feeding through 72 h, and fully-fed) to salivate into 2% pilocarpine-PBS for protein identification using LC-MS/MS. RESULTS We identified a combined 747 tick saliva proteins of uninfected and B. burgdorferi infected ticks that were classified into 25 functional categories: housekeeping-like (48%), unknown function (18%), protease inhibitors (9%), immune-related (6%), proteases (8%), extracellular matrix (7%), and small categories that account for <5% each. Notably, B. burgdorferi infected ticks secreted high number of saliva proteins (n=645) than uninfected ticks (n=376). Counter-intuitively, antimicrobial peptides, which function to block bacterial infection at tick feeding site were suppressed 23-85 folds in B. burgdorferi infected ticks. Similar to glycolysis enzymes being enhanced in mammalian cells exposed to B. burgdorferi : eight of the 10-glycolysis pathway enzymes were secreted at high abundance by B. burgdorferi infected ticks. Of significance, rabbits exposed to B. burgdorferi infected ticks acquired potent immunity that caused 40-60% mortality of B. burgdorferi infected ticks during the second infestation compared to 15-28% for the uninfected. This might be explained by ELISA data that show that high expression levels of immunogenic proteins in B. burgdorferi infected ticks. CONCLUSION Data here suggest that B. burgdorferi infection modified protein content in tick saliva to promote its survival at the tick feeding site. For instance, enzymes; copper/zinc superoxide dismutase that led to production of H2O2 that is toxic to B. burgdorferi were suppressed, while, catalase and thioredoxin that neutralize H2O2, and pyruvate kinase which yields pyruvate that protects Bb from H2O2 killing were enhanced. We conclude data here is an important resource for discovery of effective antigens for a vaccine to prevent LD.
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Affiliation(s)
- Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Department of Diagnostic Medicine and Veterinary Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Lucas Tirloni
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, Montana, United States of America
| | - Emily Bencosme-Cuevas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Tae Heung Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America.
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