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Lu P, Zhang C, Fu L, Wei Y, Huang Y, Wang X, Lv C, Chen L. Near-Infrared Fluorescent Probe for Imaging and Evaluating the Role of Vanin-1 in Chemotherapy. Anal Chem 2021; 93:10378-10387. [PMID: 34275284 DOI: 10.1021/acs.analchem.1c02386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pantetheinase (also known as Vanin-1) is highly expressed in the liver, kidneys, and intestine and is closely associated with a number of diseases. Vanin-1 can hydrolyze pantetheine to pantothenic acid (vitamin B5) and cysteamine and participate in the synthesis of glutathione (GSH). GSH is highly expressed in tumor cells and plays a major role in the resistance of tumor cells to cisplatin. Therefore, we urgently need a method to monitor the activity level of Vanin-1 in tumor cells and tissues and elucidate the relationship between the role of Vanin-1 in GSH synthesis and tumor resistance. Herein, we report a Cy-Pa fluorescent probe for imaging Vanin-1 in cells and in vivo that can qualitatively and quantitatively detect the fluctuation of Vanin-1 concentrations in HepG2 and HepG2/DDP cells or tumor tissues of tumor-bearing mice. This probe shows excellent potential in in situ real-time monitoring of endogenous Vanin-1. Moreover, we proved that Vanin-1 can inhibit GSH synthesis using the probe. When the Vanin-1 inhibitor RR6 was used in combination with cisplatin, HepG2 and HepG2/DDP cells showed increased resistance to cisplatin, while the therapeutic efficiency of cisplatin was reduced in HepG2 and HepG2/DDP xenografts. In this study, Vanin-1 was shown to play an important role in the treatment of cancer, and the study of Vanin-1 may provide an idea for the treatment of cancer in the future.
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Affiliation(s)
- Pengpeng Lu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.,CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Caiyun Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Lili Fu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.,CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yinghui Wei
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,Department of Respiratory Medicine, Binzhou Medical University Hospital, Binzhou 256603, China
| | - Yan Huang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.,CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Xiaoyan Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.,CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Changjun Lv
- Department of Respiratory Medicine, Binzhou Medical University Hospital, Binzhou 256603, China
| | - Lingxin Chen
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.,CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,College of Chemistry and Chemical Engineering, Qufu Normal University, University, Qufu 273165, China
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Epigenetic Drifts during Long-Term Intestinal Organoid Culture. Cells 2021; 10:cells10071718. [PMID: 34359888 PMCID: PMC8305684 DOI: 10.3390/cells10071718] [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: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/17/2022] Open
Abstract
Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying the mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in the growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we studied histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks and compared them with data on their tissue of origin. We found that, besides the expected changes in short-term culture, the organoids showed profound changes in their epigenomes also during the long-term culture. The most prominent were epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We showed that a long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process was disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER) stress and Wnt activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during a long-term culture involve DNA demethylation that ceases if the metabolic adaptation is disturbed.
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Neely BA, Janech MG, Fenton MB, Simmons NB, Bland AM, Becker DJ. Surveying the Vampire Bat ( Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens. J Proteome Res 2021; 20:2547-2559. [PMID: 33840197 PMCID: PMC9812275 DOI: 10.1021/acs.jproteome.0c00995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bats are increasingly studied as model systems for longevity and as natural hosts for some virulent viruses. Yet the ability to characterize immune mechanisms of viral tolerance and to quantify infection dynamics in wild bats is often limited by small sample volumes and few species-specific reagents. Here, we demonstrate how proteomics can overcome these limitations by using data-independent acquisition-based shotgun proteomics to survey the serum proteome of 17 vampire bats (Desmodus rotundus) from Belize. Using just 2 μL of sample and relatively short separations of undepleted serum digests, we identified 361 proteins across 5 orders of magnitude. Levels of immunological proteins in vampire bat serum were then compared to human plasma via published databases. Of particular interest were antiviral and antibacterial components, circulating 20S proteasome complex and proteins involved in redox activity. Lastly, we used known virus proteomes to putatively identify Rh186 from Macacine herpesvirus 3 and ORF1a from Middle East respiratory syndrome-related coronavirus, indicating that mass spectrometry-based techniques show promise for pathogen detection. Overall, these results can be used to design targeted mass-spectrometry assays to quantify immunological markers and detect pathogens. More broadly, our findings also highlight the application of proteomics in advancing wildlife immunology and pathogen surveillance.
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Affiliation(s)
- Benjamin A Neely
- Chemical Sciences Division, National Institute of Standards and Technology, NIST Charleston, Charleston, South Carolina 29412, United States
| | - Michael G Janech
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, United States
| | - M Brock Fenton
- Department of Biology, Western University, London, Ontario N6A 3K7, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York 10024, United States
| | - Alison M Bland
- Hollings Marine Laboratory, Charleston, South Carolina 29412, United States
- Department of Biology, College of Charleston, Charleston, South Carolina 29424, United States
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
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Constantino CS, Carvalho AM, Vinga S. Coupling sparse Cox models with clustering of longitudinal transcriptomics data for trauma prognosis. BioData Min 2021; 14:25. [PMID: 33853663 PMCID: PMC8048345 DOI: 10.1186/s13040-021-00257-8] [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: 10/30/2020] [Accepted: 03/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background Longitudinal gene expression analysis and survival modeling have been proved to add valuable biological and clinical knowledge. This study proposes a novel framework to discover gene signatures and patterns in a high-dimensional time series transcriptomics data and to assess their association with hospital length of stay. Methods We investigated a longitudinal and high-dimensional gene expression dataset from 168 blunt-force trauma patients followed during the first 28 days after injury. To model the length of stay, an initial dimensionality reduction step was performed by applying Cox regression with elastic net regularization using gene expression data from the first hospitalization days. Also, a novel methodology to impute missing values to the genes selected previously was proposed. We then applied multivariate time series (MTS) clustering to analyse gene expression over time and to stratify patients with similar trajectories. The validation of the patients’ partitions obtained by MTS clustering was performed using Kaplan-Meier curves and log-rank tests. Results We were able to unravel 22 genes strongly associated with hospital’s discharge. Their expression values in the first days after trauma showed to be good predictors of the length of stay. The proposed mixed imputation method allowed to achieve a complete dataset of short time series with a minimum loss of information for the 28 days of follow-up. MTS clustering enabled to group patients with similar genes trajectories and, notably, with similar discharge days from the hospital. Patients within each cluster have comparable genes’ trajectories and may have an analogous response to injury. Conclusion The proposed framework was able to tackle the joint analysis of time-to-event information with longitudinal multivariate high-dimensional data. The application to length of stay and transcriptomics data revealed a strong relationship between gene expression trajectory and patients’ recovery, which may improve trauma patient’s management by healthcare systems. The proposed methodology can be easily adapted to other medical data, towards more effective clinical decision support systems for health applications.
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Affiliation(s)
- Cláudia S Constantino
- INESC-ID, Instituto Superior Técnico, ULisboa, R. Alves Redol 9, Lisbon, 1000-029, Portugal
| | - Alexandra M Carvalho
- Instituto de Telecomunicações, Instituto Superior Técnico, ULisboa, Av. Rovisco Pais 1, Lisbon, 1049-001, Portugal
| | - Susana Vinga
- INESC-ID, Instituto Superior Técnico, ULisboa, R. Alves Redol 9, Lisbon, 1000-029, Portugal. .,IDMEC, Instituto Superior Técnico, ULisboa, Av. Rovisco Pais 1, Lisbon, 1049-001, Portugal.
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Krzemień G, Pańczyk-Tomaszewska M, Górska E, Szmigielska A. Urinary vanin-1 for predicting acute pyelonephritis in young children with urinary tract infection: a pilot study. Biomarkers 2021; 26:318-324. [PMID: 33656956 DOI: 10.1080/1354750x.2021.1893813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Vanin-1, an epithelial glycosylphosphatidylolinositol (GPI)-anchored pantetheinase, is a valuable marker of renal injury. PURPOSE The aim of this study was to assess the predictive value of vanin-1 in acute pyelonephritis (APN) in comparison to the conventional serum inflammatory markers in children aged 1-24 months with the first episode of urinary tract infection (UTI). MATERIAL AND METHODS Urinary vanin-1, vanin-1/Cr ratio, WBC, CRP, PCT were analysed in 58 children with febrile UTI and in 18 children with non-febrile UTI. Febrile UTI group was divided into APN subgroup (n = 29) and non-APN subgroup (n = 29), based on the results of Tc-99m-ethylenedicysteine scan. RESULTS The mean vanin-1 level was higher in the APN group compared to the non-febrile UTI group (p = 0.02) and did not differ between APN and non-APN subgroup. In univariate analysis, vanin-1 (p = 0.042), CRP (p < 0.001), PCT (p < 0.001), and WBC (p = 0.022), were associated with APN, but only vanin-1 (p = 0.048) and CRP (p = 0.002) were independent markers of APN. In ROC analysis, vanin-1, with its best cut-off value of 16.53 ng/mL, had worse diagnostic profile (AUC 0.629, sensitivity 58,6%, specificity 63.8%) than CRP, PCT and WBC (AUC: 0.937; 0.880; 0.667, respectively). CONCLUSIONS Vanin-1 is not useful for predicting APN, since its diagnostic value is inferior to other conventional serum inflammatory markers.
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Affiliation(s)
- Grażyna Krzemień
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | | | - Elżbieta Górska
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
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Effect of using green fluorescent proteindouble-stranded RNA as non-target negative control in Nasonia vitripennisRNA interference assays. EXPERIMENTAL RESULTS 2021. [DOI: 10.1017/exp.2020.67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractRNA interference (RNAi) is a technique used in many insects to study gene function. However, prior research suggests possible off-target effects when usingGreen Fluorescent Protein(GFP) sequence as a non-target control. We used a transcriptomic approach to study the effect ofGFPRNAi (GFP-i) inNasonia vitripennis, a widely used parasitoid wasp model system. Our study identified 3.4% of total genes being differentially expressed in response toGFP-i. A subset of these genes appears involved in microtubule and sperm functions.In silicoanalysis identified 17 potential off-targets, of which only one was differentially expressed afterGFP-i. We suggest the primary cause for differential expression afterGFP-i is the non-specific activation of the RNAi machinery at the injection site, and a potentially disturbed spermatogenesis. Still, we advise that any RNAi study involving the genes deregulated in this study, exercises caution in drawing conclusions and uses a different non-target control.
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Corinti D, Chiavarino B, Scuderi D, Fraschetti C, Filippi A, Fornarini S, Crestoni ME. Molecular Properties of Bare and Microhydrated Vitamin B5-Calcium Complexes. Int J Mol Sci 2021; 22:E692. [PMID: 33445631 PMCID: PMC7826572 DOI: 10.3390/ijms22020692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]-, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Debora Scuderi
- Institut de Chimie Physique (UMR8000), CNRS, Université Paris-Saclay, 91405 Orsay, France;
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Piazzale Aldo Moro, 5, I-00185 Roma, Italy; (D.C.); (B.C.); (C.F.); (A.F.); (S.F.)
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Qian J, Zhang L, Wang J, Teng Z, Cao T, Zheng L, Cao Y, Qin W, Liu Y, Guo H. Red emission ratio fluorescent probe for the activity of vanin-1 and imaging in vivo. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123863. [PMID: 33113750 DOI: 10.1016/j.jhazmat.2020.123863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Pantetheinase, also known as Vanin-1, catalyzes pantetheine to decompose into the precursor of CoA - pantothenic acid and aminothiol cysteamine. Studies have shown that Vanin-1 plays an important role in many important physiological pathologies. In this paper, a new red emission ratio fluorescent probe DCM-PA (I640 nm/I564 nm) has been implemented to detect the activity of Vanin-1 in cells and vivo. DCM-PA has short response time (30 min), high selectivity and low sensitivity (DL =0.69 ng/mL). Also, we have applied DCM-PA for imaging in cells and mice, and the results have indicated that the probe has a non-negligible potential for monitoring the activity of Vanin-1 in situ, benefiting further to study the role of Vanin-1 in physiology and pathology. In addition, the up-regulation of this enzyme by starvation confirmed the inevitable connection between diabetes and abnormal expression of Vanin-1.
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Affiliation(s)
- Jing Qian
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Liang Zhang
- Department of Radiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China
| | - Jiemin Wang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Zhidong Teng
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu Province 730046, PR China
| | - Ting Cao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Lei Zheng
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Yuping Cao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Wenwu Qin
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and Key Laboratory of Special Function Materials and Structure Design (MOE), College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China.
| | - Yun Liu
- Department of Radiology, Xinqiao Hospital, Army Medical University, Chongqing, 400037, PR China.
| | - Huichen Guo
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu Province 730046, PR China.
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Gurung AB, Bhutia JT, Bhattacharjee A. High-throughput virtual screening of novel potent inhibitor(s) for Human Vanin-1 enzyme. J Biomol Struct Dyn 2020; 40:4208-4223. [PMID: 33289461 DOI: 10.1080/07391102.2020.1854857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Vanin-1 (VNN1) is a glycosylphosphatidylinositol (GPI)-anchored ectoenzyme which hydrolyzes pantetheine to pantothenic acid and cysteamine. It has emerged as a promising drug target for many human diseases associated with oxidative stress and inflammatory pathways. In the present study we used structure-based virtual screening approach for the identification of small molecule inhibitors of vanin-1. A chemical library consisting of natural compounds, synthetic compounds and RRV analogs were screened for drug-like molecules. The filtered molecules were subjected to molecular docking studies. Three potential hits-ZINC04073864 (Natural compound), CID227017 (synthetic compound) and CID129558381 (RRV analog)-were identified for the target enzyme. The molecules form good number of hydrogen bonds with the catalytic residues such as Glu79, Lys178 and Cys211. The apo-VNN1 and VNN1-ligand complexes were subjected to molecular dynamics (MD) simulation for 30 ns. The geometric properties such as root mean square deviation, radius of gyration, solvent accessible surface area, number of hydrogen bonds and the distance between the catalytic triad residues-Glu79, Lys178 and Cys211 were altered upon binding of the compounds. Essential dynamics and entropic studies further confirmed that the fluctuations in VNN1 decrease upon binding of the compounds. The lead molecules were stable throughout the simulation time period. Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) studies showed that Van der Waals interaction energy contributes significantly to the total binding free energy. Thus, our study reveals three lead molecules-ZINC04073864, CID227017 and CID129558381 as potential inhibitors of Vanin-1 which can be validated through further studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arun Bahadur Gurung
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India.,Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Jigmi Tshering Bhutia
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
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Wang Y, Chen Y, Zhang X, Lu Y, Chen H. New insights in intestinal oxidative stress damage and the health intervention effects of nutrients: A review. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104248] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Yang Y, Hu Y, Shi W, Ma H. A near-infrared fluorescence probe for imaging of pantetheinase in cells and mice in vivo. Chem Sci 2020; 11:12802-12806. [PMID: 34123238 PMCID: PMC8163316 DOI: 10.1039/d0sc04537c] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Pantetheinase is an amidohydrolase that cleaves pantetheine into pantothenic acid and cysteamine. Functional studies have found that ubiquitous expression of this enzyme is associated with many inflammatory diseases. However, the lack of near-infrared fluorescence probes limits the better understanding of the functions of the enzyme. In this work, we have developed a new near-infrared fluorescence probe, CYLP, for bioimaging of pantetheinase by using pantothenic acid with a self-immolative linker as a recognition group. The probe produces a sensitive fluorescence off–on response at 710 nm to pantetheinase with a detection limit of 0.02 ng mL−1 and can be used to image the intraperitoneal pantetheinase activity in mice in vivo. Moreover, with the probe we have observed that pantetheinase is significantly increased in the tissues of mouse inflammatory models as well as in the intestines of mice with inflammatory bowel disease. Therefore, CYLP may provide a convenient and intuitive tool for studying the role of pantetheinase in diseases. A near-infrared fluorescence probe for detecting pantetheinase activity has been used for imaging pantetheinase in mice with inflammatory bowel disease.![]()
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Affiliation(s)
- Yuantao Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Yiming Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Wen Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Huimin Ma
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
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Zhang Y, Qin X. Urinary vanin-1 and chronic kidney disease in hypertensive patients. J Clin Hypertens (Greenwich) 2020; 22:1466-1468. [PMID: 32762139 DOI: 10.1111/jch.13967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanyuan Zhang
- Division of Nephrology, National Clinical Research Center for Kidney Disease, State Key Laboratory for Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xianhui Qin
- Division of Nephrology, National Clinical Research Center for Kidney Disease, State Key Laboratory for Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Roles Played by Biomarkers of Kidney Injury in Patients with Upper Urinary Tract Obstruction. Int J Mol Sci 2020; 21:ijms21155490. [PMID: 32752030 PMCID: PMC7432915 DOI: 10.3390/ijms21155490] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/25/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
Partial or complete obstruction of the urinary tract is a common and challenging urological condition caused by a variety of conditions, including ureteral calculi, ureteral pelvic junction obstruction, ureteral stricture, and malignant ureteral obstruction. The condition, which may develop in patients of any age, induces tubular and interstitial injury followed by inflammatory cell infiltration and interstitial fibrosis, eventually impairing renal function. The serum creatinine level is commonly used to evaluate global renal function but is not sensitive to early changes in the glomerular filtration rate and unilateral renal damage. Biomarkers of acute kidney injury are useful for the early detection and monitoring of kidney injury induced by upper urinary tract obstruction. These markers include levels of neutrophil gelatinase-associated lipocalin (NGAL), monocyte chemotactic protein-1, kidney injury molecule 1, N-acetyl-b-D-glucosaminidase, and vanin-1 in the urine and serum NGAL and cystatin C concentrations. This review summarizes the pathophysiology of kidney injury caused by upper urinary tract obstruction, the roles played by emerging biomarkers of obstructive nephropathy, the mechanisms involved, and the clinical utility and limitations of the biomarkers.
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Bundgaard L, Stensballe A, Elbæk KJ, Berg LC. Mass spectrometric analysis of the in vitro secretome from equine bone marrow-derived mesenchymal stromal cells to assess the effect of chondrogenic differentiation on response to interleukin-1β treatment. Stem Cell Res Ther 2020; 11:187. [PMID: 32434555 PMCID: PMC7238576 DOI: 10.1186/s13287-020-01706-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Background Similar to humans, the horse is a long-lived, athletic species. The use of mesenchymal stromal cells (MSCs) is a relatively new frontier, but has been used with promising results in treating joint diseases, e.g., osteoarthritis. It is believed that MSCs exert their main therapeutic effects through secreted trophic biomolecules. Therefore, it has been increasingly important to characterize the MSC secretome. It has been shown that the effect of the MSCs is strongly influenced by the environment in the host compartment, and it is a crucial issue when considering MSC therapy. The aim of this study was to investigate differences in the in vitro secreted protein profile between naïve and chondrogenic differentiating bone marrow-derived (BM)-MSCs when exposed to an inflammatory environment. Methods Equine BM-MSCs were divided into a naïve group and a chondrogenic group. Cells were treated with normal expansion media or chondrogenic media. Cells were treated with IL-1β for a period of 5 days (stimulation), followed by 5 days without IL-1β (recovery). Media were collected after 48 h and 10 days. The secretomes were digested and analyzed by nanoLC-MS/MS to unravel the orchestration of proteins. Results The inflammatory proteins IL6, CXCL1, CXCL6, CCL7, SEMA7A, SAA, and haptoglobin were identified in the secretome after 48 h from all cells stimulated with IL-1β. CXCL8, OSM, TGF-β1, the angiogenic proteins VCAM1, ICAM1, VEGFA, and VEGFC, the proteases MMP1 and MMP3, and the protease inhibitor TIMP3 were among the proteins only identified in the secretome after 48 h from cells cultured in normal expansion media. After 10-day incubation, the proteins CXCL1, CXCL6, and CCL7 were still identified in the secretome from BM-MSCs stimulated with IL-1β, but the essential inducer of inflammation, IL6, was only identified in the secretome from cells cultured in normal expansion media. Conclusion The findings in this study indicate that naïve BM-MSCs have a more extensive inflammatory response at 48 h to stimulation with IL-1β compared to BM-MSCs undergoing chondrogenic differentiation. This extensive inflammatory response decreased after 5 days without IL-1β (day 10), but a difference in composition of the secretome between naïve and chondrogenic BM-MSCs was still evident.
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Affiliation(s)
- Louise Bundgaard
- Department of Veterinary Clinical Sciences, University of Copenhagen, Agrovej 8, 2630, Taastrup, Denmark.
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7E, 9220, Aalborg Ø, Denmark
| | - Kirstine Juul Elbæk
- Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 7E, 9220, Aalborg Ø, Denmark
| | - Lise Charlotte Berg
- Department of Veterinary Clinical Sciences, University of Copenhagen, Agrovej 8, 2630, Taastrup, Denmark
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Naquet P, Kerr EW, Vickers SD, Leonardi R. Regulation of coenzyme A levels by degradation: the 'Ins and Outs'. Prog Lipid Res 2020; 78:101028. [PMID: 32234503 DOI: 10.1016/j.plipres.2020.101028] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/09/2020] [Accepted: 02/22/2020] [Indexed: 02/06/2023]
Abstract
Coenzyme A (CoA) is the predominant acyl carrier in mammalian cells and a cofactor that plays a key role in energy and lipid metabolism. CoA and its thioesters (acyl-CoAs) regulate a multitude of metabolic processes at different levels: as substrates, allosteric modulators, and via post-translational modification of histones and other non-histone proteins. Evidence is emerging that synthesis and degradation of CoA are regulated in a manner that enables metabolic flexibility in different subcellular compartments. Degradation of CoA occurs through distinct intra- and extracellular pathways that rely on the activity of specific hydrolases. The pantetheinase enzymes specifically hydrolyze pantetheine to cysteamine and pantothenate, the last step in the extracellular degradation pathway for CoA. This reaction releases pantothenate in the bloodstream, making this CoA precursor available for cellular uptake and de novo CoA synthesis. Intracellular degradation of CoA depends on specific mitochondrial and peroxisomal Nudix hydrolases. These enzymes are also active against a subset of acyl-CoAs and play a key role in the regulation of subcellular (acyl-)CoA pools and CoA-dependent metabolic reactions. The evidence currently available indicates that the extracellular and intracellular (acyl-)CoA degradation pathways are regulated in a coordinated and opposite manner by the nutritional state and maximize the changes in the total intracellular CoA levels that support the metabolic switch between fed and fasted states in organs like the liver. The objective of this review is to update the contribution of these pathways to the regulation of metabolism, physiology and pathology and to highlight the many questions that remain open.
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Affiliation(s)
- Philippe Naquet
- Aix Marseille Univ, INSERM, CNRS, Centre d'Immunologie de Marseille-Luminy, Marseille, France.
| | - Evan W Kerr
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States of America
| | - Schuyler D Vickers
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States of America
| | - Roberta Leonardi
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States of America.
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Phillips RA, Kraev I, Lange S. Protein Deimination and Extracellular Vesicle Profiles in Antarctic Seabirds. BIOLOGY 2020; 9:E15. [PMID: 31936359 PMCID: PMC7168935 DOI: 10.3390/biology9010015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/19/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Pelagic seabirds are amongst the most threatened of all avian groups. They face a range of immunological challenges which seem destined to increase due to environmental changes in their breeding and foraging habitats, affecting prey resources and exposure to pollution and pathogens. Therefore, the identification of biomarkers for the assessment of their health status is of considerable importance. Peptidylarginine deiminases (PADs) post-translationally convert arginine into citrulline in target proteins in an irreversible manner. PAD-mediated deimination can cause structural and functional changes in target proteins, allowing for protein moonlighting in physiological and pathophysiological processes. PADs furthermore contribute to the release of extracellular vesicles (EVs), which play important roles in cellular communication. In the present study, post-translationally deiminated protein and EV profiles of plasma were assessed in eight seabird species from the Antarctic, representing two avian orders: Procellariiformes (albatrosses and petrels) and Charadriiformes (waders, auks, gulls and skuas). We report some differences between the species assessed, with the narrowest EV profiles of 50-200 nm in the northern giant petrel Macronectes halli, and the highest abundance of larger 250-500 nm EVs in the brown skua Stercorarius antarcticus. The seabird EVs were positive for phylogenetically conserved EV markers and showed characteristic EV morphology. Post-translational deimination was identified in a range of key plasma proteins critical for immune response and metabolic pathways in three of the bird species under study; the wandering albatross Diomedea exulans, south polar skua Stercorarius maccormicki and northern giant petrel. Some differences in Gene Ontology (GO) biological and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for deiminated proteins were observed between these three species. This indicates that target proteins for deimination may differ, potentially contributing to a range of physiological functions relating to metabolism and immune response, as well as to key defence mechanisms. PAD protein homologues were identified in the seabird plasma by Western blotting via cross-reaction with human PAD antibodies, at an expected 75 kDa size. This is the first study to profile EVs and to identify deiminated proteins as putative novel plasma biomarkers in Antarctic seabirds. These biomarkers may be further refined to become useful indicators of physiological and immunological status in seabirds-many of which are globally threatened.
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Affiliation(s)
- Richard A. Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge CB3 0ET, UK;
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
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Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum. Nat Commun 2019; 10:5612. [PMID: 31819058 PMCID: PMC6901522 DOI: 10.1038/s41467-019-13577-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human myeloid-derived growth factor (hMYDGF) is a 142-residue protein with a C-terminal endoplasmic reticulum (ER) retention sequence (ERS). Extracellular MYDGF mediates cardiac repair in mice after anoxic injury. Although homologs of hMYDGF are found in eukaryotes as distant as protozoans, its structure and function are unknown. Here we present the NMR solution structure of hMYDGF, which consists of a short α-helix and ten β-strands distributed in three β-sheets. Conserved residues map to the unstructured ERS, loops on the face opposite the ERS, and the surface of a cavity underneath the conserved loops. The only protein or portion of a protein known to have a similar fold is the base domain of VNN1. We suggest, in analogy to the tethering of the VNN1 nitrilase domain to the plasma membrane via its base domain, that MYDGF complexed to the KDEL receptor binds cargo via its conserved residues for transport to the ER.
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Affiliation(s)
- Valeriu Bortnov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Woonghee Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ziqing Lin
- Departments of Cell and Regenerative Biology and Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Douglas S Annis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Omar N Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ying Ge
- Departments of Cell and Regenerative Biology and Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Deane F Mosher
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Gheita AA, Gheita TA, Kenawy SA. The potential role of B5: A stitch in time and switch in cytokine. Phytother Res 2019; 34:306-314. [DOI: 10.1002/ptr.6537] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/23/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Alaa A. Gheita
- Plastic Surgery Department, Faculty of MedicineCairo University Cairo Egypt
- Egyptian Society of Plastic and Reconstructive Surgeons Egypt
| | - Tamer A. Gheita
- Rheumatology and Clinical Immunology Department, Faculty of MedicineCairo University Cairo Egypt
- Graduate Studies and Research AffairCairo University Cairo Egypt
| | - Sanaa A. Kenawy
- Pharmacology Department, Faculty of PharmacyCairo University Cairo Egypt
- Royal College of SurgeonsLondon University London UK
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