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Baichan P, Naicker P, Augustine TN, Smith M, Candy G, Devar J, Nweke EE. Proteomic analysis identifies dysregulated proteins and associated molecular pathways in a cohort of gallbladder cancer patients of African ancestry. Clin Proteomics 2023; 20:8. [PMID: 36855072 PMCID: PMC9976386 DOI: 10.1186/s12014-023-09399-9] [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: 09/05/2022] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Gallbladder cancer (GBC) is a lethal cancer with a poor prognosis. The lack of specific and sensitive biomarkers results in delayed diagnosis with most patients presenting at late stages of the disease. Furthermore, there is little known about the molecular mechanisms associated with GBC, especially in patients of African ancestry. This study aimed to determine dysregulated proteins in South African GBC patients to identify potential mechanisms of the disease progression and plausible biomarkers. METHODS Tissues (27 GBC, 13 Gallstone disease, and 5 normal tissues) and blood plasma (54 GBC and 73 Benign biliary pathology) were obtained from consenting patients. Protein extraction was performed on all tissues and liquid chromatography-mass spectrometry was used for proteomic profiling. A project-specific spectral library was built using the Pulsar search algorithm. Principal component and Spearman's rank correlation analyses were performed using PAST (V4.07b). Pathway and Network analyses were conducted using REACTOME (v3.7) and stringAPP (v1.7.0), respectively. RESULTS In the tissue sample group, there were 62 and 194 dysregulated proteins in GBC compared to normal and gallstone groups, respectively. In the plasma group, there were 33 altered proteins in GBC compared to the benign biliary pathology group. We found 9 proteins (APOA1, APOA2, RET4, TTR, HEMO, HBB, HBA, PIGR, and APOE) to be commonly dysregulated in both tissue and plasma. Furthermore, a subset analysis demonstrated that 2 proteins, S100A8 and S100A9, were downregulated in GBC patients with GD history compared to those without. Pathway analysis showed that the dysregulated proteins in GBC patients were enriched in pathways involved in smooth muscle contraction, metabolism, ECM organization, and integrin cell surface interactions. CONCLUSION The identified dysregulated proteins help in understanding GBC molecular mechanisms in our patient group. Furthermore, the alteration of specific proteins in both tissue and plasma samples suggests their potential utility as biomarkers of GBC in this sample cohort.
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Affiliation(s)
- Pavan Baichan
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa
| | - Previn Naicker
- Council for Scientific and Industrial Research, Pretoria, 0001, South Africa
| | - Tanya Nadine Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Martin Smith
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa
- Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Geoffrey Candy
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa
| | - John Devar
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa
- Hepatopancreatobiliary Unit, Department of Surgery, Chris Hani-Baragwanath Academic Hospital, Soweto, Johannesburg, South Africa
| | - Ekene Emmanuel Nweke
- Department of Surgery, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road Parktown, Johannesburg, 2193, South Africa.
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Rajoria S, Nair D, Suvarna K, Pai MGJ, Salkar A, Palanivel V, Verma A, Barpanda A, Awasthi G, Doshi H, Dhara V, Burli A, Agrawal S, Shrivastav O, Shastri J, Srivastava S. Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:175-195. [PMID: 37378767 DOI: 10.1007/978-3-031-28012-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
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Affiliation(s)
- Sakshi Rajoria
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kruthi Suvarna
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Medha Gayathri J Pai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Akanksha Salkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Viswanthram Palanivel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Abhilash Barpanda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gaurav Awasthi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hastyn Doshi
- Department of Computer Science, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vivek Dhara
- Department of Mechanical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ananya Burli
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Om Shrivastav
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Jayanthi Shastri
- Kasturba Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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Islam Khan MZ, Tam SY, Law HKW. Advances in High Throughput Proteomics Profiling in Establishing Potential Biomarkers for Gastrointestinal Cancer. Cells 2022; 11:973. [PMID: 35326424 PMCID: PMC8946849 DOI: 10.3390/cells11060973] [Citation(s) in RCA: 2] [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: 12/24/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
Gastrointestinal cancers (GICs) remain the most diagnosed cancers and accounted for the highest cancer-related death globally. The prognosis and treatment outcomes of many GICs are poor because most of the cases are diagnosed in advanced metastatic stages. This is primarily attributed to the deficiency of effective and reliable early diagnostic biomarkers. The existing biomarkers for GICs diagnosis exhibited inadequate specificity and sensitivity. To improve the early diagnosis of GICs, biomarkers with higher specificity and sensitivity are warranted. Proteomics study and its functional analysis focus on elucidating physiological and biological functions of unknown or annotated proteins and deciphering cellular mechanisms at molecular levels. In addition, quantitative analysis of translational proteomics is a promising approach in enhancing the early identification and proper management of GICs. In this review, we focus on the advances in mass spectrometry along with the quantitative and functional analysis of proteomics data that contributes to the establishment of biomarkers for GICs including, colorectal, gastric, hepatocellular, pancreatic, and esophageal cancer. We also discuss the future challenges in the validation of proteomics-based biomarkers for their translation into clinics.
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Affiliation(s)
| | | | - Helen Ka Wai Law
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China; (M.Z.I.K.); (S.Y.T.)
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Gaither C, Popp R, Zahedi RP, Borchers CH. Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic. Mol Cell Proteomics 2022; 21:100212. [PMID: 35182769 PMCID: PMC9062485 DOI: 10.1016/j.mcpro.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/24/2022] [Accepted: 02/13/2022] [Indexed: 12/23/2022] Open
Abstract
Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays—from minutes to hours—between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. Here, we investigated, using multiple reaction monitoring mass spectrometry (MRM-MS), how delays in plasma processing affect peptide-centric “bottom-up” proteomics. We used validated assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated after whole blood had been kept at room temperature from 0 to 40 h to mimic delays that occur in the clinic. Moreover, we evaluated the impact of different plasma-thawing conditions on MRM-based plasma protein quantitation. We demonstrate that >90% of protein concentration measurements were unaffected by the thawing procedure and by up to 40-h delayed plasma generation, reflected by relative standard deviations (RSDs) of <30%. Of the 159 MRM assays that yielded quantitative results in 60% of the measured time points, 139 enabled a stable protein quantitation (RSD <20%), 14 showed a slight variation (RSD 20–30%), and 6 appeared unstable/irreproducible (RSD > 30%). These results demonstrate the high robustness and thus the potential for MRM-based plasma-protein quantitation to be used in a clinical setting. In contrast to enzyme-linked immunosorbent assay, peptide-based MRM assays do not require intact three-dimensional protein structures for an accurate and precise quantitation of protein concentrations in the original sample. Delays in whole blood processing often cannot be avoided in the clinic. These delays might affect measurements by intact protein assays such as ELISA. The impact on LC/MRM was evaluated using validated assays to quantify 270 proteins. >95% of the measured concentrations had RSDs <30% between delays of 0 to 40 h. Protein quantitation by LC/MRM-MS is robust against pitfalls in the clinical setting.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc, Montreal, Quebec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
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Jakšić Ž, Mrljak V, Horvatić A, Gelemanović A, Mičić M. Loggerhead sea turtle Caretta caretta plasma biochemistry and proteome profile modulation during recovery. J Proteomics 2022; 252:104433. [PMID: 34839037 DOI: 10.1016/j.jprot.2021.104433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/26/2022]
Abstract
The aim of the study was to monitor and analyse injured and diseased loggerhead sea turtles (Caretta caretta) plasma proteome profiles and biochemistry parameters during their recovery period in rescue centre within different age and recovery period groups, and determine the potential biomarkers that can be used in diagnostics. The plasma biochemical parameters of total protein and glucose content, accompanied by aspartate aminotransferase (AST) and N-acetyl-cystein-activated creatinine kinase (CK-NAC) are highlighted as valuable and potential biomarkers of turtle's health status and condition. Using high throughput tandem mass tag (TMT)-based proteomic approach we identified 913 plasma proteins, 12 of which shown to be modulated in loggerheads age groups, and identified as a part of (i) platelet degranulation, (ii) neutrophil degranulation, and (iii) innate immune system pathways. The neurofascin (NFASC) is shown to be differentially abundant among all the age groups, and alpha-1-acid glycoprotein 2-like (ORM2) and alpha-1-antitrypsin-like (SERPINA1) proteins were recognized as members of all three above mentioned REACTOME pathways. Furthermore, 29 of plasma proteins were significantly differentially abundant in loggerheads age and recovery period groups. Out of 15 recognized pathways, those proteins were mostly included in three specific REACTOME pathways: (i) post-translational phosphorylation, (ii) regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs), and (iii) platelet degranulation. The alpha-fetoprotein (AFP) was the only protein which showed statistically significant up-regulation patterns in all loggerhead age groups before release from the rescue centre, and the complement component 3 (C3) protein was the only protein modulated in all recovery period groups. Furthermore, C3 protein takes part in 9; and followed up with apolipoprotein A-I (APOA1) in 7; complement component 4 (C4), complement component 5 (C5) and kininogen-1 (KNG1) in 6 REACTOME pathways. Thereby, those proteins are highlighted and recommended as potential biomarkers of turtle's health status. Data are available via ProteomeXchange with identifier PXD029569. Finally, based on our results, we believe that comprehensive omics approach and routine plasma biochemical analysis, accompanied by proteins of acute phase, acid-base status and immune-response indicator analysis may significantly and reliably improve assessment of captive loggerheads rehabilitation and medication. SIGNIFICANCE: Monitoring and comparison of loggerhead sea turtles (C. caretta) blood plasma biochemistry parameters and plasma proteome profiles in relation to the age, and recovery period pointed out significantly differentially abundant proteins, along with certain biochemical parameter contents as potential biomarkers of turtle's fitness, health status and physiology.
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Affiliation(s)
- Ž Jakšić
- Ruđer Bošković Institute, Center for Marine Rresearch Rovinj, G. Paliage 5, HR - 52210 Rovinj, Croatia; Marine Educational Centre Pula, A. Negri 10, HR - 52100 Pula, Croatia.
| | - V Mrljak
- University of Zagreb, Faculty of Veterinary Medicine, Department of Pathophysiology, Heinzelova 55, HR - 10000 Zagreb, Croatia
| | - A Horvatić
- University of Zagreb, Faculty of Veterinary Medicine, Department of Pathophysiology, Heinzelova 55, HR - 10000 Zagreb, Croatia; University of Zagreb, Faculty of Food Technology and Biotechnology, Department of Chemistry and Biochemistry, Pierottieva 6, HR - 10000 Zagreb, Croatia
| | - A Gelemanović
- Mediterranean Institute for Life Sciences (MedILS), Šetalište Ivana Meštrovića 45, HR - 21000 Split, Croatia
| | - M Mičić
- Aquarium Verudela, Verudela bb, HR - 52105 Pula, Croatia; Marine Educational Centre Pula, A. Negri 10, HR - 52100 Pula, Croatia
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High-Sensitivity Biosensor Based on Glass Resonance PhC Cavities for Detection of Blood Component and Glucose Concentration in Human Urine. COATINGS 2021. [DOI: 10.3390/coatings11121555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In this work, a novel structure of an all-optical biosensor based on glass resonance cavities with high detection accuracy and sensitivity in two-dimensional photon crystal is designed and simulated. The free spectral range in which the structure performs well is about FSR = 630 nm. This sensor measures the concentration of glucose in human urine. Analyses to determine the glucose concentration in urine for a normal range (0~15 mg/dL) and urine despite glucose concentrations of 0.625, 1.25, 2.5, 5 and 10 g/dL in the wavelength range 1.326404~1.326426 μm have been conducted. The detection range is RIU = 0.2 × 10−7. The average bandwidth of the output resonance wavelengths is 0.34 nm in the lowest case. In the worst case, the percentage of optical signal power transmission is 77% with an amplitude of 1.303241 and, in the best case, 100% with an amplitude of 1.326404. The overall dimensions of the biosensor are 102.6 µm2 and the sensitivity is equal to S = 1360.02 nm/RIU and the important parameter of the Figure of Merit (FOM) for the proposed biosensor structure is equal to FOM = 1320.23 RIU−1.
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Huang J, Ali N, Quansah E, Guo S, Noutsias M, Meyer-Zedler T, Bocklitz T, Popp J, Neugebauer U, Ramoji A. Vibrational Spectroscopic Investigation of Blood Plasma and Serum by Drop Coating Deposition for Clinical Application. Int J Mol Sci 2021; 22:2191. [PMID: 33671841 PMCID: PMC7926873 DOI: 10.3390/ijms22042191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
In recent decades, vibrational spectroscopic methods such as Raman and FT-IR spectroscopy are widely applied to investigate plasma and serum samples. These methods are combined with drop coating deposition techniques to pre-concentrate the biomolecules in the dried droplet to improve the detected vibrational signal. However, most often encountered challenge is the inhomogeneous redistribution of biomolecules due to the coffee-ring effect. In this study, the variation in biomolecule distribution within the dried-sample droplet has been investigated using Raman and FT-IR spectroscopy and fluorescence lifetime imaging method. The plasma-sample from healthy donors were investigated to show the spectral differences between the inner and outer-ring region of the dried-sample droplet. Further, the preferred location of deposition of the most abundant protein albumin in the blood during the drying process of the plasma has been illustrated by using deuterated albumin. Subsequently, two patients with different cardiac-related diseases were investigated exemplarily to illustrate the variation in the pattern of plasma and serum biomolecule distribution during the drying process and its impact on patient-stratification. The study shows that a uniform sampling position of the droplet, both at the inner and the outer ring, is necessary for thorough clinical characterization of the patient's plasma and serum sample using vibrational spectroscopy.
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Affiliation(s)
- Jing Huang
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Nairveen Ali
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Elsie Quansah
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Shuxia Guo
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Michel Noutsias
- Department of Cardiology Internal Medicine, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany;
- Mid-German Heart Center, Department of Internal Medicine III (KIM-III), Division of Cardiology, Angiology and Intensive Medical Care, University Hospital Halle, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Strasse 40, D-06120 Halle (Saale), Germany
| | - Tobias Meyer-Zedler
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Thomas Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
- InfectoGnostics Research Campus Jena, Centre of Applied Research, Philosophenweg 7, D-07743 Jena, Germany
| | - Ute Neugebauer
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
- InfectoGnostics Research Campus Jena, Centre of Applied Research, Philosophenweg 7, D-07743 Jena, Germany
| | - Anuradha Ramoji
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, D-07743 Jena, Germany; (J.H.); (N.A.); (E.Q.); (S.G.); (T.M.-Z.); (T.B.); (J.P.); (U.N.)
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Albert-Einstein-Straße 9, D-07745 Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
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Monu, Kharb R, Sharma A, Chaddar MK, Yadav R, Agnihotri P, Kar A, Biswas S. Plasma Proteome Profiling of Coronary Artery Disease Patients: Downregulation of Transthyretin-An Important Event. Mediators Inflamm 2020; 2020:3429541. [PMID: 33299376 PMCID: PMC7707994 DOI: 10.1155/2020/3429541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/24/2020] [Indexed: 02/07/2023] Open
Abstract
Coronary artery disease (CAD) is a prevalent chronic inflammatory cardiac disorder. An early diagnosis is likely to help in the prevention and proper management of this disease. As the study of proteomics provides the potential markers for detection of a disease, in the present investigation, attempt has been made to identify disease-associated differential proteins involved in CAD pathogenesis. For this study, a total of 200 selected CAD patients were considered, who were recruited for percutaneous coronary intervention (PCI) treatment. The proteomic analysis was performed using two-dimensional gel electrophoresis (2-DE) and MALDI-TOF MS/MS. Samples were also subjected to Western blot analysis, enzyme-linked immunosorbent assay (ELISA), peripheral blood mononuclear cells isolation immunofluorescence (IF) analysis, analytical screening by fluorescence-activated cell sorting (FACS), and in silico analysis. The representative data were shown as mean ± SD of at least three experiments. A total of 19 proteins were identified. Among them, the most abundant five proteins (serotransferrin, talin-1, alpha-2HS glycoprotein, transthyretin (TTR), fibrinogen-α chain) were found to have altered level in CAD. Serotransferrin, talin-1, alpha-2HS glycoprotein, and transthyretin (TTR) were found to have lower level, whereas fibrinogen-α chain was found to have higher level in CAD plasma compared to healthy, confirmed by Western blot analysis. TTR, an important acute phase transport protein, was validated low level in 200 CAD patients who confirmed to undergo PCI treatment. Further, in silico and in vitro studies of TTR indicated a downexpression of CAD in plasma as compared to the plasma of healthy individuals. Lower level of plasma TTR was determined to be an important risk marker in the atherosclerotic-approved CAD patients. We suggest that the TTR lower level predicts disease severity and hence may serve as an important marker tool for CAD screening. However, further large-scale studies are required to determine the clinical significance of TTR.
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Affiliation(s)
- Monu
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
| | - Rupsi Kharb
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), University of Delhi, Pushpvihar, New Delhi 110017, India
| | - Ankita Sharma
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
| | - Monu Kumar Chaddar
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
| | - Rakesh Yadav
- All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Prachi Agnihotri
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
| | - Anand Kar
- School of Life Sciences, Takshashila Campus, Devi Ahilya University, 452017, Indore, India
| | - Sagarika Biswas
- Council of Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, 110007, Delhi, India
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Deng L, Han Y, Tang C, Liao Q, Li Z. Label-Free Mass Spectrometry-Based Quantitative Proteomics Analysis of Serum Proteins During Early Pregnancy in Jennies ( Equus asinus). Front Vet Sci 2020; 7:569587. [PMID: 33195553 PMCID: PMC7642908 DOI: 10.3389/fvets.2020.569587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 11/17/2022] Open
Abstract
Early pregnancy in jennies is routinely determined by palpation per rectum or ultrasonography and also by detecting steroid hormone and chorionic gonadotropin levels in the blood, plasma, and serum. Herein we applied label-free mass spectrometry-based quantitative proteomics to identify serum proteins that were differentially expressed between early pregnant (day 45 after ovulation) and non-pregnant jennies. Bioinformatics analysis allowed illustration of pathways potentially involved in early pregnancy. We identified 295 proteins from a total of 2,569 peptides. Twenty-five proteins (22 upregulated and three downregulated) were significantly differentially expressed between the early pregnant and non-pregnant groups. The majority of the differentially expressed proteins were involved in defense response, early embryonic development, and hormone signaling pathways. Furthermore, functional protein analyses suggested that proteins were involved in binding, enzyme inhibitor activity, and enzyme regulator activity. Five serum proteins—granulin precursor/acrogranin, transgelin-2, fibronectin, fibrinogen-like 1, and thrombospondin 1—can be considered as novel, reliable candidates to detect pregnancy in jennies. To the best of our knowledge, this is the first study to use label-free mass spectrometry-based quantitative proteomics to analyze serum proteins during early pregnancy in jennies. Our results should facilitate the identification of valuable pregnancy diagnostic markers in early pregnant jennies.
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Affiliation(s)
- Liang Deng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuwei Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chi Tang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingchao Liao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zheng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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10
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Patient Management in Aortic Stenosis: Towards Precision Medicine Through Protein Analysis, Imaging and Diagnostic Tests. J Clin Med 2020; 9:jcm9082421. [PMID: 32731585 PMCID: PMC7463596 DOI: 10.3390/jcm9082421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/12/2023] Open
Abstract
Aortic stenosis is the most frequent valvular disease in developed countries. It progresses from mild fibrocalcific leaflet changes to a more severe leaflet calcification at the end stages of the disease. Unfortunately, symptoms of aortic stenosis are unspecific and only appear when it is too late, complicating patients' management. The global impact of aortic stenosis is increasing due to the growing elderly population. The disease supposes a great challenge because of the multiple comorbidities of these patients. Nowadays, the only effective treatment is valve replacement, which has a high cost in both social and economic terms. For that reason, it is crucial to find potential diagnostic, prognostic and therapeutic indicators that could help us to detect this disease in its earliest stages. In this article, we comprehensively review several key observations and translational studies related to protein markers that are promising for being implemented in the clinical field as well as a discussion about the role of precision medicine in aortic stenosis.
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11
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Han Y, Tang C, Liao Q, Li Z, Deng L. Characterizing the Serum Proteome of Donkeys (Equus asinus). J Equine Vet Sci 2020; 92:103174. [PMID: 32797796 DOI: 10.1016/j.jevs.2020.103174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Abstract
Serum and plasma are commonly used in clinical practice considering the widely accepted fact that the "normal" protein expression pattern of a healthy animal changes under disease conditions. We herein used a label-free mass spectrometry-based quantitative proteomics approach to characterize the serum proteome of donkeys. A total of 277 unique proteins were identified from 2,388 unique peptides. Gene ontology analyses showed that the most frequent processes were related to metabolic activities and biological regulation, response to stimulus, and immune system processes. The main annotated areas of origin were the extracellular region, extracellular region part, and organelle, and their molecular functions included binding, catalytic activity, and molecular function regulator. Analyses using the Clusters of Orthologous Groups for Eukaryotic Complete Genomes database indicated that the identified proteins could be categorized into three main groups: signal transduction mechanisms, amino acid transport and metabolism, and defense mechanisms. Most of the unique proteins were associated with the complement and coagulation cascades, and they participated in several disease-related metabolic pathways. Our results should be crucial for further analyses of changes in different physiological and pathophysiological conditions in donkeys.
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Affiliation(s)
- Yuwei Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Chi Tang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Qingchao Liao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Zheng Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China
| | - Liang Deng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning Province, PR China.
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12
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Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)-Based Proteomics of Drug-Metabolizing Enzymes and Transporters. Molecules 2020; 25:molecules25112718. [PMID: 32545386 PMCID: PMC7321193 DOI: 10.3390/molecules25112718] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples, outperforming conventional antibody-based methods in many aspects. LC-MS/MS-based proteomics studies have revealed the protein abundances of many drug-metabolizing enzymes and transporters (DMETs) in tissues relevant to drug metabolism and disposition. Previous studies have consistently demonstrated marked interindividual variability in DMET protein expression, suggesting that varied DMET function is an important contributing factor for interindividual variability in pharmacokinetics (PK) and pharmacodynamics (PD) of medications. Moreover, differential DMET expression profiles were observed across different species and in vitro models. Therefore, caution must be exercised when extrapolating animal and in vitro DMET proteomics findings to humans. In recent years, DMET proteomics has been increasingly utilized for the development of physiologically based pharmacokinetic models, and DMET proteins have also been proposed as biomarkers for prediction of the PK and PD of the corresponding substrate drugs. In sum, despite the existence of many challenges in the analytical technology and data analysis methods of LC-MS/MS-based proteomics, DMET proteomics holds great potential to advance our understanding of PK behavior at the individual level and to optimize treatment regimens via the DMET protein biomarker-guided precision pharmacotherapy.
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13
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Radko S, Ptitsyn K, Novikova S, Kiseleva Y, Moysa A, Kurbatov L, Mannanova M, Zgoda V, Ponomarenko E, Lisitsa A, Archakov A. Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma. Biomedicines 2020; 8:E133. [PMID: 32456365 PMCID: PMC7277749 DOI: 10.3390/biomedicines8050133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma.
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Affiliation(s)
- Sergey Radko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Svetlana Novikova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Yana Kiseleva
- Russian Scientific Center of Roentgenoradiology, Moscow 117485, Russia;
| | - Alexander Moysa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Maria Mannanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
| | - Alexander Archakov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (K.P.); (S.N.); (A.M.); (L.K.); (M.M.); (V.Z.); (E.P.); (A.L.); (A.A.)
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14
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Boudon S, Ounaissi D, Viala D, Monteils V, Picard B, Cassar-Malek I. Label free shotgun proteomics for the identification of protein biomarkers for beef tenderness in muscle and plasma of heifers. J Proteomics 2020; 217:103685. [DOI: 10.1016/j.jprot.2020.103685] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/15/2020] [Accepted: 02/08/2020] [Indexed: 12/21/2022]
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15
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Abstract
Systems medicine is a holistic approach to deciphering the complexity of human physiology in health and disease. In essence, a living body is constituted of networks of dynamically interacting units (molecules, cells, organs, etc) that underlie its collective functions. Declining resilience because of aging and other chronic environmental exposures drives the system to transition from a health state to a disease state; these transitions, triggered by acute perturbations or chronic disturbance, manifest as qualitative shifts in the interactions and dynamics of the disease-perturbed networks. Understanding health-to-disease transitions poses a high-dimensional nonlinear reconstruction problem that requires deep understanding of biology and innovation in study design, technology, and data analysis. With a focus on the principles of systems medicine, this Review discusses approaches for deciphering this biological complexity from a novel perspective, namely, understanding how disease-perturbed networks function; their study provides insights into fundamental disease mechanisms. The immediate goals for systems medicine are to identify early transitions to cardiovascular (and other chronic) diseases and to accelerate the translation of new preventive, diagnostic, or therapeutic targets into clinical practice, a critical step in the development of personalized, predictive, preventive, and participatory (P4) medicine.
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Affiliation(s)
- Kalliopi Trachana
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Rhishikesh Bargaje
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Gustavo Glusman
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Nathan D Price
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
| | - Sui Huang
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.).,Department of Biological Sciences, University of Calgary, Alberta, Canada (S.H.)
| | - Leroy E Hood
- From the Institute for Systems Biology, Seattle, WA (K.T., R.B., G.G., N.D.P., S.H., L.E.H.)
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16
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Whittaker K, Burgess R, Jones V, Yang Y, Zhou W, Luo S, Wilson J, Huang R. Quantitative proteomic analyses in blood: A window to human health and disease. J Leukoc Biol 2019; 106:759-775. [PMID: 31329329 DOI: 10.1002/jlb.mr1118-440r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | | | | | | | - Shuhong Luo
- RayBiotech Life Norcross Georgia USA
- RayBiotech Life Guangzhou Guangdong China
- South China Biochip Research Center Guangzhou Guangdong China
| | | | - Ruo‐Pan Huang
- RayBiotech Life Norcross Georgia USA
- RayBiotech Life Guangzhou Guangdong China
- South China Biochip Research Center Guangzhou Guangdong China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical UniversityGuangzhou Medical University Guangzhou China
- Guangdong Provincial Hospital of Chinese Medicine Guangzhou China
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17
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Corbacho-Alonso N, Rodríguez-Sánchez E, Martin-Rojas T, Mouriño-Alvarez L, Sastre-Oliva T, Hernandez-Fernandez G, Padial LR, Ruilope LM, Ruiz-Hurtado G, Barderas MG. Proteomic investigations into hypertension: what's new and how might it affect clinical practice? Expert Rev Proteomics 2019; 16:583-591. [PMID: 31195841 DOI: 10.1080/14789450.2019.1632197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Introduction: Hypertension is a multifactorial disease that has, thus far, proven to be a difficult target for pharmacological intervention. The application of proteomic strategies may help to identify new biomarkers for the early diagnosis and prompt treatment of hypertension, in order to control blood pressure and prevent organ damage. Areas covered: Advances in proteomics have led to the discovery of new biomarkers to help track the pathophysiological processes implicated in hypertension. These findings not only help to better understand the nature of the disease, but will also contribute to the clinical needs for a timely diagnosis and more precise treatment. In this review, we provide an overview of new biomarkers identified in hypertension through the application of proteomic techniques, and we also discuss the difficulties and challenges in identifying biomarkers in this clinical setting. We performed a literature search in PubMed with the key words 'hypertension' and 'proteomics', and focused specifically on the most recent literature on the utility of proteomics in hypertension research. Expert opinion: There have been several promising biomarkers of hypertension identified by proteomics, but too few have been introduced to the clinic. Thus, further investigations in larger cohorts are necessary to test the feasibility of this strategy for patients. Also, this emerging field would profit from more collaboration between clinicians and researchers.
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Affiliation(s)
- N Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - E Rodríguez-Sánchez
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain
| | - T Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - L Mouriño-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - T Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - G Hernandez-Fernandez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
| | - L R Padial
- c Department of Cardiology , Hospital Virgen de la Salud, SESCAM , Toledo , Spain
| | - L M Ruilope
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain.,d Department of Preventive Medicine and Public Health, School of Medicine , Universidad Autónoma de Madrid/IdiPAZ and CIBER in Epidemiology and Public Health (CIBERESP) , Madrid , Spain.,e School of Doctoral Studies and Research , Universidad Europea de Madrid , Madrid , Spain
| | - G Ruiz-Hurtado
- b Cardiorenal Translational Laboratory , Instituto de Investigación i+12, Hospital Universitario 12 de Octubre , Madrid , Spain
| | - M G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos (HNP), SESCAM , Toledo , Spain
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18
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Rice SJ, Liu X, Zhang J, Belani CP. Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. Proteomics 2019; 19:e1800135. [DOI: 10.1002/pmic.201800135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/27/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Shawn J. Rice
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Xin Liu
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Jianhong Zhang
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
| | - Chandra P. Belani
- Penn State Cancer InstitutePenn State College of Medicine Hershey PA 17033 USA
- Department of MedicinePenn State College of Medicine Hershey PA 17033 USA
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19
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Parachalil DR, Bruno C, Bonnier F, Blasco H, Chourpa I, McIntyre J, Byrne HJ. Raman spectroscopic screening of high and low molecular weight fractions of human serum. Analyst 2019; 144:4295-4311. [DOI: 10.1039/c9an00599d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This study explores the suitability of Raman spectroscopy as a bioanalytical tool, when coupled with ultra-filtration and multivariate analysis, to detect imbalances in both high molecular weight and low molecular weight fractions of the same samples of human patient serum, in the native liquid form.
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Affiliation(s)
- Drishya Rajan Parachalil
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
- School of Physics and Optometric & Clinical Sciences
| | - Clément Bruno
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Franck Bonnier
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Hélène Blasco
- CHRU de Tours
- Laboratoire de Biochimie et Biologie Moléculaire
- Tours
- France
- Université de Tours
| | - Igor Chourpa
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Jennifer McIntyre
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
| | - Hugh J. Byrne
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
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20
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Barbosa AI, Reis NM. A critical insight into the development pipeline of microfluidic immunoassay devices for the sensitive quantitation of protein biomarkers at the point of care. Analyst 2018; 142:858-882. [PMID: 28217778 DOI: 10.1039/c6an02445a] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The latest clinical procedures for the timely and cost-effective diagnosis of chronic and acute clinical conditions, such as cardiovascular diseases, cancer, chronic respiratory diseases, diabetes or sepsis (i.e. the biggest causes of death worldwide), involve the quantitation of specific protein biomarkers released into the blood stream or other physiological fluids (e.g. urine or saliva). The clinical thresholds are usually in the femtomolar to picolomar range, and consequently the measurement of these protein biomarkers heavily relies on highly sophisticated, bulky and automated equipment in centralised pathology laboratories. The first microfluidic devices capable of measuring protein biomarkers in miniaturised immunoassays were presented nearly two decades ago and promised to revolutionise point-of-care (POC) testing by offering unmatched sensitivity and automation in a compact POC format; however, the development and adoption of microfluidic protein biomarker tests has fallen behind expectations. This review presents a detailed critical overview into the pipeline of microfluidic devices developed in the period 2005-2016 capable of measuring protein biomarkers from the pM to fM range in formats compatible with POC testing, with a particular focus on the use of affordable microfluidic materials and compact low-cost signal interrogation. The integration of these two important features (essential unique selling points for the successful microfluidic diagnostic products) has been missed in previous review articles and explain the poor adoption of microfluidic technologies in this field. Most current miniaturised devices compromise either on the affordability, compactness and/or performance of the test, making current tests unsuitable for the POC measurement of protein biomarkers. Seven core technical areas, including (i) the selected strategy for antibody immobilisation, (ii) the surface area and surface-area-to-volume ratio, (iii) surface passivation, (iv) the biological matrix interference, (v) fluid control, (vi) the signal detection modes and (vii) the affordability of the manufacturing process and detection system, were identified as the key to the effective development of a sensitive and affordable microfluidic protein biomarker POC test.
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Affiliation(s)
- Ana I Barbosa
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK
| | - Nuno M Reis
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK and Department of Chemical Engineering, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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21
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Serra R, Ielapi N, Barbetta A, Andreucci M, de Franciscis S. Novel biomarkers for cardiovascular risk. Biomark Med 2018; 12:1015-1024. [PMID: 30126290 DOI: 10.2217/bmm-2018-0056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cardiovascular disease refers to different diseases involving the heart and/or the arteries and/or the veins. Cardiovascular disease, overall considered, is a notable source of morbidity and mortality worldwide. Therefore, several research studies are dedicated to explore, by means of biomarkers, the possiblity to calculate the cardiovascular risk both for the onset and for the complications of the related clinical manifestations such as coronary artery disease, carotid artery stenosis, peripheral artery disease, arterial aneurysm, chronic venous disease and venous thromboembolism. This review discusses the most updated information in the area of the novel biomarkers related to omics, imaging techniques and clinical data, that may help physicians in order to improve the knowledge and the management of the cardiovascular risk.
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Affiliation(s)
- Raffaele Serra
- Interuniversity Center of Phlebolymphology (CIFL). International Research & Educational Program in Clinical & Experimental Biotechnology' at the Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy.,Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy
| | - Nicola Ielapi
- Interuniversity Center of Phlebolymphology (CIFL). International Research & Educational Program in Clinical & Experimental Biotechnology' at the Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy
| | - Andrea Barbetta
- Interuniversity Center of Phlebolymphology (CIFL). International Research & Educational Program in Clinical & Experimental Biotechnology' at the Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy
| | - Michele Andreucci
- Department of Health Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy
| | - Stefano de Franciscis
- Interuniversity Center of Phlebolymphology (CIFL). International Research & Educational Program in Clinical & Experimental Biotechnology' at the Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy.,Department of Surgical & Medical Sciences University Magna Graecia of Catanzaro, Viale Europa 88100 Catanzaro, Italy
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22
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Manfredi M, Chiariello C, Conte E, Castagna A, Robotti E, Gosetti F, Patrone M, Martinelli N, Bassi A, Cecconi D, Marengo E, Olivieri O. Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels. Proteomics Clin Appl 2018; 13:e1800023. [DOI: 10.1002/prca.201800023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/30/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Marcello Manfredi
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
- ISALIT S.r.l. Via Canobia 4/6 28100 Novara Italy
| | - Carmela Chiariello
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | | | - Annalisa Castagna
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Elisa Robotti
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
- ISALIT S.r.l. Via Canobia 4/6 28100 Novara Italy
| | - Fabio Gosetti
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Mauro Patrone
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Nicola Martinelli
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Antonella Bassi
- Laboratory of Clinical Chemistry and HematologyUniversity Hospital of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Daniela Cecconi
- Department of BiotechnologyProteomics and Mass Spectrometry LaboratoryUniversity of Verona Strada le grazie 15 37134 Verona Italy
| | - Emilio Marengo
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Oliviero Olivieri
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
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Mahdavi S, Jenkins DJA, Borchers CH, El-Sohemy A. Genetic Variation in 9p21 and the Plasma Proteome. J Proteome Res 2018; 17:2649-2656. [DOI: 10.1021/acs.jproteome.8b00117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sara Mahdavi
- Department of Nutritional Sciences, University of Toronto, 150 College Street, Room 310, Toronto, Ontario M5S 3E2, Canada
| | - David J. A. Jenkins
- Department of Nutritional Sciences, University of Toronto, 150 College Street, Room 310, Toronto, Ontario M5S 3E2, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 209 Victoria Street, Toronto, Ontario M5B 1T8, Canada
- Risk Factor Modification Centre and Division of Endocrinology and Metabolism, St. Michael’s Hospital, St. Michael’s Health Centre, 61 Queen Street East, Toronto, Ontario M5C 2T2, Canada
| | - Christoph H. Borchers
- University of Victoria−Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Colombia V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H4A 3T2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, University of Toronto, 150 College Street, Room 310, Toronto, Ontario M5S 3E2, Canada
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Abstract
Conventional workup of rare neurological disease is frequently hampered by diagnostic delay or lack of diagnosis. While biomarkers have been established for many neurometabolic disorders, improved methods are required for diagnosis of previously unidentified or underreported causes of rare neurological disease. This would result in a higher diagnostic yield and increased patient numbers required for interventional studies. Recent studies using next-generation sequencing and metabolomics have led to identification of novel disease-causing genes and biomarkers. This combined approach can assist in overcoming challenges associated with analyzing and interpreting the large amount of data obtained from each technique. In particular, metabolomics can support the pathogenicity of sequence variants in genes encoding enzymes or transporters involved in metabolic pathways. Moreover, metabolomics can show the broader perturbation caused by inborn errors of metabolism and identify a metabolic fingerprint of metabolic disorders. As such, using "omics" has great potential to meet the current needs for improved diagnosis and elucidation of rare neurological disease.
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Affiliation(s)
- L M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - M Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland.
- CRC Clinical Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
- Radiz - Rare Disease Intiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Zurich, Switzerland.
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, University Childrens' Hospital Graz, Auenbruggerplatz 34/2, 8036, Graz, Austria.
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Baetta R, Pontremoli M, Fernandez AM, Spickett CM, Banfi C. Reprint of: Proteomics in cardiovascular diseases: Unveiling sex and gender differences in the era of precision medicine. J Proteomics 2018; 178:57-72. [PMID: 29622522 DOI: 10.1016/j.jprot.2018.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 01/19/2023]
Abstract
Cardiovascular diseases (CVDs) represent the most important cause of mortality in women and in men. Contrary to the long-standing notion that the effects of the major risk factors on CVD outcomes are the same in both sexes, recent evidence recognizes new, potentially independent, sex/gender-related risk factors for CVDs, and sex/gender-differences in the clinical presentation of CVDs have been demonstrated. Furthermore, some therapeutic options may not be equally effective and safe in men and women. In this context, proteomics offers an extremely useful and versatile analytical platform for biomedical researches that expand from the screening of early diagnostic and prognostic biomarkers to the investigation of the molecular mechanisms underlying CDVs. In this review, we summarized the current applications of proteomics in the cardiovascular field, with emphasis on sex and gender-related differences in CVDs. SIGNIFICANCE Increasing evidence supports the profound effect of sex and gender on cardiovascular physio-pathology and the response to drugs. A clear understanding of the mechanisms underlying sexual dimorphisms in CVDs would not only improve our knowledge of the etiology of these diseases, but could also inform health policy makers and guideline committees in tailoring specific interventions for the prevention, treatment and management of CVDs in both men and women.
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Baetta R, Pontremoli M, Martinez Fernandez A, Spickett CM, Banfi C. Proteomics in cardiovascular diseases: Unveiling sex and gender differences in the era of precision medicine. J Proteomics 2017; 173:62-76. [PMID: 29180046 DOI: 10.1016/j.jprot.2017.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 02/07/2023]
Abstract
Cardiovascular diseases (CVDs) represent the most important cause of mortality in women and in men. Contrary to the long-standing notion that the effects of the major risk factors on CVD outcomes are the same in both sexes, recent evidence recognizes new, potentially independent, sex/gender-related risk factors for CVDs, and sex/gender-differences in the clinical presentation of CVDs have been demonstrated. Furthermore, some therapeutic options may not be equally effective and safe in men and women. In this context, proteomics offers an extremely useful and versatile analytical platform for biomedical researches that expand from the screening of early diagnostic and prognostic biomarkers to the investigation of the molecular mechanisms underlying CDVs. In this review, we summarized the current applications of proteomics in the cardiovascular field, with emphasis on sex and gender-related differences in CVDs. SIGNIFICANCE Increasing evidence supports the profound effect of sex and gender on cardiovascular physio-pathology and the response to drugs. A clear understanding of the mechanisms underlying sexual dimorphisms in CVDs would not only improve our knowledge of the etiology of these diseases, but could also inform health policy makers and guideline committees in tailoring specific interventions for the prevention, treatment and management of CVDs in both men and women.
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28
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Corbo C, Molinaro R, Tabatabaei M, Farokhzad OC, Mahmoudi M. Personalized protein corona on nanoparticles and its clinical implications. Biomater Sci 2017; 5:378-387. [PMID: 28133653 PMCID: PMC5592724 DOI: 10.1039/c6bm00921b] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is now well understood that once in contact with biological fluids, nanoscale objects lose their original identity and acquire a new biological character, referred to as a protein corona. The protein corona changes many of the physicochemical properties of nanoparticles, including size, surface charge, and aggregation state. These changes, in turn, affect the biological fate of nanoparticles, including their pharmacokinetics, biodistribution, and therapeutic efficacy. It is progressively being accepted that even slight variations in the composition of a protein source (e.g., plasma and serum) can substantially change the composition of the corona formed on the surface of the exact same nanoparticles. Recently it has been shown that the protein corona is strongly affected by the patient's specific disease. Therefore, the same nanomaterial incubated with plasma proteins of patients with different pathologies adsorb protein coronas with different compositions, giving rise to the concept of personalized protein corona. Herein, we review this concept along with recent advances on the topic, with a particular focus on clinical relevance.
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Affiliation(s)
- Claudia Corbo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Roberto Molinaro
- Center for Biomimetic Medicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Mateen Tabatabaei
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Omid C Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. and King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. and Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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29
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Fontana P, Reny JL. Will proteomics design next-generation management of cardiovascular diseases? TRANSLATIONAL PROTEOMICS 2015. [DOI: 10.1016/j.trprot.2015.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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