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Pazoki A, Dadfar S, Shadab A, Haghmorad D, Oksenych V. Soluble CD40 Ligand as a Promising Biomarker in Cancer Diagnosis. Cells 2024; 13:1267. [PMID: 39120299 PMCID: PMC11311304 DOI: 10.3390/cells13151267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Cancer remains a significant challenge in medicine due to its complexity and heterogeneity. Biomarkers have emerged as vital tools for cancer research and clinical practice, facilitating early detection, prognosis assessment, and treatment monitoring. Among these, CD40 ligand (CD40L) has gained attention for its role in immune response modulation. Soluble CD40 ligand (sCD40L) has shown promise as a potential biomarker in cancer diagnosis and progression, reflecting interactions between immune cells and the tumor microenvironment. This review explores the intricate relationship between sCD40L and cancer, highlighting its diagnostic and prognostic potential. It discusses biomarker discovery, emphasizing the need for reliable markers in oncology, and elucidates the roles of CD40L in inflammatory responses and interactions with tumor cells. Additionally, it examines sCD40L as a biomarker, detailing its significance across various cancer types and clinical applications. Moreover, the review focuses on therapeutic interventions targeting CD40L in malignancies, providing insights into cellular and gene therapy approaches and recombinant protein-based strategies. The clinical effectiveness of CD40L-targeted therapy is evaluated, underscoring the need for further research to unlock the full potential of this signaling pathway in cancer management.
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Affiliation(s)
- Alireza Pazoki
- Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan 35147-99442, Iran
| | - Sepehr Dadfar
- Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan 35147-99442, Iran
| | - Alireza Shadab
- Department of Health Science, Iran University of Medical Sciences, Tehran 14496-14535, Iran
| | - Dariush Haghmorad
- Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan 35147-99442, Iran
- Cancer Research Center, Semnan University of Medical Sciences, Semnan 35147-99442, Iran
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
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Tielemans B, Van Slambrouck J, Özsoy B, Ceulemans LJ. Phenotyping of primary graft dysfunction after lung transplantation by in-depth biomarker analysis. ERJ Open Res 2024; 10:00439-2024. [PMID: 39104953 PMCID: PMC11299001 DOI: 10.1183/23120541.00439-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 08/07/2024] Open
Abstract
This editorial highlights the importance of research towards PGD-specific biomarkers, suggesting strategic sample collection and advanced analysis techniques to expand our knowledge of PGD mechanisms and potential phenotyping https://bit.ly/3UUElw0.
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Affiliation(s)
- Birger Tielemans
- Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Jan Van Slambrouck
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Balin Özsoy
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, KU Leuven, Leuven, Belgium
| | - Laurens J. Ceulemans
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
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3
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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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Hidese S. Search for cerebrospinal fluid biomarkers in patients with major psychiatric disorders: Multiplex immunoassay findings and proximity extension assay prospects. Neuropsychopharmacol Rep 2024; 44:314-320. [PMID: 38686540 PMCID: PMC11144604 DOI: 10.1002/npr2.12439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/05/2024] [Accepted: 03/24/2024] [Indexed: 05/02/2024] Open
Abstract
Multiplex immunoassays have been developed to detect multiple proteins simultaneously and are used to search for biomarkers, including those present in major psychiatric disorders. This study aimed to review multiplex immunoassay studies on cerebrospinal fluid (CSF) biomarkers in patients with schizophrenia, bipolar disorder (BD), and major depressive disorder (MDD) and examine future research directions using improved proteomic techniques. According to the results of previous multiplex immunoassay studies, increased CSF IFN-β, IL-8, MCP-2, MMP-2, PAI-1, sICAM-1, and sVCAM-1 and decreased CSF ACE, APP, fibrinogen, and GDNF were observed in patients with schizophrenia, while CSF HGF and S100B were positively correlated with psychotic symptom and CSF IL-11, IL-29/IFN-λ1, and TSLP were negatively correlated. Increased CSF IFN-β and IL-1β and decreased CSF Aβ42, APP, IL-6, and NCAM-1 were observed, while CSF S100B was positively correlated with manic symptom in patients with BD. Increased CSF IL-4, MCP-1, MIP-1β, and MMP-2 were observed in patients with MDD, while CSF HGF and MMP-2 were positively correlated with depressive symptom and CSF IL-15 and MCP-1 were negatively correlated. However, signal cross-talk and cross-reactivity problems have been observed in previous studies using multiplex immunoassay. The proximity extension assay can be used to overcome cross-reactivity and enable ultrasensitive multiplexed detection and quantification of more than 1000 target proteins. However, proteomic studies using proximity extension assay technology in patients with schizophrenia, BD, or MDD are still scarce. Therefore, future high-quality proteomic studies are required to identify CSF biomarkers for larger sets of target proteins in patients with major psychiatric disorders.
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Affiliation(s)
- Shinsuke Hidese
- Department of PsychiatryTeikyo University School of MedicineTokyoJapan
- Department of Mental Disorder Research, National Center of Neurology and PsychiatryNational Institute of NeuroscienceKodaira, TokyoJapan
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de Boer FL, van der Molen HF, Wang JH, Raun E, Pereda J, Hwu EET, Jakasa I, Dubrac S, Rustemeyer T, Kezic S. Skin Barrier- and Immune Response-Related Biomarkers of Solar UVR Exposure Comparing Indoor and Outdoor Workers. JID INNOVATIONS 2024; 4:100280. [PMID: 38756236 PMCID: PMC11097112 DOI: 10.1016/j.xjidi.2024.100280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 05/18/2024] Open
Abstract
Outdoor workers have increased risk of developing keratinocyte cancer due to accumulated skin damage resulting from chronic and excessive exposure to UVR. This study aims to identify potential noninvasive biomarkers to assess chronic UVR exposure. We analyzed stratum corneum biomarkers collected from 2 skin locations and 2 occupational groups with contrasting solar UVR exposure: the forehead and retroauricular skin among outdoor workers and indoor workers. Using a linear mixed model adjusting for age and skin phototype, we compared biomarkers between both skin sites in indoor and outdoor workers. We measured markers of the immune response and skin barrier, including cytokines, GFs, 15-hydroxyeicosatetraenoic acid, cis- and trans-urocanic acid, and corneocyte topography, indicated by circular nano objects. Differences between the 2 skin sites were found for cis-urocanic acid, total urocanic acid, IL-1α, IL-1RA, IL-1RA/IL-1α, IL-18, 15-hydroxyeicosatetraenoic acid, CCL4, and circular nano objects. The levels of cis-urocanic acid and CCL4 also differed between indoor and outdoor workers. These findings underscore changes in both immune response and skin barrier induced by UVR. They indicate the potential utility of stratum corneum biomarkers in detecting both chronic UVR exposure in occupational setting and aiding in the development of preventive measures.
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Affiliation(s)
- Florentine L. de Boer
- Amsterdam Public Health Research Institute, Department of Public and Occupational Health, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk F. van der Molen
- Amsterdam Public Health Research Institute, Department of Public and Occupational Health, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jen-Hung Wang
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ellen Raun
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jorge Pereda
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Edwin En-Te Hwu
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Sandrine Dubrac
- Epidermal Biology Laboratory, Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Rustemeyer
- Dermato-Allergology and Occupational Dermatology, Amsterdam University Medical Centers, Noord-Holland, The Netherlands
| | - Sanja Kezic
- Amsterdam Public Health Research Institute, Department of Public and Occupational Health, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Cheng HP, Yang TH, Wang JC, Chuang HS. Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection. SENSORS (BASEL, SWITZERLAND) 2024; 24:2904. [PMID: 38733011 PMCID: PMC11086254 DOI: 10.3390/s24092904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Demand is strong for sensitive, reliable, and cost-effective diagnostic tools for cancer detection. Accordingly, bead-based biosensors have emerged in recent years as promising diagnostic platforms based on wide-ranging cancer biomarkers owing to the versatility, high sensitivity, and flexibility to perform the multiplexing of beads. This comprehensive review highlights recent trends and innovations in the development of bead-based biosensors for cancer-biomarker detection. We introduce various types of bead-based biosensors such as optical, electrochemical, and magnetic biosensors, along with their respective advantages and limitations. Moreover, the review summarizes the latest advancements, including fabrication techniques, signal-amplification strategies, and integration with microfluidics and nanotechnology. Additionally, the challenges and future perspectives in the field of bead-based biosensors for cancer-biomarker detection are discussed. Understanding these innovations in bead-based biosensors can greatly contribute to improvements in cancer diagnostics, thereby facilitating early detection and personalized treatments.
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Affiliation(s)
- Hui-Pin Cheng
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
| | - Tai-Hua Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Department of Orthopedic Surgery, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
| | - Jhih-Cheng Wang
- Department of Urology, Chimei Medical Center, Tainan 710, Taiwan
- Department of Electrical Engineering, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
- School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (T.-H.Y.)
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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7
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Lee MJ, Cho JY, Bae S, Jung HS, Kang CM, Kim SH, Choi HJ, Lee CK, Kim H, Jo D, Paik YK. Inhibition of the Alternative Complement Pathway May Cause Secretion of Factor B, Enabling an Early Detection of Pancreatic Cancer. J Proteome Res 2024; 23:985-998. [PMID: 38306169 DOI: 10.1021/acs.jproteome.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
This study aims to elucidate the cellular mechanisms behind the secretion of complement factor B (CFB), known for its dual roles as an early biomarker for pancreatic ductal adenocarcinoma (PDAC) and as the initial substrate for the alternative complement pathway (ACP). Using parallel reaction monitoring analysis, we confirmed a consistent ∼2-fold increase in CFB expression in PDAC patients compared with that in both healthy donors (HD) and chronic pancreatitis (CP) patients. Elevated ACP activity was observed in CP and other benign conditions compared with that in HD and PDAC patients, suggesting a functional link between ACP and PDAC. Protein-protein interaction analyses involving key complement proteins and their regulatory factors were conducted using blood samples from PDAC patients and cultured cell lines. Our findings revealed a complex control system governing the ACP and its regulatory factors, including Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation, adrenomedullin (AM), and complement factor H (CFH). Particularly, AM emerged as a crucial player in CFB secretion, activating CFH and promoting its predominant binding to C3b over CFB. Mechanistically, our data suggest that the KRAS mutation stimulates AM expression, enhancing CFH activity in the fluid phase through binding. This heightened AM-CFH interaction conferred greater affinity for C3b over CFB, potentially suppressing the ACP cascade. This sequence of events likely culminated in the preferential release of ductal CFB into plasma during the early stages of PDAC. (Data set ID PXD047043.).
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Affiliation(s)
- Min Jung Lee
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Jin-Young Cho
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
| | - Sumi Bae
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Hye Soo Jung
- JW BioScience Corp., 38 Gwacheon-daero, Gwacheon-si, Gyeonggi-do 13840, South Korea
| | - Chang Moo Kang
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sung Hyun Kim
- Department of Surgery, Division of HBP Surgery, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hye Jin Choi
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Daewoong Jo
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul 03722, South Korea
- Cellivery R&D Institute, Cellivery Therapeutics, Inc., Seoul 03929, Korea
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Iacobescu M, Pop C, Uifălean A, Mogoşan C, Cenariu D, Zdrenghea M, Tănase A, Bergthorsson JT, Greiff V, Cenariu M, Iuga CA, Tomuleasa C, Tătaru D. Unlocking protein-based biomarker potential for graft-versus-host disease following allogenic hematopoietic stem cell transplants. Front Immunol 2024; 15:1327035. [PMID: 38433830 PMCID: PMC10904603 DOI: 10.3389/fimmu.2024.1327035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Despite the numerous advantages of allogeneic hematopoietic stem cell transplants (allo-HSCT), there exists a notable association with risks, particularly during the preconditioning period and predominantly post-intervention, exemplified by the occurrence of graft-versus-host disease (GVHD). Risk stratification prior to symptom manifestation, along with precise diagnosis and prognosis, relies heavily on clinical features. A critical imperative is the development of tools capable of early identification and effective management of patients undergoing allo-HSCT. A promising avenue in this pursuit is the utilization of proteomics-based biomarkers obtained from non-invasive biospecimens. This review comprehensively outlines the application of proteomics and proteomics-based biomarkers in GVHD patients. It delves into both single protein markers and protein panels, offering insights into their relevance in acute and chronic GVHD. Furthermore, the review provides a detailed examination of the site-specific involvement of GVHD. In summary, this article explores the potential of proteomics as a tool for timely and accurate intervention in the context of GVHD following allo-HSCT.
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Affiliation(s)
- Maria Iacobescu
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Pop
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Uifălean
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Mogoşan
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Cenariu
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Tănase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Jon Thor Bergthorsson
- Department of Laboratory Hematology, Stem Cell Research Unit, Biomedical Center, School of Health Sciences, University Iceland, Reykjavik, Iceland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Mihai Cenariu
- Department of Animal Reproduction, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristina Adela Iuga
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Tătaru
- Department of Internal Medicine, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Sitkov N, Ryabko A, Moshnikov V, Aleshin A, Kaplun D, Zimina T. Hybrid Impedimetric Biosensors for Express Protein Markers Detection. MICROMACHINES 2024; 15:181. [PMID: 38398911 PMCID: PMC10890403 DOI: 10.3390/mi15020181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
Impedimetric biosensors represent a powerful and promising tool for studying and monitoring biological processes associated with proteins and can contribute to the development of new approaches in the diagnosis and treatment of diseases. The basic principles, analytical methods, and applications of hybrid impedimetric biosensors for express protein detection in biological fluids are described. The advantages of this type of biosensors, such as simplicity and speed of operation, sensitivity and selectivity of analysis, cost-effectiveness, and an ability to be integrated into hybrid microfluidic systems, are demonstrated. Current challenges and development prospects in this area are analyzed. They include (a) the selection of materials for electrodes and formation of nanostructures on their surface; (b) the development of efficient methods for biorecognition elements' deposition on the electrodes' surface, providing the specificity and sensitivity of biosensing; (c) the reducing of nonspecific binding and interference, which could affect specificity; (d) adapting biosensors to real samples and conditions of operation; (e) expanding the range of detected proteins; and, finally, (f) the development of biosensor integration into large microanalytical system technologies. This review could be useful for researchers working in the field of impedimetric biosensors for protein detection, as well as for those interested in the application of this type of biosensor in biomedical diagnostics.
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Affiliation(s)
- Nikita Sitkov
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
- Engineering Centre for Microtechnology and Diagnostics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
| | - Andrey Ryabko
- Laboratory of Nonequilibrium Processes in Semiconductors, Ioffe Institute, 26 Politekhnicheskaya, 194021 Saint Petersburg, Russia;
| | - Vyacheslav Moshnikov
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
| | - Andrey Aleshin
- Laboratory of Nonequilibrium Processes in Semiconductors, Ioffe Institute, 26 Politekhnicheskaya, 194021 Saint Petersburg, Russia;
| | - Dmitry Kaplun
- Artificial Intelligence Research Institute, China University of Mining and Technology, 1 Daxue Road, Xuzhou 221116, China;
- Department of Automation and Control Processes, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
| | - Tatiana Zimina
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia; (V.M.); (T.Z.)
- Engineering Centre for Microtechnology and Diagnostics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
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10
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Qin J, Wang S, Liang Y, Ye Y, Guo Y, Li S, Liang Y. A SERS substrate based on perovskite quantum dots and graphene for the determination of cardiac troponin I. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123543. [PMID: 37862840 DOI: 10.1016/j.saa.2023.123543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/14/2023] [Indexed: 10/22/2023]
Abstract
Noble metal has always been used as a preferred base for SERS substrate. However, the preparation cost of such materials is trully high. Therefore, many researchers have begun to search for succedanea which cost were lower. In this work, CsPbBr3@ZIF-8 was synthesized by in-situ reduction method and combined with graphene nanosheets to construct a SERS substrate. The SERS performance of this substrate could be further enhanced by the synergistic effect of perovskite quantum dots and graphene. Base on this material, a sensitive SERS strategy composed of CsPbBr3@ZIF-8@G, antibody, and Bradford method was developed for the quantitative determination of cardiac troponin I (cTnI) in human serum. It's worth noting that the sensitivity and accuracy of this method could approach the level of other SERS methods using noble metals. The "reverse"-SERS method could improve the uniformity and stability of detection platform obviously. The detection range of this method was 0.01-100 ng/mL, and the estimated detection of limit (LOD) was 4.7 pg/mL. The recovery rate of this method range was between 93.1 % and 104.8 %, and RSD range was between 4.47 % and 7.06 %.
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Affiliation(s)
- Jinli Qin
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Shuqian Wang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Yin Liang
- Science and Tecnology Innovation Center, China GDE Engineering Co., LTD., Guangzhou 511447, China
| | - Youai Ye
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Yamei Guo
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Shushu Li
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Yong Liang
- School of Chemistry, South China Normal University, Guangzhou 510006, China.
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11
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Kumar Barik A, Mathew C, Sanoop PM, John RV, Adigal SS, Bhat S, Pai KM, Bhandary SV, Devasia T, Upadhya R, Kartha VB, Chidangil S. Protein profile pattern analysis: A multifarious, in vitro diagnosis technique for universal screening. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1232:123944. [PMID: 38056315 DOI: 10.1016/j.jchromb.2023.123944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Universal health care is attracting increased attention nowadays, because of the large increase in population all over the world, and a similar increase in life expectancy, leading to an increase in the incidence of non-communicable (various cancers, coronary diseases, neurological and old-age-related diseases) and communicable diseases/pandemics like SARS-COVID 19. This has led to an immediate need for a healthcare technology that should be cost-effective and accessible to all. A technology being considered as a possible one at present is liquid biopsy, which looks for markers in readily available samples like body fluids which can be accessed non- or minimally- invasive manner. Two approaches are being tried now towards this objective. The first involves the identification of suitable, specific markers for each condition, using established methods like various Mass Spectroscopy techniques (Surface-Enhanced Laser Desorption/Ionization Mass Spectroscopy (SELDI-MS), Matrix-Assisted Laser Desorption/Ionization (MALDI-MS), etc., immunoassays (Enzyme-Linked Immunoassay (ELISA), Proximity Extension Assays, etc.) and separation methods like 2-Dimensional Polyacrylamide Gel Electrophoresis (2-D PAGE), Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE), Capillary Electrophoresis (CE), etc. In the second approach, no attempt is made the identification of specific markers; rather an efficient separation method like High-Performance Liquid Chromatography/ Ultra-High-Performance Liquid Chromatography (HPLC/UPLC) is used to separate the protein markers, and a profile of the protein pattern is recorded, which is analysed by Artificial Intelligence (AI)/Machine Learning (MI) methods to derive characteristic patterns and use them for identifying the disease condition. The present report gives a summary of the current status of these two approaches and compares the two in the use of their suitability for universal healthcare.
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Affiliation(s)
- Ajaya Kumar Barik
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Clint Mathew
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pavithran M Sanoop
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Reena V John
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sphurti S Adigal
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sujatha Bhat
- Division of Microbiology, Department of Basic Medical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keerthilatha M Pai
- Department of Dental Surgery, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok, Sikkim 737102, India
| | - Sulatha V Bhandary
- Department of Ophthalmology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Tom Devasia
- Department of Cardiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rekha Upadhya
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - V B Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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12
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Röwer C, Olaleye OO, Bischoff R, Glocker MO. Mass Spectrometric ITEM-ONE and ITEM-TWO Analyses Confirm and Refine an Assembled Epitope of an Anti-Pertuzumab Affimer. Biomolecules 2023; 14:24. [PMID: 38254624 PMCID: PMC10813730 DOI: 10.3390/biom14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Intact Transition Epitope Mapping-One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab's heavy chain and together form a surface area of 1381.46 Å2. Despite not being part of Pertuzumab's CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (KD m0g#) of 3.07 × 10-12. The experimentally determined apparent enthalpy (ΔHm0g#) and apparent free energy (ΔGm0g#) of the complex dissociation reaction indicate that the opposite reaction-complex formation-is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab's unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids.
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
| | - Oladapo O. Olaleye
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
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13
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Repetto O, Vettori R, Steffan A, Cannizzaro R, De Re V. Circulating Proteins as Diagnostic Markers in Gastric Cancer. Int J Mol Sci 2023; 24:16931. [PMID: 38069253 PMCID: PMC10706891 DOI: 10.3390/ijms242316931] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has a poor prognosis. Most GC cases are detected at advanced stages due to the cancer lacking early detectable symptoms. Therefore, there is great interest in improving early diagnosis by implementing targeted prevention strategies. Markers are necessary for early detection and to guide clinicians to the best personalized treatment. The current semi-invasive endoscopic methods to detect GC are invasive, costly, and time-consuming. Recent advances in proteomics technologies have enabled the screening of many samples and the detection of novel biomarkers and disease-related signature signaling networks. These biomarkers include circulating proteins from different fluids (e.g., plasma, serum, urine, and saliva) and extracellular vesicles. We review relevant published studies on circulating protein biomarkers in GC and detail their application as potential biomarkers for GC diagnosis. Identifying highly sensitive and highly specific diagnostic markers for GC may improve patient survival rates and contribute to advancing precision/personalized medicine.
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Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Roberto Vettori
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy; (R.V.); (A.S.)
| | - Renato Cannizzaro
- Oncological Gastroenterology, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy;
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), National Cancer Institute, IRCCS, 33081 Aviano, Italy
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14
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Blanco-Pintos T, Regueira-Iglesias A, Seijo-Porto I, Balsa-Castro C, Castelo-Baz P, Nibali L, Tomás I. Accuracy of periodontitis diagnosis obtained using multiple molecular biomarkers in oral fluids: A systematic review and meta-analysis. J Clin Periodontol 2023; 50:1420-1443. [PMID: 37608638 DOI: 10.1111/jcpe.13854] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 08/24/2023]
Abstract
AIM To determine the accuracy of biomarker combinations in gingival crevicular fluid (GCF) and saliva through meta-analysis to diagnose periodontitis in systemically healthy subjects. METHODS Studies on combining two or more biomarkers providing a binary classification table, sensitivity/specificity values or group sizes in subjects diagnosed with periodontitis were included. The search was performed in August 2022 through PUBMED, EMBASE, Cochrane, LILACS, SCOPUS and Web of Science. The methodological quality of the articles selected was evaluated using the QUADAS-2 checklist. Hierarchical summary receiver operating characteristic modelling was employed to perform the meta-analyses (CRD42020175021). RESULTS Twenty-one combinations in GCF and 47 in saliva were evaluated. Meta-analyses were possible for six salivary combinations (median sensitivity/specificity values): IL-6 with MMP-8 (86.2%/80.5%); IL-1β with IL-6 (83.0%/83.7%); IL-1β with MMP-8 (82.7%/80.8%); MIP-1α with MMP-8 (71.0%/75.6%); IL-1β, IL-6 and MMP-8 (81.8%/84.3%); and IL-1β, IL-6, MIP-1α and MMP-8 (76.6%/79.7%). CONCLUSIONS Two-biomarker combinations in oral fluids show high diagnostic accuracy for periodontitis, which is not substantially improved by incorporating more biomarkers. In saliva, the dual combinations of IL-1β, IL-6 and MMP-8 have an excellent ability to detect periodontitis and a good capacity to detect non-periodontitis. Because of the limited number of biomarker combinations evaluated, further research is required to corroborate these observations.
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Affiliation(s)
- T Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - A Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - I Seijo-Porto
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - C Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - P Castelo-Baz
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - L Nibali
- Periodontology Unit, Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - I Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
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15
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Haller N, Reichel T, Zimmer P, Behringer M, Wahl P, Stöggl T, Krüger K, Simon P. Blood-Based Biomarkers for Managing Workload in Athletes: Perspectives for Research on Emerging Biomarkers. Sports Med 2023; 53:2039-2053. [PMID: 37341908 PMCID: PMC10587296 DOI: 10.1007/s40279-023-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
At present, various blood-based biomarkers have found their applications in the field of sports medicine. This current opinion addresses biomarkers that warrant consideration in future research for monitoring the athlete training load. In this regard, we identified a variety of emerging load-sensitive biomarkers, e.g., cytokines (such as IL-6), chaperones (such as heat shock proteins) or enzymes (such as myeloperoxidase) that could improve future athlete load monitoring as they have shown meaningful increases in acute and chronic exercise settings. In some cases, they have even been linked to training status or performance characteristics. However, many of these markers have not been extensively studied and the cost and effort of measuring these parameters are still high, making them inconvenient for practitioners so far. We therefore outline strategies to improve knowledge of acute and chronic biomarker responses, including ideas for standardized study settings. In addition, we emphasize the need for methodological advances such as the development of minimally invasive point-of-care devices as well as statistical aspects related to the evaluation of these monitoring tools to make biomarkers suitable for regular load monitoring.
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Affiliation(s)
- Nils Haller
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
| | - Thomas Reichel
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Philipp Zimmer
- Division of Performance and Health (Sports Medicine), Institute for Sport and Sport Science, TU Dortmund University, Dortmund, Germany
| | - Michael Behringer
- Department of Sports Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Wahl
- Department of Exercise Physiology, German Sport University Cologne, Cologne, Germany
| | - Thomas Stöggl
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
- Red Bull Athlete Performance Center, Salzburg, Austria
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany.
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16
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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de Jesus JR, de Araujo Andrade T, de Figueiredo EC. Biomarkers in psychiatric disorders. Adv Clin Chem 2023; 116:183-208. [PMID: 37852719 DOI: 10.1016/bs.acc.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Psychiatric disorders represent a significant socioeconomic and healthcare burden worldwide. Of these, schizophrenia, bipolar disorder, major depressive disorder and anxiety are among the most prevalent. Unfortunately, diagnosis remains problematic and largely complicated by the lack of disease specific biomarkers. Accordingly, much research has focused on elucidating these conditions to more fully understand underlying pathophysiology and potentially identify biomarkers, especially those of early stage disease. In this chapter, we review current status of this endeavor as well as the potential development of novel biomarkers for clinical applications and future research study.
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Affiliation(s)
| | | | - Eduardo Costa de Figueiredo
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, Alfenas, Minas Gerais, Brazil
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18
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Mousseau F, Féraudet Tarisse C, Simon S, Gacoin T, Alexandrou A, Bouzigues CI. Multititration: The New Method for Implementing Ultrasensitive and Quantitative Multiplexed In-Field Immunoassays Despite Cross-Reactivity? Anal Chem 2023; 95:13509-13518. [PMID: 37639578 DOI: 10.1021/acs.analchem.3c01846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The accurate in-field titration of multiple pathogens is essential to efficiently describe and monitor environmental or biological contamination, isolate, act, and treat adequately. This underscores the requirement of portable, fast, quantitative, and multiplexed detection technologies, which, however, have not been properly developed so far, notably because it has been hindered by the phenomenon of cross-reactivity. In this work, we proposed a new analytical method based on the imaging through a portable device of lanthanide-based nanoparticles (YVO4:Eu) for spatially multiplexed detection, relying on a multiparameter analysis, i.e., a simultaneous analysis of all of the luminescence signals through the comparison to a calibration surface built in the presence of multiple analytes of interest. We then demonstrated the possibility to simultaneously quantify by multiplexed lateral flow assay (xLFA) the three enterotoxins SEG, SEH, and SEI in unknown mixtures, over two concentration decades (from a dozen of pg·mL-1 to few ng·mL-1). Assays were performed in less than an hour (25 min of strip migration followed by 30 min of drying at room temperature), the time during which the presence of the operator was not required for more than 5 min, in order to dip the strip and have it imaged by the reader. The concepts of nominal concentration recovery, coefficient of variation (CV), limit of blank (LOB), and limit of detection (LOD) were discussed in detail in the context of multiplexed assays. With our new definitions, quantitative results demonstrated a high recovery of the nominal concentrations (115%), reliability (CV = 20%), and sensitivity (LOBs of 3, 27, and 6 pg·mL-1 for SEG, SEH, and SEI respectively, and LODs of 6, 48, and 11 pg·mL-1 for SEG, SEH, and SEI, respectively). Based on this method, we observed an increase in sensitivity of 100 compared to the other multiplexed LFA labeled with gold particles and we approached the sensitivity of the simplex enzyme-linked immunosorbent assay (ELISA) performed with the same capture and detection antibodies. To conclude, our results, which are applicable to virtually any kind of multiplexed test, pave the way to the next generation of in-field analytical immunoassays by providing fast, quantitative, and highly sensitive multiplexed detection of biomarkers or pathogens.
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Affiliation(s)
- Fanny Mousseau
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut Polytechnique de Paris, CNRS, INSERM, Route de Saclay, 91128 Palaiseau, France
| | - Cécile Féraudet Tarisse
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Stéphanie Simon
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 91191 Gif-sur-Yvette, France
| | - Thierry Gacoin
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, Institut Polytechnique de Paris, CNRS, Route de Saclay, 91128 Palaiseau, France
| | - Antigoni Alexandrou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut Polytechnique de Paris, CNRS, INSERM, Route de Saclay, 91128 Palaiseau, France
| | - Cédric Ismael Bouzigues
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Institut Polytechnique de Paris, CNRS, INSERM, Route de Saclay, 91128 Palaiseau, France
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Garcia-Vaquero M, Mirzapour-Kouhdasht A. A review on proteomic and genomic biomarkers for gelatin source authentication: Challenges and future outlook. Heliyon 2023; 9:e16621. [PMID: 37303544 PMCID: PMC10248112 DOI: 10.1016/j.heliyon.2023.e16621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 05/05/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
Biomarkers are compounds that could be detected and used as indicators of normal and/or abnormal functioning of different biological systems, including animal tissues and food matrices. Gelatin products of animal origin, mainly bovine and porcine, are currently under scrutiny mainly due to the specific needs of some sectors of the population related to religious beliefs and their dietary prohibitions, as well as some potential health threats associated with these products. Thus, manufacturers are currently in need of a reliable, convenient, and easy procedure to discern and authenticate the origin of animal-based gelatins (bovine, porcine, chicken, or fish). This work aims to review current advances in the creation of reliable gelatin biomarkers for food authentication purposes based on proteomic and DNA biomarkers that could be applied in the food sector. Overall, the presence of specific proteins and peptides in gelatin can be chemically analysed (i.e., by chromatography, mass spectroscopy, electrophoresis, lateral flow devices, and enzyme-linked immunosorbent assay), and different polymerase chain reaction (PCR) methods have been applied for the detection of nucleic acid substances in gelatin. Altogether, despite the fact that numerous methods are currently being developed for the purpose of detecting gelatin biomarkers, their widespread application is highly dependent on the cost of the equipment and reagents as well as the ease of use of the various methods. Combining different methods and approaches targeting multiple biomarkers may be key for manufacturers to achieve reliable authentication of gelatin's origin.
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20
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Zatloukalova M, Poltorak L, Bilewicz R, Vacek J. Lipid-based liquid crystalline materials in electrochemical sensing and nanocarrier technology. Mikrochim Acta 2023; 190:187. [PMID: 37071228 PMCID: PMC10113356 DOI: 10.1007/s00604-023-05727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/02/2023] [Indexed: 04/19/2023]
Abstract
Some biologically active substances are unstable and poorly soluble in aqueous media, at the same time exhibiting low bioavailability. The incorporation of these biologically active compounds into the structure of a lipid-based lyotropic liquid crystalline phase or nanoparticles can increase or improve their stability and transport properties, subsequent bioavailability, and applicability in general. The aim of this short overview is (1) to clarify the principle of self-assembly of lipidic amphiphilic molecules in an aqueous environment and (2) to present lipidic bicontinuous cubic and hexagonal phases and their current biosensing (with a focus on electrochemical protocols) and biomedical applications.
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Affiliation(s)
- Martina Zatloukalova
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
| | - Lukasz Poltorak
- Electrochemistry@Soft Interfaces Team, Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403, Lodz, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15, Olomouc, Czech Republic.
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21
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Zammataro A, Koy C, Ruß M, Röwer C, Glocker MO. Intact Transition Epitope Mapping—Serological Inspection by Epitope EXtraction (ITEM—SIX). Molecules 2023; 28:molecules28073092. [PMID: 37049857 PMCID: PMC10096252 DOI: 10.3390/molecules28073092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Precision medicine requests accurate serological inspections to precisely stratify patients for targeted treatment. Intact transition epitope mapping analysis proved surrogate seroconversion of a model organism’s serum when spiked with a monoclonal murine anti-Ovalbumin antibody (mAb) with epitope resolution. Isolation of the IgG fraction from blood serum applied two consecutive protein precipitation steps followed by ultrafiltration and resulted in an ESI-MS analysis-ready IgG preparation. For epitope mapping by epitope extraction, the Ovalbumin antigen was digested with trypsin. After desalting, the peptide mixture was added to the ESI-MS-ready IgG preparation from mAb-spiked serum and the solution was incubated to form an immune complex between the Ovalbumin-derived epitope peptide and the anti-Ovalbumin mAb. Then, the entire mixture of proteins and peptides was directly electrosprayed. Sorting of ions in the mass spectrometer’s gas phase, dissociation of the immune complex ions by collision-induced dissociation, and recording of the epitope peptide ion that had been released from the immune complex proved the presence of the anti-Ovalbumin mAb in serum. Mass determination of the complex-released epitope peptide ion with isotope resolution is highly accurate, guaranteeing high specificity of this novel analysis approach, which is termed Intact Transition Epitope Mapping—Serological Inspections by Epitope EXtraction (ITEM—SIX).
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22
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Maráková K, Renner BJ, Thomas SL, Opetová M, Tomašovský R, Rai AJ, Schug KA. Solid phase extraction as sample pretreatment method for top-down quantitative analysis of low molecular weight proteins from biological samples using liquid chromatography - triple quadrupole mass spectrometry. Anal Chim Acta 2023; 1243:340801. [PMID: 36697174 DOI: 10.1016/j.aca.2023.340801] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023]
Abstract
Targeting and quantifying intact proteins from biological samples is still a very challenging research area. Several crucial steps exist in the analytical workflow, including development of a reliable sample preparation method. Here, we developed and applied for the first time a non-immunoaffinity sample preparation method based on a generally widely available micro-elution solid phase extraction (μSPE) strategy for the extraction of multiple lower molecular weight intact proteins (<30 kDa) from various biological matrices. Omission of a time-consuming drying and reconstitution step after extraction resulted in a more simple and rapid sample preparation procedure. A model set of eleven intact proteins (molecular weights: 5.5-29 kDa; isoelectric points: 4.5-11.3) were analyzed in multiple biological fluids using reversed-phase liquid chromatography with a triple quadrupole mass spectrometer operated in multiple reaction monitoring mode. Various sample pre-treatment reagents, sorbent types, and washing and elution solvents were experimentally tested and optimized to obtain the μSPE clean-up condition for a broad mixture of intact proteins having variable physicochemical properties. 1% trifluoroacetic acid and 0.2% Triton 100-X were selected as suitable sample pre-treatment reagents for releasing protein-protein interactions in human serum/plasma and human urine, respectively. Hydrophilic lipophilic balanced μSPE sorbent was selected as a high performing stationary phase. Addition of 1% trifluoroacetic acid to all washing and elution solutions showed the most beneficial effect for the extraction recovery of the proteins. Under the optimized conditions, reproducible extraction recoveries >65% for all targeted proteins (up to 30 kDa) in human urine and >50% for most of the proteins in serum/plasma were achieved. The selected conditions were applied also for the analysis of clinical serum and urine samples to demonstrate the feasibility of the developed method to target intact proteins directly by more affordable μSPE sample preparation and triple quadrupole mass spectrometry, which could be beneficial in many application fields.
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Affiliation(s)
- Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Beatriz J Renner
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, TX, USA
| | - Shannon L Thomas
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, TX, USA
| | - Martina Opetová
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Comenius University in Bratislava, Bratislava, Slovakia
| | - Radovan Tomašovský
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alex J Rai
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, USA
| | - Kevin A Schug
- Department of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, TX, USA.
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23
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Coverdale JPC, Harrington CF, Solovyev N. Review: Advances in the Accuracy and Traceability of Metalloprotein Measurements Using Isotope Dilution Inductively Coupled Plasma Mass Spectrometry. Crit Rev Anal Chem 2023:1-18. [PMID: 36637361 DOI: 10.1080/10408347.2022.2162811] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Advances in inductively coupled plasma mass spectrometry and the methods used to prepare isotopically enriched standards, allow for the high accuracy measurement of metalloproteins by isotope dilution mass spectrometry. This technique has now reached a level of maturity whereby a step change in the accuracy, precision, and traceability of, in particular, clinical, and biomedical measurements is achievable. Current clinical measurements, which require low limits of detection in the presence of complex sample matrices, use indirect methods based on immunochemistry for the study of human disease. However, this approach suffers from poor traceability, requiring comparisons based on provision of matrix-based reference materials, used as analytical standards. This leads to difficulty when changes in the reference material are required, often resulting in a lack of interlaboratory and temporal comparability in clinical results and reference ranges. In this review, we focus on the most important metalloproteins for clinical studies, to illustrate how the attributes of chromatography coupled to inorganic mass spectrometry can be used for the direct measurement of metalloproteins such as hemoglobin, transferrin, and ceruloplasmin. By using this approach, we hope to demonstrate how isotope dilution analysis can be used as a reference method to improve traceability and underpin clinical, biomedical, and other biological measurements.
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Affiliation(s)
- James P C Coverdale
- Supra-Regional Assay Service, Trace Element Laboratory, Surrey Research Park, Guildford, United Kingdom
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Chris F Harrington
- Supra-Regional Assay Service, Trace Element Laboratory, Surrey Research Park, Guildford, United Kingdom
- Royal Surrey NHS Foundation Trust, Guildford, United Kingdom
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24
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Hrušková H, Voráčová I, Laštovičková M, Killinger M, Foret F. Preparative protein concentration from biofluids by epitachophoresis. J Chromatogr A 2022; 1685:463591. [DOI: 10.1016/j.chroma.2022.463591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
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25
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Plasma proteomic profiling in postural orthostatic tachycardia syndrome (POTS) reveals new disease pathways. Sci Rep 2022; 12:20051. [PMID: 36414707 PMCID: PMC9681882 DOI: 10.1038/s41598-022-24729-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Postural orthostatic tachycardia syndrome (POTS) is a cardiovascular autonomic disorder characterized by excessive heart rate increase on standing, leading to debilitating symptoms with limited therapeutic possibilities. Proteomics is a large-scale study of proteins that enables a systematic unbiased view on disease and health, allowing stratification of patients based on their protein background. The aim of the present study was to determine plasma protein biomarkers of POTS and to reveal proteomic pathways differentially regulated in POTS. We performed an age- and sex-matched, case-control study in 130 individuals (case-control ratio 1:1) including POTS and healthy controls. Mean age in POTS was 30 ± 9.8 years (84.6% women) versus controls 31 ± 9.8 years (80.0% women). We analyzed plasma proteins using data-independent acquisition (DIA) mass spectrometry. Pathway analysis of significantly differently expressed proteins was executed using a cutoff log2 fold change set to 1.2 and false discovery rate (p-value) of < 0.05. A total of 393 differential plasma proteins were identified. Label-free quantification of DIA-data identified 30 differentially expressed proteins in POTS compared with healthy controls. Pathway analysis identified the strongest network interactions particularly for proteins involved in thrombogenicity and enhanced platelet activity, but also inflammation, cardiac contractility and hypertrophy, and increased adrenergic activity. Our observations generated by the first use a label-free unbiased quantification reveal the proteomic footprint of POTS in terms of a hypercoagulable state, proinflammatory state, enhanced cardiac contractility and hypertrophy, skeletal muscle expression, and adrenergic activity. These findings support the hypothesis that POTS may be an autoimmune, inflammatory and hyperadrenergic disorder.
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26
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Suica VI, Uyy E, Ivan L, Boteanu RM, Cerveanu-Hogas A, Hansen R, Antohe F. Cardiac Alarmins as Residual Risk Markers of Atherosclerosis under Hypolipidemic Therapy. Int J Mol Sci 2022; 23:ijms231911174. [PMID: 36232476 PMCID: PMC9569654 DOI: 10.3390/ijms231911174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 12/01/2022] Open
Abstract
Increased levels of low-density lipoproteins are the main risk factor in the initiation and progression of atherosclerosis. Although statin treatment can effectively lower these levels, there is still a residual risk of cardiovascular events. We hypothesize that a specific panel of stress-sensing molecules (alarmins) could indicate the persistence of silent atherosclerosis residual risk. New Zealand White rabbits were divided into: control group (C), a group that received a high-fat diet for twelve weeks (Au), and a treated hyperlipidemic group with a lipid diet for eight weeks followed by a standard diet and hypolipidemic treatment (atorvastatin and PCSK9 siRNA-inhibitor) for four weeks (Asi). Mass spectrometry experiments of left ventricle lysates were complemented by immunologic and genomic studies to corroborate the data. The hyperlipidemic diet determined a general alarmin up-regulation tendency over the C group. A significant spectral abundance increase was measured for specific heat shock proteins, S100 family members, HMGB1, and Annexin A1. The hypolipidemic treatment demonstrated a reversed regulation trend with non-significant spectral alteration over the C group for some of the identified alarmins. Our study highlights the discriminating potential of alarmins in hyperlipidemia or following hypolipidemic treatment. Data are available via ProteomeXchange with identifier PXD035692.
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Affiliation(s)
- Viorel I. Suica
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
| | - Elena Uyy
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
| | - Luminita Ivan
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
| | - Raluca M. Boteanu
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
| | - Aurel Cerveanu-Hogas
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
| | - Rune Hansen
- SINTEF Digital, 7465 Trondheim, Norway
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Felicia Antohe
- Institute of Cellular Biology and Pathology “Nicolae Simionescu”, 050568 Bucharest, Romania
- Correspondence: ; Tel.: +40-213194518
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27
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Zhang K, Cao H, Ma Y, Si H, Zang J, Bai H, Yu L, Pang X, Zhou F, Xing J, Dong J. Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1000039. [PMID: 36186065 PMCID: PMC9521605 DOI: 10.3389/fpls.2022.1000039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Proteins post-translational modification (PTMs) is necessary in the whole life process of organisms. Among them, lysine 2-hydroxyisobutyrylation (Khib) plays an important role in protein synthesis, transcriptional regulation, and cell metabolism. Khib is a newly identified PTM in several plant species. However, the function of Khib in maize was unclear. In this study, western blotting results showed that Khib modification level increased significantly after Fusarium graminearum infection, and 2,066 Khib modified sites on 728 proteins were identified in maize, among which 24 Khib sites occurred on core histones. Subcellular localization results showed that these Khib modified proteins were localized in cytoplasm, chloroplast, and nucleus. Then, comparative proteomic analysis of the defense response to F. graminearum infection showed that Khib modification participated in plant resistance to pathogen infection by regulating glycolysis, TCA cycle, protein synthesis, peroxisome, and secondary metabolic processes, such as benzoxazinoid biosynthesis, phenylpropanoid biosynthesis, jasmonic acid synthesis, and tyrosine and tryptophan biosynthesis. In addition, we also demonstrated that lysine 2-hydroxyisobutyrylation sites on histones were involved in the gene expression of pathogenesis-related proteins. Our results provide a new perspective for the study of plant disease resistance, and had directive significance of maize disease resistance for molecular breeding.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongzhe Cao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuxin Ma
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Helong Si
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jinping Zang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hua Bai
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Lu Yu
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Xi Pang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Zhou
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
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28
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Technical steps towards enhanced localization of proteins in cultural heritage samples by immunofluorescence microscopy and micro-reflectance imaging spectroscopy. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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30
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Havran L, Vacek J, Dorčák V. Free and Bound Histidine in Reactions at Mercury Electrode. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Mishra S, Rajput N, Jadav T, Sahu AK, Tekade RK, Sengupta P. Advancement in Analytical Strategies for Quantification of Biomarkers with a Special Emphasis on Surrogate Approaches. Crit Rev Anal Chem 2022; 53:1515-1530. [PMID: 35138951 DOI: 10.1080/10408347.2022.2035210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Accurate quantification of biomarkers has always been a challenge for many bioanalytical scientists due to their endogenous nature and low concentration in biological matrices. Different analytical approaches have been developed for quantifying biomarkers including enzyme-linked immunosorbent assay, immunohistochemistry, western blotting, and chromatographic techniques assisted with mass spectrometry. Liquid chromatography-tandem mass spectrometry-based quantification of biomarkers has gained more attention over other traditional techniques due to its higher sensitivity and selectivity. However, the primary challenge lies with this technique includes the unavailability of a blank matrix for method development. To overcome this challenge, different analytical approaches are being developed including surrogate analyte and surrogate matrix approach. Such approaches include quantification of biomarkers in a surrogate matrix or quantification of an isotopically labeled surrogate analyte in an authentic matrix. To demonstrate the authenticity of the surrogate approach, it is mandatory to establish quantitative parallelism through validation employing respective surrogate analytes and surrogate matrices. In this review, different bioanalytical approaches for biomarker quantification and recent advancements in the field aiming for improvement in the specificity of the techniques have been discussed. Liquid chromatography-tandem mass spectrometry-based surrogate approaches for biomarker quantification and significance of parallelism establishment in both surrogate matrix and surrogate analyte-based approaches have been critically discussed. In addition, different methods for demonstrating parallelism in the surrogate method have been explained.
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Affiliation(s)
- Sonam Mishra
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
| | - Niraj Rajput
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
| | - Tarang Jadav
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
| | - Amit Kumar Sahu
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
| | - Rakesh K Tekade
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
| | - Pinaki Sengupta
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Gandhinagar, Gujarat, India
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32
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Macchia E, Torricelli F, Bollella P, Sarcina L, Tricase A, Di Franco C, Österbacka R, Kovács-Vajna ZM, Scamarcio G, Torsi L. Large-Area Interfaces for Single-Molecule Label-free Bioelectronic Detection. Chem Rev 2022; 122:4636-4699. [PMID: 35077645 DOI: 10.1021/acs.chemrev.1c00290] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioelectronic transducing surfaces that are nanometric in size have been the main route to detect single molecules. Though enabling the study of rarer events, such methodologies are not suited to assay at concentrations below the nanomolar level. Bioelectronic field-effect-transistors with a wide (μm2-mm2) transducing interface are also assumed to be not suited, because the molecule to be detected is orders of magnitude smaller than the transducing surface. Indeed, it is like seeing changes on the surface of a one-kilometer-wide pond when a droplet of water falls on it. However, it is a fact that a number of large-area transistors have been shown to detect at a limit of detection lower than femtomolar; they are also fast and hence innately suitable for point-of-care applications. This review critically discusses key elements, such as sensing materials, FET-structures, and target molecules that can be selectively assayed. The amplification effects enabling extremely sensitive large-area bioelectronic sensing are also addressed.
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Affiliation(s)
- Eleonora Macchia
- Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, 25123 Brescia, Italy
| | - Paolo Bollella
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy.,Centre for Colloid and Surface Science - Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Angelo Tricase
- Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Cinzia Di Franco
- CNR, Istituto di Fotonica e Nanotecnologie, Sede di Bari, 70125 Bari, Italy
| | - Ronald Österbacka
- Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Zsolt M Kovács-Vajna
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, 25123 Brescia, Italy
| | - Gaetano Scamarcio
- CNR, Istituto di Fotonica e Nanotecnologie, Sede di Bari, 70125 Bari, Italy.,Dipartimento Interateneo di Fisica "M. Merlin", Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Luisa Torsi
- Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland.,Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy.,Centre for Colloid and Surface Science - Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
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33
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Ventura C, Torres V, Vieira L, Gomes B, Rodrigues AS, Rueff J, Penque D, Silva MJ. New “Omics” Approaches as Tools to Explore Mechanistic Nanotoxicology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:179-194. [DOI: 10.1007/978-3-030-88071-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Renner CM, Visetsouk MR, Kreeger PK, Masters KS. Multispectral Staining and Analysis of Extracellular Matrix. Methods Mol Biol 2022; 2424:105-119. [PMID: 34918289 DOI: 10.1007/978-1-0716-1956-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiplexed immunofluorescent (IF) techniques enable the detection of multiple antigens within the same sample and are therefore useful in situations where samples are rare or small in size. Similar to standard IF, multiplexed IF yields information on both the location and relative amount of detected antigens. While this method has been used primarily to detail cell phenotypes, we have recently adapted it to profile the extracellular matrix (ECM), which provides technical challenges due to autofluorescence and spatial overlap. This chapter details the planning, execution, optimization, and troubleshooting to use multiplexed IF to profile the ECM of human fallopian tube tissue.
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Affiliation(s)
- Carine M Renner
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Mike R Visetsouk
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Pamela K Kreeger
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, Department of Obstetrics and Gynecology, and University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kristyn S Masters
- Department of Biomedical Engineering and Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Departments of Medicine, University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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35
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Protein discrimination using erythrosin B-based GUMBOS in combination with UV-Vis spectroscopy and chemometrics. Talanta 2021; 240:123164. [PMID: 34972064 DOI: 10.1016/j.talanta.2021.123164] [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] [Received: 09/02/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
GUMBOS (Group of Uniform Materials Based on Organic Salts) have recently emerged as interesting materials for protein analysis due to their unique features and high tunability. In this regard, four novel erythrosin B (EB)-based GUMBOS were synthesized and their potential to discriminate among proteins with distinct properties (e.g., size, charge, and hydrophobicity) was assessed. These solid-phase materials were prepared using a single-step metathesis reaction between EB and various phosphonium and ammonium cations, namely tetrabutylphosphonium (P4444+), tributylhexadecylphosphonium (P44416+), tetrabutylammonium (N4444+), and benzyldimethylhexadecylammonium (BDHA+). Subsequently, the effect of pH (3.0, 4.5, and 6.0) and reaction time (5, 10, and 15 min) on the discriminatory power of synthesized GUMBOS was evaluated. Absorption spectra resulting from the interaction between EB-based GUMBOS and proteins were analyzed using partial least squares discriminant analysis (PLSDA). Unlike time, the pH value was determined to have influence over GUMBOS discrimination potential. Correct protein assignments varied from 86.5% to 100.0%, and the best discriminatory results were observed for [P4444]2[EB] and [N4444]2[EB] at pH 6.0. Additionally, these two GUMBOS allowed discrimination of protein mixtures containing different ratios of albumin and myoglobin, which appeared as individualized clusters in the PLSDA scores plots. Overall, this study showcases EB-based GUMBOS as simple synthetic targets to provide a label-free, cost-effective, rapid, and successful approach for discrimination of single proteins and their mixtures.
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36
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Bile Processing Protocol for Improved Proteomic Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:1-10. [PMID: 34905161 DOI: 10.1007/978-1-0716-1936-0_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
One of the critical issues to warrant the success of a proteome-wide analysis is sample preparation. Efficient protein extraction in the absence of interferent material is mandatory to achieve an ample proteome coverage by mass spectrometry. The study of biological fluids is always challenging due to their specific biochemical composition. However, there is increasing interest in their characterization as it will provide proteins that may advice disease setting, state, and progression. In particular, bile is proximal to liver and pancreas, and its study is especially attractive since it might provide valuable information for the clinical management of severe diseases afflicting these organs, which are at an urgent need of new biomarkers. Though previous efforts have been made to optimize protocols to analyze bile proteome, only partial descriptions were achieved due to its complex composition, where proteins represent less than 5% of the organic components. Here we describe a new method that significantly increases the bile proteome coverage while reducing by a factor of six the amount of sample required for the proteomic analysis.
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Lin C, Li L, Feng J, Zhang Y, Lin X, Guo H, Li R. Aptamer-modified magnetic SERS substrate for label-based determination of cardiac troponin I. Mikrochim Acta 2021; 189:22. [PMID: 34882274 DOI: 10.1007/s00604-021-05121-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 12/28/2022]
Abstract
A sensitive label-based SERS strategy composed of magnetic bimetallic nanoparticles Fe3O4@Ag@Au, specific aptamer, and Bradford method was developed for the quantitative determination of cardiac troponin I (cTnI) in human serum. The prepared substrate with high magnetic character, signal enhancement, and uniformity exhibited significant Raman response. After the substrate was bound to the aptamer, the target protein cTnI was specifically captured, and it showed the Raman signal when the signal reporter Coomassie Brilliant Blue G-250 (CBBG) was supplied. The Raman signal intensity at 1621 cm-1 showed a wide linear relationship with the log value of the cTnI concentration in the range 0.01 to 100 ng·mL-1, and the estimated limit of detection (LOD) was 5.50 pg·mL-1. The recovery and relative standard deviation (RSD) of the spike experiment in human serum samples were 92-115% and 7.4-12.7%, respectively.
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Affiliation(s)
- Chubing Lin
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Lijun Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China. .,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China.
| | - Jun Feng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Yan Zhang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Xin Lin
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Heyuanxi Guo
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Rui Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No.268 Donghuan Road, Chengzhong District, Liuzhou City, 545006, Guangxi Zhuang Autonomous Region, China.,Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugarcane and Sugar Industry, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
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Castro RC, Saraiva MLM, Santos JL, Ribeiro DS. Multiplexed detection using quantum dots as photoluminescent sensing elements or optical labels. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ornelas-González A, Ortiz-Martínez M, González-González M, Rito-Palomares M. Enzymatic Methods for Salivary Biomarkers Detection: Overview and Current Challenges. Molecules 2021; 26:7026. [PMID: 34834116 PMCID: PMC8624596 DOI: 10.3390/molecules26227026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 12/12/2022] Open
Abstract
Early detection is a key factor in patient fate. Currently, multiple biomolecules have been recognized as biomarkers. Nevertheless, their identification is only the starting line on the way to their implementation in disease diagnosis. Although blood is the biofluid par excellence for the quantification of biomarkers, its extraction is uncomfortable and painful for many patients. In this sense, there is a gap in which saliva emerges as a non-invasive and valuable source of information, as it contains many of the biomarkers found in blood. Recent technological advances have made it possible to detect and quantify biomarkers in saliva samples. However, there are opportunity areas in terms of cost and complexity, which could be solved using simpler methodologies such as those based on enzymes. Many reviews have focused on presenting the state-of-the-art in identifying biomarkers in saliva samples. However, just a few of them provide critical analysis of technical elements for biomarker quantification in enzymatic methods for large-scale clinical applications. Thus, this review proposes enzymatic assays as a cost-effective alternative to overcome the limitations of current methods for the quantification of biomarkers in saliva, highlighting the technical and operational considerations necessary for sampling, method development, optimization, and validation.
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Affiliation(s)
| | | | - Mirna González-González
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Monterrey 64710, N.L., Mexico; (A.O.-G.); (M.O.-M.)
| | - Marco Rito-Palomares
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Monterrey 64710, N.L., Mexico; (A.O.-G.); (M.O.-M.)
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Tezel G. Multiplex protein analysis for the study of glaucoma. Expert Rev Proteomics 2021; 18:911-924. [PMID: 34672220 PMCID: PMC8712406 DOI: 10.1080/14789450.2021.1996232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/15/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Glaucoma, a leading cause of irreversible blindness in the world, is a chronic neurodegenerative disease of multifactorial origin. Extensive research is ongoing to better understand, prevent, and treat progressive degeneration of retinal ganglion cells in glaucoma. While experimental models of glaucoma and postmortem tissues of human donors are analyzed for pathophysiological comprehension and improved treatment of this blinding disease, clinical samples of intraocular biofluids and blood collected from glaucoma patients are analyzed to identify predictive, diagnostic, and prognostic biomarkers. Multiplexing techniques for protein analysis offer a valuable approach for translational glaucoma research. AREAS COVERED This review provides an overview of the increasing applications of multiplex protein analysis for glaucoma research and also highlights current research challenges in the field and expected solutions from emerging technological advances. EXPERT OPINION Analytical techniques for multiplex analysis of proteins can help uncover neurodegenerative processes for enhanced treatment of glaucoma and can help identify molecular biomarkers for improved clinical testing and monitoring of this complex disease. This evolving field and continuously growing availability of new technologies are expected to broaden the comprehension of this complex neurodegenerative disease and speed up the progress toward new therapeutics and personalized patient care to prevent blindness from glaucoma.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology, Vagelos College of Physicians and Surgeons, Columbia University, Edward S. Harkness Eye Institute, New York, NY, USA
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Güzel C, van Sten-Van't Hoff J, de Kok IMCM, Govorukhina NI, Boychenko A, Luider TM, Bischoff R. Molecular markers for cervical cancer screening. Expert Rev Proteomics 2021; 18:675-691. [PMID: 34551656 DOI: 10.1080/14789450.2021.1980387] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cervical cancer remains a significant healthcare problem, notably in low- to middle-income countries. While a negative test for hrHPV has a predictive value of more than 99.5%, its positive predictive value is less than 10% for CIN2+ stages. This makes the use of a so-called triage test indispensable for population-based screening to avoid referring women, that are ultimately at low risk of developing cervical cancer, to a gynecologist. This review will give an overview of tests that are based on epigenetic marker panels and protein markers. AREAS COVERED There is a medical need for molecular markers with a better predictive value to discriminate hrHPV-positive women that are at risk of developing cervical cancer from those that are not. Areas covered are epigenetic and protein markers as well as health economic considerations in view of the fact that most cases of cervical cancer arise in low-to-middle-income countries. EXPERT OPINION While there are biomarker assays based on changes at the nucleic acid (DNA methylation patterns, miRNAs) and at the protein level, they are not widely used in population screening. Combining nucleic acid-based and protein-based tests could improve the overall specificity for discriminating CIN2+ lesions that carry a low risk of progressing to cervical cancer within the screening interval from those that carry an elevated risk. The challenge is to reduce unnecessary referrals without an undesired increase in false-negative diagnoses resulting in cases of cervical cancer that could have been prevented. A further challenge is to develop tests for low-and middle-income countries, which is critical to reduce the worldwide burden of cervical cancer.
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Affiliation(s)
- Coşkun Güzel
- Erasmus MC, Department of Neurology, University of Groningen, Rotterdam, The Netherlands
| | | | | | - Natalia I Govorukhina
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | | | - Theo M Luider
- Erasmus MC, Department of Neurology, University of Groningen, Rotterdam, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
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Novel Approaches to an Integrated Route for Trisomy 21 Evaluation. Biomolecules 2021; 11:biom11091328. [PMID: 34572541 PMCID: PMC8465311 DOI: 10.3390/biom11091328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 12/31/2022] Open
Abstract
Trisomy 21 (T21) is one of the most commonly occurring genetic disorders, caused by the partial or complete triplication of chromosome 21. Despite the significant progress in the diagnostic tools applied for prenatal screening, commonly used methods are still imprecise and involve invasive diagnostic procedures that are related to a maternal risk of miscarriage. In this case, novel prenatal biomarkers are still being evaluated using highly specialized techniques, which could increase the diagnostic usefulness of biochemical prenatal screening for T21. From the other hand, the T21′s pathogenesis, caused by the improper division of genetic material, disrupting many metabolic pathways, could be further evaluated with the use of omics methods, which could result in bringing relevant insights for the evaluation of potential medical targets. Accordingly, a literature search was undertaken to collect novel information about prenatal screening for Down syndrome with the use of advanced technology, with a particular emphasis on the evaluation of novel screening biomarkers and the discovery of potential medical targets. These meta-analyses are focused on novel approaches designed with the use of omics techniques, representing the most rapidly developing and promising field in research today. Considering the limitations and progress of these methods, the use of omics techniques in evaluating T21 pathogenesis could bring beneficial results in prenatal screening, simultaneously uncovering novel potential medical targets.
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Ren A, Prassas I, Sugumar V, Soosaipillai A, Bernardini M, Diamandis EP, Kulasingam V. Comparison of two multiplexed technologies for profiling >1,000 serum proteins that may associate with tumor burden. F1000Res 2021; 10:509. [PMID: 34868557 PMCID: PMC8609392 DOI: 10.12688/f1000research.53364.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background: In this pilot study, we perform a preliminary comparison of two targeted multiplex proteomics technologies for discerning serum protein concentration changes that may correlate to tumor burden in ovarian cancer (OC) patients. Methods: Using the proximity extension assay (PEA) and Quantibody® Kiloplex Array (QKA), we measured >1,000 proteins in the pre-surgical and post-surgical serum from nine OC patients (N=18 samples). We expect that proteins that have decreased significantly in the post-surgical serum concentration may correlate to tumor burden in each patient. Duplicate sera from two healthy individuals were used as controls (N=4 samples). We employed in-house ELISAs to measure five proteins with large serum concentration changes in pre- and post-surgical sera, from four of the original nine patients and the two original controls. Results: Both platforms showed a weak correlation with clinical cancer antigen 125 (CA125) data. The two multiplexed platforms showed a significant correlation with each other for >400 overlapping proteins. PEA uncovered 15 proteins, while QKA revealed 11 proteins, with more than a two-fold post-surgical decrease in at least six of the nine patients. Validation using single enzyme-linked immunosorbent assays (ELISAs) showed at least a two-fold post-surgical decrease in serum concentration of the same patients, as indicated by the two multiplex assays. Conclusion: Both methods identified proteins that had significantly decreased in post-surgical serum concentration, as well as recognizing proteins that had been implicated in OC patients. Our findings from a limited sample size suggest that novel targeted proteomics platforms are promising tools for identifying candidate serological tumor-related proteins. However further studies are essential for the improvement of accuracy and avoidance of false results.
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Affiliation(s)
- Annie Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vijithan Sugumar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antoninus Soosaipillai
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marcus Bernardini
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
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Aalami AH, Abdeahad H, Mesgari M, Sathyapalan T, Sahebkar A. Urinary Angiogenin as a Marker for Bladder Cancer: A Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5557309. [PMID: 33997007 PMCID: PMC8099530 DOI: 10.1155/2021/5557309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/27/2021] [Accepted: 04/16/2021] [Indexed: 01/20/2023]
Abstract
AIMS Bladder cancer (BCa) is a common cancer in North America and Europe that carries considerable morbidity and mortality. A reliable biomarker for early detection of the bladder is crucial for improving the prognosis of BCA. In this meta-analysis, we examine the diagnostic role of the angiogenin (ANG) protein in patients' urine with bladder neoplasm. METHODS We performed a systematic literature search using ScienceDirect, Web of Science, PubMed/MEDLINE, Scopus, Google Scholar, and Embase, up to 10th October 2020 databases. Meta-Disc V.1.4 and Comprehensive Meta-Analysis V.2.2 software calculated the pooled specificity, sensitivity, area under the curve (AUC), diagnostic odds ratio (DOR), positive likelihood ratio (LR+), negative likelihood ratio (LR-), Q ∗ index, and summary receiver-operating characteristic (SROC) for the role of ANG as a urinary biomarker for BCa patients. RESULTS Four case-control studies were included with 656 participants (417 cases and 239 controls) in this meta-analysis. The pooled sensitivity of 0.71 (95% CI: 0.66-0.75), specificity of 0.78 (95% CI: 0.73-0.81), LR+ of 3.34 (95% CI: 2.02-5.53), LR- of 0.37 (95% CI: 0.32-0.44), DOR of 9.99 (95% CI: 4.69-21.28), and AUC of 0.789 and Q ∗ index of 0.726 demonstrate acceptable diagnostic precision of ANG in identifying BCa. CONCLUSION This meta-analysis showed that ANG could be a fair biomarker for the diagnosis of BCa patients.
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Affiliation(s)
- Amir Hossein Aalami
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hossein Abdeahad
- Department of Nutrition and Integrative Physiology, Collogue of Health, University of Utah, Salt Lake City, UT, USA
| | - Mohammad Mesgari
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Thozhukat Sathyapalan
- Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, UK
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Genomics-based approaches to identify and predict the health-promoting and safety activities of promising probiotic strains – A probiogenomics review. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.12.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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Bringans S, Peters K, Casey T, Ito J, Lipscombe R. The New and the Old: Platform Cross-Validation of Immunoaffinity MASS Spectrometry versus ELISA for PromarkerD, a Predictive Test for Diabetic Kidney Disease. Proteomes 2020; 8:proteomes8040031. [PMID: 33126588 PMCID: PMC7709118 DOI: 10.3390/proteomes8040031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022] Open
Abstract
PromarkerD is a proteomics derived test for predicting diabetic kidney disease that measures the concentrations of three plasma protein biomarkers, APOA4, CD5L and IBP3. Antibodies against these proteins were developed and applied to a multiplexed immunoaffinity capture mass spectrometry assay. In parallel, and facilitating current clinical laboratory workflows, a standard ELISA was also developed to measure each protein. The performance characteristics of the two technology platforms were compared using a cohort of 100 samples, with PromarkerD test scores demonstrating a high correlation (R = 0.97). These technologies illustrate the potential for large scale, high throughput clinical applications of proteomics now and into the future.
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Sensors and microarrays in protein biomarker monitoring: an electrochemical perspective spots. Bioanalysis 2020; 12:1337-1345. [PMID: 32915086 DOI: 10.4155/bio-2020-0166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The development of clinically applicable portable sensors and multiplex protein biomarker assays is one of the most important goals of laboratory medicine today. Sensing strategies based on electrochemical devices are discussed in this overview, with special emphasis on detection principles derived from voltammetry, electrogenerated chemiluminescence, bipolar electrochemistry and impedance-based measurements. Up-to-date examples of electrochemical methods in biomedical research and development are highlighted here, including critical evaluation and future directions of the analysis, development and validation of new protein biomarkers.
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Boelens JJ, Hosszu KK, Nierkens S. Immune Monitoring After Allogeneic Hematopoietic Cell Transplantation: Toward Practical Guidelines and Standardization. Front Pediatr 2020; 8:454. [PMID: 32974239 PMCID: PMC7472532 DOI: 10.3389/fped.2020.00454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic cell transplantation (HCT) is often a last resort, but potentially curative treatment option for children suffering from hematological malignancies and a variety of non-malignant disorders, such as bone marrow failure, inborn metabolic disease or immune deficiencies. Although efficacy and safety of the HCT procedure has increased significantly over the last decades, the majority of the patients still suffer from severe acute toxicity, viral reactivation, acute or chronic graft-versus-host disease (GvHD) and/or, in case of malignant disease, relapses. Factors influencing HCT outcomes are numerous and versatile. For example, there is variation in the selected graft sources, type of infused cell subsets, cell doses, and the protocols used for conditioning, as well as immune suppression and treatment of adverse events. Moreover, recent pharmacokinetic studies show that medications used in the conditioning regimen (e.g., busulphan, fludarabine, anti-thymocyte globulin) should be dosed patient-specific to achieve optimal exposure in every individual patient. Due to this multitude of variables and site-specific policies/preferences, harmonization between HCT centers is still difficult to achieve. Literature shows that adequate immune recovery post-HCT limits both relapse and non-relapse mortality (death due to viral reactivations and GvHD). Monitoring immune parameters post-HCT may facilitate a timely prediction of outcome. The use of standardized assays to measure immune parameters would facilitate a fast comparison between different strategies tested in different centers or between different clinical trials. We here discuss immune cell markers that may contribute to clinical decision making and may be worth to standardize in multicenter collaborations for future trials.
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Affiliation(s)
- Jaap Jan Boelens
- Stem Cell Transplantation and Cellular Therapies, MSK Kids, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Kinga K Hosszu
- Stem Cell Transplantation and Cellular Therapies, MSK Kids, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology and UMC Utrecht, Utrecht, Netherlands
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