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Jebari N, Dufour-Gergam E, Ammar M. 3D Simulation-Driven Design of a Microfluidic Immunosensor for Real-Time Monitoring of Sweat Biomarkers. MICROMACHINES 2024; 15:936. [PMID: 39203587 PMCID: PMC11356042 DOI: 10.3390/mi15080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 09/03/2024]
Abstract
This study presents the design and comprehensive 3D multiphysics simulation of a novel microfluidic immunosensor for non-invasive, real-time detection of pro-inflammatory biomarkers in human sweat. The patch-like device integrates magnetofluidic manipulation of antibody-functionalized magnetic nanoparticles (MNPs) with direct-field capacitive sensing (DF-CS). This unique combination enhances sensitivity, reduces parasitic capacitance, and enables a more compact design compared to traditional fringing-field approaches. A comprehensive 3D multiphysics simulation of the device, performed using COMSOL Multiphysics, demonstrates its operating principle by analyzing the sensor's response to changes in the dielectric properties of the medium due to the presence of magnetic nanoparticles. The simulation reveals a sensitivity of 42.48% at 85% MNP occupancy within the detection zone, highlighting the sensor's ability to detect variations in MNP concentration, and thus indirectly infer biomarker levels, with high precision. This innovative integration of magnetofluidic manipulation and DF-CS offers a promising new paradigm for continuous, non-invasive health monitoring, with potential applications in point-of-care diagnostics, personalized medicine, and preventive healthcare.
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Affiliation(s)
- Nessrine Jebari
- Center for Nanosciences and Nanotechnology (C2N), CNRS UMR 9001, University of Paris-Saclay, 91120 Palaiseau, France
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Elguoshy A, Yamamoto K, Hirao Y, Uchimoto T, Yanagita K, Yamamoto T. Investigating and Annotating the Human Peptidome Profile from Urine under Normal Physiological Conditions. Proteomes 2024; 12:18. [PMID: 39051237 PMCID: PMC11270373 DOI: 10.3390/proteomes12030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Examining the composition of the typical urinary peptidome and identifying the enzymes responsible for its formation holds significant importance, as it mirrors the normal physiological state of the human body. Any deviation from this normal profile could serve as an indicator of pathological processes occurring in vivo. Consequently, this study focuses on characterizing the normal urinary peptidome and investigating the various catalytic enzymes that are involved in generating these native peptides in urine. Our findings reveal that 1503 endogenous peptides, corresponding to 436 precursor proteins, were consistently identified robustly in at least 10 samples out of a total of 19 samples. Notably, the liver and kidneys exhibited the highest number of tissue-enriched or enhanced genes in the analyzed urinary peptidome. Furthermore, among the catalytic types, CTSD (cathepsin D) and MMP2 (matrix metalloproteinase-2) emerged as the most prominent peptidases in the aspartic and metallopeptidases categories, respectively. A comparison of our dataset with two of the most comprehensive urine peptidome datasets to date indicates a consistent relative abundance of core endogenous peptides for different proteins across all three datasets. These findings can serve as a foundational reference for the discovery of biomarkers in various human diseases.
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Affiliation(s)
- Amr Elguoshy
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Keiko Yamamoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Tomohiro Uchimoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Kengo Yanagita
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Kidney Research Center, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-2181, Japan; (A.E.); (K.Y.); (Y.H.); (T.U.); (K.Y.)
- Department of Clinical Laboratory, Shinrakuen Hospital, Niigata 950-2087, Japan
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Makhammajanov Z, Kabayeva A, Auganova D, Tarlykov P, Bukasov R, Turebekov D, Kanbay M, Molnar MZ, Kovesdy CP, Abidi SH, Gaipov A. Candidate protein biomarkers in chronic kidney disease: a proteomics study. Sci Rep 2024; 14:14014. [PMID: 38890379 PMCID: PMC11189417 DOI: 10.1038/s41598-024-64833-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Proteinuria poses a substantial risk for the progression of chronic kidney disease (CKD) and its related complications. Kidneys excrete hundreds of individual proteins, some with a potential impact on CKD progression or as a marker of the disease. However, the available data on specific urinary proteins and their relationship with CKD severity remain limited. Therefore, we aimed to investigate the urinary proteome and its association with kidney function in CKD patients and healthy controls. The proteomic analysis of urine samples showed CKD stage-specific differences in the number of detected proteins and the exponentially modified protein abundance index for total protein (p = 0.007). Notably, specific urinary proteins such as B2MG, FETUA, VTDB, and AMBP exhibited robust negative associations with kidney function in CKD patients compared to controls. Also, A1AG2, CD44, CD59, CERU, KNG1, LV39, OSTP, RNAS1, SH3L3, and UROM proteins showed positive associations with kidney function in the entire cohort, while LV39, A1BG, and CERU consistently displayed positive associations in patients compared to controls. This study suggests that specific urinary proteins, which were found to be negatively or positively associated with the kidney function of CKD patients, can serve as markers of dysfunctional or functional kidneys, respectively.
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Affiliation(s)
| | - Assem Kabayeva
- Department of Internal Medicine, Astana Medical University, Astana, Kazakhstan
| | - Dana Auganova
- Department of Proteomics and Mass Spectroscopy, National Center for Biotechnology, Astana, Kazakhstan
| | - Pavel Tarlykov
- Department of Proteomics and Mass Spectroscopy, National Center for Biotechnology, Astana, Kazakhstan
| | - Rostislav Bukasov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Duman Turebekov
- Department of Internal Medicine, Astana Medical University, Astana, Kazakhstan
| | - Mehmet Kanbay
- Division of Nephrology, Department of Internal Medicine, Koc University, Istanbul, Turkey
| | - Miklos Z Molnar
- Division of Nephrology & Hypertension, Department of Internal Medicine, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, USA
| | - Csaba P Kovesdy
- Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Syed Hani Abidi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Abduzhappar Gaipov
- Department of Medicine, School of Medicine, Nazarbayev University, Astana, Kazakhstan.
- Clinical Academic Department of Internal Medicine, University Medical Center, Astana, Kazakhstan.
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Grange C, Dalmasso A, Cortez JJ, Spokeviciute B, Bussolati B. Exploring the role of urinary extracellular vesicles in kidney physiology, aging, and disease progression. Am J Physiol Cell Physiol 2023; 325:C1439-C1450. [PMID: 37842748 PMCID: PMC10861146 DOI: 10.1152/ajpcell.00349.2023] [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: 07/27/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Extracellular vesicles (EVs), membranous vesicles present in all body fluids, are considered important messengers, carrying their information over long distance and modulating the gene expression profile of recipient cells. EVs collected in urine (uEVs) are mainly originated from the apical part of urogenital tract, following the urine flow. Moreover, bacterial-derived EVs are present within urine and may reflect the composition of microbiota. Consolidated evidence has established the involvement of uEVs in renal physiology, being responsible for glomerular and tubular cross talk and among different tubular segments. uEVs may also be involved in other physiological functions such as modulation of innate immunity, coagulation, or metabolic activities. Furthermore, it has been recently remonstrated that age, sex, endurance excise, and lifestyle may influence uEV composition and release, modifying their cargo. On the other hand, uEVs appear modulators of different urogenital pathological conditions, triggering disease progression. uEVs sustain fibrosis and inflammation processes, both involved in acute and chronic kidney diseases, aging, and stone formation. The molecular signature of uEVs collected from diseased patients can be of interest for understanding kidney physiopathology and for identifying diagnostic and prognostic biomarkers.
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Affiliation(s)
- Cristina Grange
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessia Dalmasso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Judiel John Cortez
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Beatrice Spokeviciute
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
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