1
|
Elgamal RM, Melton RL, Chiou J, McGrail CW, Gaulton KJ. Circulating pancreatic enzyme levels are a causal biomarker of type 1 diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.08.24311619. [PMID: 39148858 PMCID: PMC11326359 DOI: 10.1101/2024.08.08.24311619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Novel biomarkers of type 1 diabetes (T1D) are needed for earlier detection of disease and identifying therapeutic targets. We identified biomarkers of T1D by combining plasma cis and trans protein QTLs (pQTLs) for 2,922 proteins in the UK Biobank with a T1D genome-wide association study (GWAS) in 157k samples. T1D risk variants at over 20% of known loci colocalized with cis or trans pQTLs, and distinct sets of T1D loci colocalized with immune, pancreatic secretion, or gut-related proteins. We identified 23 proteins with evidence for a causal role in using pQTLs as genetic instruments in Mendelian Randomization which included multiple sensitivity analyses. Proteins increasing T1D risk were involved in immune processes (e.g. HLA-DRA) and, more surprisingly, T1D protective proteins were enriched in pancreatic secretions (e.g. CPA1), cholesterol metabolism (e.g. APOA1), and gut homeostasis. Genetic variants associated with plasma levels of T1D-protective pancreatic enzymes such as CPA1 were enriched in cis-regulatory elements in pancreatic exocrine and gut enteroendocrine cells, and the protective effects of CPA1 and other enzymes on T1D were consistent when using instruments specific to acinar cells. Finally, pancreatic enzymes had decreased acinar expression in T1D, including CPA1 which was altered prior to onset. Together, these results reveal causal biomarkers and highlight processes in the exocrine pancreas, immune system, and gut that modulate T1D risk.
Collapse
Affiliation(s)
- Ruth M Elgamal
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla CA
- Department of Pediatrics, UC San Diego, La Jolla CA
| | - Rebecca L Melton
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla CA
- Department of Pediatrics, UC San Diego, La Jolla CA
| | - Joshua Chiou
- Pfizer Research and Discovery, Pfizer Inc., Cambridge, MA
| | - Carolyn W McGrail
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla CA
- Department of Pediatrics, UC San Diego, La Jolla CA
| | | |
Collapse
|
2
|
Liang Z, Guo Y, Sharma A, McCurdy CR, Prentice BM. Multimodal Image Fusion Workflow Incorporating MALDI Imaging Mass Spectrometry and Microscopy for the Study of Small Pharmaceutical Compounds. Anal Chem 2024; 96:11869-11880. [PMID: 38982936 DOI: 10.1021/acs.analchem.4c01553] [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: 07/11/2024]
Abstract
Multimodal imaging analyses of dosed tissue samples can provide more comprehensive insights into the effects of a therapeutically active compound on a target tissue compared to single-modal imaging. For example, simultaneous spatial mapping of pharmaceutical compounds and endogenous macromolecule receptors is difficult to achieve in a single imaging experiment. Herein, we present a multimodal workflow combining imaging mass spectrometry with immunohistochemistry (IHC) fluorescence imaging and brightfield microscopy imaging. Imaging mass spectrometry enables direct mapping of pharmaceutical compounds and metabolites, IHC fluorescence imaging can visualize large proteins, and brightfield microscopy imaging provides tissue morphology information. Single-cell resolution images are generally difficult to acquire using imaging mass spectrometry but are readily acquired with IHC fluorescence and brightfield microscopy imaging. Spatial sharpening of mass spectrometry images would thus allow for higher fidelity coregistration with other higher-resolution microscopy images. Imaging mass spectrometry spatial resolution can be predicted to a finer value via a computational image fusion workflow, which models the relationship between the intensity values in the mass spectrometry image and the features of a high-spatial resolution microscopy image. As a proof of concept, our multimodal workflow was applied to brain tissue extracted from a Sprague-Dawley rat dosed with a kratom alkaloid, corynantheidine. Four candidate mathematical models, including linear regression, partial least-squares regression, random forest regression, and two-dimensional convolutional neural network (2-D CNN), were tested. The random forest and 2-D CNN models most accurately predicted the intensity values at each pixel as well as the overall patterns of the mass spectrometry images, while also providing the best spatial resolution enhancements. Herein, image fusion enabled predicted mass spectrometry images of corynantheidine, GABA, and glutamine to approximately 2.5 μm spatial resolutions, a significant improvement compared to the original images acquired at 25 μm spatial resolution. The predicted mass spectrometry images were then coregistered with an H&E image and IHC fluorescence image of the μ-opioid receptor to assess colocalization of corynantheidine with brain cells. Our study also provides insights into the different evaluation parameters to consider when utilizing image fusion for biological applications.
Collapse
Affiliation(s)
- Zhongling Liang
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Abhisheak Sharma
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Christopher R McCurdy
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
3
|
Garg P, Krishna M, Subbalakshmi AR, Ramisetty S, Mohanty A, Kulkarni P, Horne D, Salgia R, Singhal SS. Emerging biomarkers and molecular targets for precision medicine in cervical cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189106. [PMID: 38701936 DOI: 10.1016/j.bbcan.2024.189106] [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: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Cervical cancer remains a significant global health burden, necessitating innovative approaches for improved diagnostics and personalized treatment strategies. Precision medicine has emerged as a promising paradigm, leveraging biomarkers and molecular targets to tailor therapy to individual patients. This review explores the landscape of emerging biomarkers and molecular targets in cervical cancer, highlighting their potential implications for precision medicine. By integrating these biomarkers into comprehensive diagnostic algorithms, clinicians can identify high-risk patients at an earlier stage, enabling timely intervention and improved patient outcomes. Furthermore, the identification of specific molecular targets has paved the way for the development of targeted therapies aimed at disrupting key pathways implicated in cervical carcinogenesis. In conclusion, the evolving landscape of biomarkers and molecular targets presents exciting opportunities for advancing precision medicine in cervical cancer. By harnessing these insights, clinicians can optimize treatment selection, enhance patient outcomes, and ultimately transform the management of this devastating disease.
Collapse
Affiliation(s)
- Pankaj Garg
- Department of Chemistry, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Madhu Krishna
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ayalur Raghu Subbalakshmi
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sravani Ramisetty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Prakash Kulkarni
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - David Horne
- Departments of Molecular Medicine, Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Ravi Salgia
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA
| | - Sharad S Singhal
- Departments of Medical Oncology & Therapeutics Research and Beckman Research Institute of City of Hope, Comprehensive Cancer Center and National Medical Center, Duarte, CA 91010, USA.
| |
Collapse
|
4
|
Vergouwen DPC, van Beek AA, de Hoog J, de Boer JH, Los LI, Gijs M, Erckens RJ, Verdijk RM, Haasnoot GW, Roelen DL, Rothova A, Rönnelid J, Ten Berge JC, Schreurs MWJ. The enigma of sclera-specific autoimmunity in scleritis. J Autoimmun 2024; 144:103178. [PMID: 38368769 DOI: 10.1016/j.jaut.2024.103178] [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: 07/05/2023] [Revised: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 02/20/2024]
Abstract
Scleritis is a severe and painful ophthalmic disorder, in which a pathogenic role for collagen-directed autoimmunity was repeatedly suggested. We evaluated the presence of sclera-specific antibodies in a large cohort of patients with non-infectious scleritis. Therefore, we prospectively collected serum samples from 121 patients with non-infectious scleritis in a multicenter cohort study in the Netherlands. In addition, healthy (n = 39) and uveitis controls (n = 48) were included. Serum samples were tested for anti-native human type II collagen antibodies using a validated enzyme-linked immunosorbent assay (ELISA). Further, sclera-specific antibodies were determined using indirect immunofluorescence (IIF) on primate retinal/scleral cryosections. Lastly, human leukocyte antigen (HLA) typing was performed in 111 patients with scleritis. Anti-type II collagen antibodies were found in 13% of scleritis patients, in 10% of healthy controls and in 11% of uveitis controls (p = 0.91). A specific reaction to scleral nerve tissue on IIF was observed in 33% of patients with scleritis, which was higher than in healthy controls (11%; p = 0.01), but similar to uveitis controls (25%; p = 0.36). Reactivity to the scleral nerve tissue was significantly associated with earlier onset of scleritis (48 versus 56 years; p < 0.001), bilateral involvement (65% versus 42%; p = 0.01), and less frequent development of scleral necrosis (5% versus 22%; p = 0.02). HLA-B27 was found to be twice as prevalent in patients with scleritis (15.3%) compared to a healthy population (7.2%). In conclusion, scleral nerve autoantibody reactivity was more common in scleritis and uveitis patients in contrast to healthy controls. Further research is needed to characterize these scleral-nerve directed antibodies and assess their clinical value.
Collapse
Affiliation(s)
- Daphne P C Vergouwen
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Adriaan A van Beek
- Department of Immunology, HLA laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Joeri de Hoog
- Department of Ophthalmology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, UMC Utrecht, Utrecht, the Netherlands
| | - Leonoor I Los
- Department of Ophthalmology, UMC Groningen, Groningen, the Netherlands
| | - Marlies Gijs
- University Eye Clinic, Maastricht UMC+, Maastricht, the Netherlands
| | - Roel J Erckens
- University Eye Clinic, Maastricht UMC+, Maastricht, the Netherlands
| | - Rob M Verdijk
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Geert W Haasnoot
- Eurotransplant Reference Laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Dave L Roelen
- Department of Immunology, HLA laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Josianne C Ten Berge
- Department of Ophthalmology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marco W J Schreurs
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| |
Collapse
|
5
|
Liang Z, Guo Y, Sharma A, McCurdy CR, Prentice BM. A multi-modal image fusion workflow incorporating MALDI imaging mass spectrometry and microscopy for the study of small pharmaceutical compounds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584673. [PMID: 38559145 PMCID: PMC10980041 DOI: 10.1101/2024.03.12.584673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Multi-modal imaging analyses of dosed tissue samples can provide more comprehensive insight into the effects of a therapeutically active compound on a target tissue compared to single-modal imaging. For example, simultaneous spatial mapping of pharmaceutical compounds and endogenous macromolecule receptors is difficult to achieve in a single imaging experiment. Herein, we present a multi-modal workflow combining imaging mass spectrometry with immunohistochemistry (IHC) fluorescence imaging and brightfield microscopy imaging. Imaging mass spectrometry enables direct mapping of pharmaceutical compounds and metabolites, IHC fluorescence imaging can visualize large proteins, and brightfield microscopy imaging provides tissue morphology information. Single-cell resolution images are generally difficult to acquire using imaging mass spectrometry, but are readily acquired with IHC fluorescence and brightfield microscopy imaging. Spatial sharpening of mass spectrometry images would thus allow for higher fidelity co-registration with higher resolution microscopy images. Imaging mass spectrometry spatial resolution can be predicted to a finer value via a computational image fusion workflow, which models the relationship between the intensity values in the mass spectrometry image and the features of a high spatial resolution microscopy image. As a proof of concept, our multi-modal workflow was applied to brain tissue extracted from a Sprague Dawley rat dosed with a kratom alkaloid, corynantheidine. Four candidate mathematical models including linear regression, partial least squares regression (PLS), random forest regression, and two-dimensional convolutional neural network (2-D CNN), were tested. The random forest and 2-D CNN models most accurately predicted the intensity values at each pixel as well as the overall patterns of the mass spectrometry images, while also providing the best spatial resolution enhancements. Herein, image fusion enabled predicted mass spectrometry images of corynantheidine, GABA, and glutamine to approximately 2.5 μm spatial resolutions, a significant improvement compared to the original images acquired at 25 μm spatial resolution. The predicted mass spectrometry images were then co-registered with an H&E image and IHC fluorescence image of the μ-opioid receptor to assess co-localization of corynantheidine with brain cells. Our study also provides insight into the different evaluation parameters to consider when utilizing image fusion for biological applications.
Collapse
Affiliation(s)
- Zhongling Liang
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| | - Abhisheak Sharma
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610
| | - Christopher R. McCurdy
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, FL 32611
| |
Collapse
|
6
|
Vergouwen DP, Kolijn PM, de Hoog J, de Boer JH, Los LI, Gijs M, Erckens RJ, de Jong PH, Rothova A, Ten Berge JC, Schreurs MW. Potential Biomarkers for Noninfectious Scleritis Identified by Serum and Tear Fluid Proteomics. OPHTHALMOLOGY SCIENCE 2024; 4:100407. [PMID: 38054106 PMCID: PMC10694766 DOI: 10.1016/j.xops.2023.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 12/07/2023]
Abstract
Purpose Scleritis is an extremely painful and potentially blinding inflammation of the sclera with unknown pathogenesis and unpredictable course. To gain insight in its disease process and identify biomarker candidates, we performed extensive proteomics in serum and tear fluid. Design Prospective multicenter cohort study. Participants A total of 121 patients with noninfectious scleritis (of which 39 active cases), 30 healthy controls, and 23 disease controls (uveitis and rheumatoid arthritis) were enrolled in the Netherlands from 2020 to 2022. Methods Serum, tear fluid of both eyes, and clinical data were gathered. The level of 368 inflammatory proteins was measured using proximity extension assays. Results were validated in an independent cohort of 15 patients with scleritis, and using addressable laser bead immunoassay, or enzyme-linked immunoassays. In addition, we studied an extended panel of matrix metalloproteinases in tear fluid of necrotizing scleritis with addressable laser bead immunoassay. Main Outcome Measures Statistically significant differences in the level of inflammatory proteins between patients with scleritis and control groups. Results Proteomics revealed 18 significantly upregulated or downregulated serum proteins in active scleritis cases compared with all control groups in both the discovery cohort and the validation cohort. The most upregulated protein was nuclear migration protein nudC (NudC; P = 0.0032), a protein involved in neurogenesis. The other significant hits included proteins involved in T-cell activation, apoptosis, epithelial barrier maintenance, and angiogenesis. Our tear fluid analysis showed matrix metalloproteinase 9 (MMP9) to be upregulated in the tear fluid of patients with scleral necrosis. Conclusions The results of our proteomics analysis suggest a role for neurogenesis, T-cell activation, disruption of epithelial barrier, and angiogenesis in the pathogenesis of scleritis, and highlight MMP9 and NudC as biomarkers with potential clinical relevance. Funding Disclosures The authors have no proprietary or commercial interest in any materials discussed in this article.
Collapse
Affiliation(s)
- Daphne P.C. Vergouwen
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - P. Martijn Kolijn
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joeri de Hoog
- Department of Ophthalmology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonoor I. Los
- Department of Ophthalmology, University Medical Center Groningen, Groningen, The Netherlands
| | - Marlies Gijs
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Roel J. Erckens
- University Eye Clinic, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Pascal H.P. de Jong
- Department of Rheumatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aniki Rothova
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Josianne C. Ten Berge
- Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marco W.J. Schreurs
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
7
|
Bouwens E, Vanmaele A, Hoeks SE, Verhagen HJM, Fioole B, Moelker A, ten Raa S, Hussain B, Oliveira-Pinto J, Bastos Gonçalves F, Ijpma AS, Hoefer IE, van Lier F, Akkerhuis KM, Majoor-Krakauer DF, Boersma E, Kardys I. Circulating biomarkers of cardiovascular disease are related to aneurysm volume in abdominal aortic aneurysm. Vasc Med 2023; 28:433-442. [PMID: 37395286 PMCID: PMC10559648 DOI: 10.1177/1358863x231181159] [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] [Indexed: 07/04/2023]
Abstract
BACKGROUND Surveillance programs in abdominal aortic aneurysms (AAA) are mainly based on imaging and leave room for improvement to timely identify patients at risk for AAA growth. Many biomarkers are dysregulated in patients with AAA, which fuels interest in biomarkers as indicators of disease progression. We examined associations of 92 cardiovascular disease (CVD)-related circulating biomarkers with AAA and sac volume. METHODS In a cross-sectional analysis, we separately investigated (1) 110 watchful waiting (WW) patients (undergoing periodic surveillance imaging without planned intervention) and (2) 203 patients after endovascular aneurysm repair (EVAR). The Cardiovascular Panel III (Olink Proteomics AB, Sweden) was used to measure 92 CVD-related circulating biomarkers. We used cluster analyses to investigate protein-based subphenotypes, and linear regression to examine associations of biomarkers with AAA and sac volume on CT scans. RESULTS Cluster analyses revealed two biomarker-based subgroups in both WW and EVAR patients, with higher levels of 76 and 74 proteins, respectively, in one subgroup versus the other. In WW patients, uPA showed a borderline significant association with AAA volume. Adjusting for clinical characteristics, there was a difference of -0.092 (-0.148, -0.036) loge mL in AAA volume per SD uPA. In EVAR patients, after multivariable adjustment, four biomarkers remained significantly associated with sac volume. The mean effects on sac volume per SD difference were: LDLR: -0.128 (-0.212, -0.044), TFPI: 0.139 (0.049, 0.229), TIMP4: 0.110 (0.023, 0.197), IGFBP-2: 0.103 (0.012, 0.194). CONCLUSION LDLR, TFPI, TIMP4, and IGFBP-2 were independently associated with sac volume after EVAR. Subgroups of patients with high levels of the majority of CVD-related biomarkers emphasize the intertwined relationship between AAA and CVD.ClinicalTrials.gov Identifier: NCT03703947.
Collapse
Affiliation(s)
- Elke Bouwens
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Anesthesiology, Erasmus MC, Rotterdam, The Netherlands
| | - Alexander Vanmaele
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Sanne E Hoeks
- Department of Anesthesiology, Erasmus MC, Rotterdam, The Netherlands
| | - Hence JM Verhagen
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Bram Fioole
- Department of Vascular Surgery, Maasstad Hospital, Rotterdam, The Netherlands
| | - Adriaan Moelker
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Sander ten Raa
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Burhan Hussain
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiology, Beatrix Hospital, Gorinchem, The Netherlands
| | - José Oliveira-Pinto
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Angiology and Vascular Surgery, Centro Hospitalar São João, Porto, Portugal
- Department of Surgery and Physiology, Faculty of Medicine of Oporto, Porto, Portugal
| | - Frederico Bastos Gonçalves
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- NOVA Medical School, Universidade NOVA de Lisboa, Lisbon, Portugal
- Department of Angiology and Vascular Surgery, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Arne S Ijpma
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Imo E Hoefer
- Central Diagnostic Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Felix van Lier
- Department of Anesthesiology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Eric Boersma
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| | - Isabella Kardys
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| |
Collapse
|
8
|
Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
Collapse
Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
| |
Collapse
|
9
|
Hok‐A‐Hin YS, Bolsewig K, Ruiters DN, Lleó A, Alcolea D, Lemstra AW, van der Flier WM, Teunissen CE, del Campo M. Thimet oligopeptidase as a potential CSF biomarker for Alzheimer's disease: A cross-platform validation study. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12456. [PMID: 37502019 PMCID: PMC10369371 DOI: 10.1002/dad2.12456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION Our previous antibody-based cerebrospinal fluid (CSF) proteomics study showed that Thimet oligopeptidase (THOP1), an amyloid beta (Aβ) neuropeptidase, was increased in mild cognitive impairment with amyloid pathology (MCI-Aβ+) and Alzheimer's disease (AD) dementia compared with controls and dementia with Lewy bodies (DLB), highlighting the potential of CSF THOP1 as an early specific biomarker for AD. We aimed to develop THOP1 immunoassays for large-scale analysis and validate our proteomics findings in two independent cohorts. METHODS We developed in-house CSF THOP1 immunoassays on automated Ella and Simoa platforms. The performance of the different assays were compared using Passing-Bablok regression analysis in a subset of CSF samples from the discovery cohort (n = 72). Clinical validation was performed in two independent cohorts (cohort 1: n = 200; cohort 2: n = 165) using the Ella platform. RESULTS THOP1 concentrations moderately correlated between proteomics analysis and our novel assays (Rho > 0.580). In both validation cohorts, CSF THOP1 was increased in MCI-Aβ+ (>1.3-fold) and AD (>1.2-fold) compared with controls; and between MCI-Aβ+ and DLB (>1.2-fold). Higher THOP1 concentrations were detected in AD compared with DLB only when both cohorts were analyzed together. In both cohorts, THOP1 correlated with CSF total tau (t-tau), phosphorylated tau (p-tau), and Aβ40 (Rho > 0.540) but not Aβ42. DISCUSSION Validation of our proteomics findings underpins the potential of CSF THOP1 as an early specific biomarker associated with AD pathology. The use of antibody-based platforms in both the discovery and validation phases facilitated the translation of proteomics findings, providing an additional workflow that may accelerate the development of biofluid-based biomarkers.
Collapse
Affiliation(s)
- Yanaika S. Hok‐A‐Hin
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam NeuroscienceVU University Medical Center, Amsterdam UMCAmsterdamThe Netherlands
| | - Katharina Bolsewig
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam NeuroscienceVU University Medical Center, Amsterdam UMCAmsterdamThe Netherlands
| | - Daimy N. Ruiters
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam NeuroscienceVU University Medical Center, Amsterdam UMCAmsterdamThe Netherlands
| | - Alberto Lleó
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau ‐ Hospital de Sant PauUniversitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Daniel Alcolea
- Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau ‐ Hospital de Sant PauUniversitat Autònoma de Barcelona, Hospital de la Santa Creu i Sant PauBarcelonaSpain
| | - Afina W. Lemstra
- Alzheimer Center Amsterdam, Department of NeurologyAmsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMCAmsterdamThe Netherlands
| | - Wiesje M. van der Flier
- Alzheimer Center Amsterdam, Department of NeurologyAmsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMCAmsterdamThe Netherlands
- Department of Epidemiology and Data ScienceVU University Medical CentersAmsterdamThe Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam NeuroscienceVU University Medical Center, Amsterdam UMCAmsterdamThe Netherlands
| | - Marta del Campo
- Neurochemistry Laboratory, Department of Laboratory Medicine, Amsterdam NeuroscienceVU University Medical Center, Amsterdam UMCAmsterdamThe Netherlands
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
- Bareclonaβeta Brain Research Center (BBRC)Pasqual Maragall FoundationBarcelonaSpain
| |
Collapse
|
10
|
Thijssen CGE, Dekker S, Bons LR, Geenen LW, Gökalp AL, Takkenberg JJM, Mokhles MM, Bekkers JA, Boersma E, Bouwens E, van Kimmenade RRJ, Roos-Hesselink JW. Novel biomarkers associated with thoracic aortic disease. Int J Cardiol 2023; 378:115-122. [PMID: 36796491 DOI: 10.1016/j.ijcard.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Biomarkers might help to improve diagnosis, surveillance and risk stratification of thoracic aortic disease (TAD). We explored the association between a broad spectrum of cardiovascular biomarkers with clinical characteristics and thoracic aortic diameter in TAD patients. METHODS Venous blood-samples were obtained in 158 clinically stable TAD patients visiting our outpatient clinic (2017-2020). TAD was defined as a thoracic aortic diameter ≥ 40 mm, or genetic confirmation (hereditary TAD). The cardiovascular panel III of the Olink multiplex platform was used for batch analysis of 92 proteins. A comparison was made between biomarker levels in patients with and without previous aortic dissection and/or surgery, and with and without hereditary TAD. Linear regression analyses were applied to identify (relative, normalized) biomarker concentrations associated with the absolute thoracic aortic diameter (ADmax), and thoracic aortic diameter indexed for body surface area (IDmax). RESULTS Median age of study patients was 61.0 (IQR 50.3-68.8) years, 37.3% females. Mean ADmax and IDmax were 43.3 ± 5.4 mm and 21.3 ± 3.3 mm/m2. After multivariable adjustment, Matrix Metalloproteinase-3 (MMP-3) and Insulin-like growth factor binding protein 2 (IGFBP-2) showed a significant positive association with ADmax and IDmax, respectively. Patients with previous aortic surgery/dissection had higher N-terminal-pro hormone BNP (NTproBNP) (median 3.67 [IQR 3.01-3.99] vs 2.84 [2.32-3.26], p ≤0.001). Patients with hereditary TAD had higher Trem-like transcript protein 2 (TLT-2) (median 4.64 [IQR 4.45-4.84]) than those with non-heriditary TAD (4.40 [4.17-4.64]; p = 0.00042). CONCLUSIONS Among a broad range of biomarkers, MMP-3 and IGFBP-2 were associated with disease severity in TAD patients. The pathophysiological pathways uncovered by these biomarkers, and their potential clinical use warrants further research.
Collapse
Affiliation(s)
- Carlijn G E Thijssen
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands; Department of Cardiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Silvy Dekker
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Lidia R Bons
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Laurie W Geenen
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Arjen L Gökalp
- Department of Cardiothoracic Surgery, Erasmus MC, Rotterdam, the Netherlands
| | | | - Mostafa M Mokhles
- Department of Cardiothoracic Surgery, Erasmus MC, Rotterdam, the Netherlands; Department of Cardiothoracic Surgery, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jos A Bekkers
- Department of Cardiothoracic Surgery, Erasmus MC, Rotterdam, the Netherlands
| | - Eric Boersma
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands
| | - Elke Bouwens
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands; Department of Anesthesiology, Erasmus MC, Rotterdam, the Netherlands
| | - Roland R J van Kimmenade
- Department of Cardiology, Erasmus MC, Rotterdam, the Netherlands; Department of Cardiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | |
Collapse
|
11
|
Romano A, Rižner TL, Werner HMJ, Semczuk A, Lowy C, Schröder C, Griesbeck A, Adamski J, Fishman D, Tokarz J. Endometrial cancer diagnostic and prognostic algorithms based on proteomics, metabolomics, and clinical data: a systematic review. Front Oncol 2023; 13:1120178. [PMID: 37091170 PMCID: PMC10118013 DOI: 10.3389/fonc.2023.1120178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/09/2023] Open
Abstract
Endometrial cancer is the most common gynaecological malignancy in developed countries. Over 382,000 new cases were diagnosed worldwide in 2018, and its incidence and mortality are constantly rising due to longer life expectancy and life style factors including obesity. Two major improvements are needed in the management of patients with endometrial cancer, i.e., the development of non/minimally invasive tools for diagnostics and prognostics, which are currently missing. Diagnostic tools are needed to manage the increasing number of women at risk of developing the disease. Prognostic tools are necessary to stratify patients according to their risk of recurrence pre-preoperatively, to advise and plan the most appropriate treatment and avoid over/under-treatment. Biomarkers derived from proteomics and metabolomics, especially when derived from non/minimally-invasively collected body fluids, can serve to develop such prognostic and diagnostic tools, and the purpose of the present review is to explore the current research in this topic. We first provide a brief description of the technologies, the computational pipelines for data analyses and then we provide a systematic review of all published studies using proteomics and/or metabolomics for diagnostic and prognostic biomarker discovery in endometrial cancer. Finally, conclusions and recommendations for future studies are also given.
Collapse
Affiliation(s)
- Andrea Romano
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Tea Lanišnik Rižner
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Henrica Maria Johanna Werner
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Andrzej Semczuk
- Department of Gynaecology, Lublin Medical University, Lublin, Poland
| | | | | | | | - Jerzy Adamski
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dmytro Fishman
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Janina Tokarz
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| |
Collapse
|
12
|
de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
Collapse
|
13
|
Using Artificial Intelligence to Better Predict and Develop Biomarkers. Clin Lab Med 2023; 43:99-114. [PMID: 36764811 DOI: 10.1016/j.cll.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Advancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.
Collapse
|
14
|
Skau E, Wagner P, Leppert J, Ärnlöv J, Hedberg P. Are the results from a multiplex proteomic assay and a conventional immunoassay for NT-proBNP and GDF-15 comparable? Clin Proteomics 2023; 20:5. [PMID: 36694116 PMCID: PMC9872369 DOI: 10.1186/s12014-023-09393-1] [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: 06/08/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND We aimed to compare absolute plasma concentrations of N-terminal pro-brain natriuretic peptide (NT-proBNP) and growth differentiation factor 15 (GDF-15) obtained by a conventional immunoassay with the corresponding relative concentrations from a proximity extension assay (PEA) and compare the prognostic impact of the protein levels obtained from these assays. METHODS We evaluated 437 patients with peripheral arterial disease (PAD) and a population-based cohort of 643 individuals without PAD. Correlations were calculated using Spearman's rank correlation coefficients (rho). The discriminatory accuracy of the protein levels to predict future cardiovascular events was analyzed with Cox regression and presented as time-dependent areas under the receiver-operator-characteristic curves (tdAUCs). RESULTS For NT-proBNP, the two assays correlated with rho 0.93 and 0.93 in the respective cohort. The PEA values leveled off at higher values in both cohorts. The corresponding correlations for GDF-15 were 0.91 and 0.89. At 5 years follow-up, the tdAUCs in the patient cohort were similar for NT-proBNP and GDF-15 regardless of assay used (0.65-0.66). The corresponding tdAUCs in the population-based cohort were between 0.72 and 0.77. CONCLUSION Except for the highest levels of NT-proBNP, we suggest that PEA data for NT-proBNP and GDF-15 reliably reflects absolute plasma levels and contains similar prognostic information.
Collapse
Affiliation(s)
- Emma Skau
- grid.8993.b0000 0004 1936 9457Centre for Clinical Research, Västmanland County Hospital, Uppsala University, SE-72 189 Västerås, Sweden ,grid.412154.70000 0004 0636 5158Department of Cardiology, Danderyd University Hospital, Stockholm, Sweden
| | - Philippe Wagner
- grid.8993.b0000 0004 1936 9457Centre for Clinical Research, Västmanland County Hospital, Uppsala University, SE-72 189 Västerås, Sweden
| | - Jerzy Leppert
- grid.8993.b0000 0004 1936 9457Centre for Clinical Research, Västmanland County Hospital, Uppsala University, SE-72 189 Västerås, Sweden
| | - Johan Ärnlöv
- grid.411953.b0000 0001 0304 6002School of Health and Social Studies, Dalarna University, Falun, Sweden ,grid.4714.60000 0004 1937 0626Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, Huddinge, Sweden
| | - Pär Hedberg
- grid.8993.b0000 0004 1936 9457Centre for Clinical Research, Västmanland County Hospital, Uppsala University, SE-72 189 Västerås, Sweden ,Department of Clinical Physiology, Västmanland County Hospital, Västerås, Sweden
| |
Collapse
|
15
|
Rusevski A, Plaseska-Karanfilska D, Davalieva K. Proteomics of azoospermia: Towards the discovery of reliable markers for non-invasive diagnosis. Proteomics Clin Appl 2023; 17:e2200060. [PMID: 36177695 DOI: 10.1002/prca.202200060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 01/28/2023]
Abstract
PURPOSE Azoospermia, as the most severe form of male infertility, no longer indicates sterility due to modern medical advancements. The current diagnostic procedure based on testicular biopsy has several drawbacks which urges the development of novel, non-invasive diagnostic procedures based on biomarkers. In the last two decades, there have been many proteomics studies investigating potential azoospermia biomarkers. In this review, we aimed to provide a critical evaluation of these studies. EXPERIMENTAL DESIGN Published articles were gathered by systematic literature search using Pubmed, Science Direct, and Google Scholar databases until March 2022 and were further preselected to include only studies on human samples. RESULTS A detailed review of these studies encompassed the proteomics platforms, sources of material, proposed candidate biomarkers, and their potential diagnostic specificity and sensitivity. In addition, emphasis was put on the top, most identified and validated biomarker candidates and their potential for discriminating azoospermia types and subtypes as well as predicting sperm retrieval success rate. CONCLUSIONS Proteomics research of azoospermia has laid the groundwork for the development of a more streamlined biomarker testing. The future research should be focused on well-designed studies including samples from all types/subtypes as well as further testing of the most promising biomarkers identified so far.
Collapse
Affiliation(s)
- Aleksandar Rusevski
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| |
Collapse
|
16
|
Proteomic investigations of acute ischemic stroke in animal models: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
17
|
Waury K, Willemse EAJ, Vanmechelen E, Zetterberg H, Teunissen CE, Abeln S. Bioinformatics tools and data resources for assay development of fluid protein biomarkers. Biomark Res 2022; 10:83. [DOI: 10.1186/s40364-022-00425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractFluid protein biomarkers are important tools in clinical research and health care to support diagnosis and to monitor patients. Especially within the field of dementia, novel biomarkers could address the current challenges of providing an early diagnosis and of selecting trial participants. While the great potential of fluid biomarkers is recognized, their implementation in routine clinical use has been slow. One major obstacle is the often unsuccessful translation of biomarker candidates from explorative high-throughput techniques to sensitive antibody-based immunoassays. In this review, we propose the incorporation of bioinformatics into the workflow of novel immunoassay development to overcome this bottleneck and thus facilitate the development of novel biomarkers towards clinical laboratory practice. Due to the rapid progress within the field of bioinformatics many freely available and easy-to-use tools and data resources exist which can aid the researcher at various stages. Current prediction methods and databases can support the selection of suitable biomarker candidates, as well as the choice of appropriate commercial affinity reagents. Additionally, we examine methods that can determine or predict the epitope - an antibody’s binding region on its antigen - and can help to make an informed choice on the immunogenic peptide used for novel antibody production. Selected use cases for biomarker candidates help illustrate the application and interpretation of the introduced tools.
Collapse
|
18
|
Kamali H, Golmohammadzadeh S, Zare H, Nosrati R, Fereidouni M, Safarpour H. The recent advancements in the early detection of cancer biomarkers by DNAzyme-assisted aptasensors. J Nanobiotechnology 2022; 20:438. [PMID: 36195928 PMCID: PMC9531510 DOI: 10.1186/s12951-022-01640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Clinical diagnostics rely heavily on the detection and quantification of cancer biomarkers. The rapid detection of cancer-specific biomarkers is of great importance in the early diagnosis of cancers and plays a crucial role in the subsequent treatments. There are several different detection techniques available today for detecting cancer biomarkers. Because of target-related conformational alterations, high stability, and target variety, aptamers have received considerable interest as a biosensing system component. To date, several sensitivity-enhancement strategies have been used with a broad spectrum of nanomaterials and nanoparticles (NPs) to improve the limit and sensitivity of analyte detection in the construction of innovative aptasensors. The present article aims to outline the research developments on the potential of DNAzymes-based aptasensors for cancer biomarker detection.
Collapse
Affiliation(s)
- Hossein Kamali
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shiva Golmohammadzadeh
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmaceutics, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Zare
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Fereidouni
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| |
Collapse
|
19
|
Cummins TD, Korte EA, Bhayana S, Merchant ML, Barati MT, Smoyer WE, Klein JB. Advances in proteomic profiling of pediatric kidney diseases. Pediatr Nephrol 2022; 37:2255-2265. [PMID: 35220505 PMCID: PMC9398920 DOI: 10.1007/s00467-022-05497-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/22/2023]
Abstract
Chronic kidney disease (CKD) can progress to kidney failure and require dialysis or transplantation, while early diagnosis can alter the course of disease and lead to better outcomes in both pediatric and adult patients. Significant CKD comorbidities include the manifestation of cardiovascular disease, heart failure, coronary disease, and hypertension. The pathogenesis of chronic kidney diseases can present as subtle and especially difficult to distinguish between different glomerular pathologies. Early detection of adult and pediatric CKD and detailed mechanistic understanding of the kidney damage can be helpful in delaying or curtailing disease progression via precise intervention toward diagnosis and prognosis. Clinically, serum creatinine and albumin levels can be indicative of CKD, but often are a lagging indicator only significantly affected once kidney function has severely diminished. The evolution of proteomics and mass spectrometry technologies has begun to provide a powerful research tool in defining these mechanisms and identifying novel biomarkers of CKD. Many of the same challenges and advances in proteomics apply to adult and pediatric patient populations. Additionally, proteomic analysis of adult CKD patients can be transferred directly toward advancing our knowledge of pediatric CKD as well. In this review, we highlight applications of proteomics that have yielded such biomarkers as PLA2R, SEMA3B, and other markers of membranous nephropathy as well as KIM-1, MCP-1, and NGAL in lupus nephritis among other potential diagnostic and prognostic markers. The potential for improving the clinical toolkit toward better treatment of pediatric kidney diseases is significantly aided by current and future development of proteomic applications.
Collapse
Affiliation(s)
- Timothy D Cummins
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA.
| | - Erik A Korte
- Bluewater Diagnostics, Mount Washington, KY, USA
| | - Sagar Bhayana
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Michael L Merchant
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
| | - Michelle T Barati
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
| | - William E Smoyer
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA
| | - Jon B Klein
- Division of Nephrology and Hypertension, Clinical Proteomics Center, University of Louisville School of Medicine, 570 S. Preston St, Louisville, KY, 40202, USA
| |
Collapse
|
20
|
Sugai H, Tomita S, Ishihara S, Shiraki K, Kurita R. Damage-free evaluation of cultured cells based on multivariate analysis with a single-polymer probe. Chem Commun (Camb) 2022; 58:11083-11086. [PMID: 36124543 DOI: 10.1039/d2cc03308a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a pattern-recognition-based sensor that targets cell-derived components in culture media and evaluates cultured cells without damaging them. An array sensor made of a single-polymer probe was employed to obtain fluorescence response patterns of the analyte media, allowing successful identification of the type and state of the cells via multivariate analysis.
Collapse
Affiliation(s)
- Hiroka Sugai
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan. .,Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Sayaka Ishihara
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan.
| | - Ryoji Kurita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan. .,Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| |
Collapse
|
21
|
Veettil TCP, Wood BR. A Combined Near-Infrared and Mid-Infrared Spectroscopic Approach for the Detection and Quantification of Glycine in Human Serum. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22124528. [PMID: 35746311 PMCID: PMC9228712 DOI: 10.3390/s22124528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 05/16/2023]
Abstract
Serum is an important candidate in proteomics analysis as it potentially carries key markers on health status and disease progression. However, several important diagnostic markers found in the circulatory proteome and the low-molecular-weight (LMW) peptidome have become analytically challenging due to the high dynamic concentration range of the constituent protein/peptide species in serum. Herein, we propose a novel approach to improve the limit of detection (LoD) of LMW amino acids by combining mid-IR (MIR) and near-IR spectroscopic data using glycine as a model LMW analyte. This is the first example of near-IR spectroscopy applied to elucidate the detection limit of LMW components in serum; moreover, it is the first study of its kind to combine mid-infrared (25-2.5 μm) and near-infrared (2500-800 nm) to detect an analyte in serum. First, we evaluated the prediction model performance individually with MIR (ATR-FTIR) and NIR spectroscopic methods using partial least squares regression (PLS-R) analysis. The LoD was found to be 0.26 mg/mL with ATR spectroscopy and 0.22 mg/mL with NIR spectroscopy. Secondly, we examined the ability of combined spectral regions to enhance the detection limit of serum-based LMW amino acids. Supervised extended wavelength PLS-R resulted in a root mean square error of prediction (RMSEP) value of 0.303 mg/mL and R2 value of 0.999 over a concentration range of 0-50 mg/mL for glycine spiked in whole serum. The LoD improved to 0.17 mg/mL from 0.26 mg/mL. Thus, the combination of NIR and mid-IR spectroscopy can improve the limit of detection for an LMW compound in a complex serum matrix.
Collapse
Affiliation(s)
- Thulya Chakkumpulakkal Puthan Veettil
- Centre for Biospectroscopy, Monash University, Clayton, VIC 3800, Australia;
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath BA2 7AY, UK
| | - Bayden R. Wood
- Centre for Biospectroscopy, Monash University, Clayton, VIC 3800, Australia;
- Correspondence:
| |
Collapse
|
22
|
Schrijver B, Kolijn PM, Berge JC, Nagtzaam NM, Rijswijk AL, Swagemakers SM, Spek PJ, Missotten TO, Velthoven ME, Hoog J, Hagen PM, Langerak AW, Dik WA. Vitreous proteomics, a gateway to improved understanding and stratification of diverse uveitis aetiologies. Acta Ophthalmol 2022; 100:403-413. [PMID: 34318583 PMCID: PMC9292680 DOI: 10.1111/aos.14993] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE The vitreous proteome might provide an attractive gateway to discriminate between various uveitis aetiologies and gain novel insights into the underlying pathophysiological processes. Here, we investigated 180 vitreous proteins to discover novel biomarkers and broaden disease insights by comparing (1). primary vitreoretinal lymphoma ((P)VRL) versus other aetiologies, (2). sarcoid uveitis versus tuberculosis (TB)-associated uveitis and (3). granulomatous (sarcoid and TB) uveitis versus other aetiologies. METHODS Vitreous protein levels were determined by proximity extension assay in 47 patients with intraocular inflammation and a prestudy diagnosis (cohort 1; training) and 22 patients with a blinded diagnosis (cohort 2; validation). Differentially expressed proteins identified by t-tests on cohort 1 were used to calculate Youden's indices. Pathway and network analysis was performed by ingenuity pathway analysis. A random forest classifier was trained to predict the diagnosis of blinded patients. RESULTS For (P)VRL stratification, the previously reported combined diagnostic value of IL-10 and IL-6 was confirmed. Additionally, CD70 was identified as potential novel marker for (P)VRL. However, the classifier trained on the entire cohort (cohort 1 and 2) relied primarily on the interleukin score for intraocular lymphoma diagnosis (ISOLD) or IL-10/IL-6 ratio and only showed a supportive role for CD70. Furthermore, sarcoid uveitis displayed increased levels of vitreous CCL17 as compared to TB-associated uveitis. CONCLUSION We underline the previously reported value of the ISOLD and the IL-10/IL-6 ratio for (P)VRL identification and present CD70 as a potentially valuable target for (P)VRL stratification. Finally, we also show that increased CCL17 levels might help to distinguish sarcoid uveitis from TB-associated uveitis.
Collapse
Affiliation(s)
- Benjamin Schrijver
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - P. Martijn Kolijn
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Josianne C.E.M. Berge
- Department of Ophthalmology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Nicole M.A. Nagtzaam
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Angelique L.C.T. Rijswijk
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Sigrid M.A. Swagemakers
- Department of Bioinformatics Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Peter J. Spek
- Department of Bioinformatics Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | | | | | - Joeri Hoog
- Department of Ophthalmology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - P. Martin Hagen
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
- Department of Internal Medicine Section Clinical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Anton W. Langerak
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| | - Willem A. Dik
- Department of Immunology Laboratory Medical Immunology Erasmus MC University Medical Center Rotterdam Rotterdam the Netherlands
| |
Collapse
|
23
|
Kazemi Y, Dehghani S, Nosrati R, Taghdisi SM, Abnous K, Alibolandi M, Ramezani M. Recent progress in the early detection of cancer based on CD44 biomarker; nano-biosensing approaches. Life Sci 2022; 300:120593. [PMID: 35500679 DOI: 10.1016/j.lfs.2022.120593] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/06/2023]
Abstract
CD44 is a cell matrix adhesion molecule overexpressed on the cell surfaces of the major cancers. CD44 as a cancer-related biomarker has an essential role in the invasion and metastasis of cancer. The detection and quantification of CD44 can provide essential information useful for clinical cancer diagnosis. In this regard, biosensors with sensitive and specific properties, give prominence to the development of CD44 detection platforms. To date, various aptamer-based sensitive-enhancers together with nanoparticles (NPs) have been combined into the biosensors systems to provide an innovative biosensing method (aptasensors/nano-aptasensors) with substantially improved detection limit. This review article discusses the recent advances in the field of biosensors, nanobiosensors, and aptasensors for the quantitative determination of CD44 and the detection of CD44-expressing cancer cells.
Collapse
Affiliation(s)
- Youkabed Kazemi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sadegh Dehghani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
24
|
|
25
|
Chen D, Zhang X, Zhu L, Liu C, Li Z. All on size-coded single bead set: a modular enrich-amplify-amplify strategy for attomolar level multi-immunoassay. Chem Sci 2022; 13:3501-3506. [PMID: 35432875 PMCID: PMC8943839 DOI: 10.1039/d1sc07048g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/17/2022] [Indexed: 12/04/2022] Open
Abstract
Ultrasensitive protein analysis is of great significance for early diagnosis and biological studies. The core challenge is that many critical protein markers at extremely low aM to fM levels are difficult to accurately quantify because the target-induced weak signal may be easily masked by the surrounding background. Hence, we propose herein an ultrasensitive immunoassay based on a modular Single Bead Enrich-Amplify-Amplify (SBEAA) strategy. The highly efficient enrichment of targets on only a single bead (enrich) could confine the target-responsive signal output within a limited tiny space. Furthermore, a cascade tyramide signal amplification design enables remarkable in situ signal enhancement just affixed to the target. As a result, the efficient but space-confined fluorescence deposition on a single bead will significantly exceed the background and provide a wide dynamic range. Importantly, the SBEAA system can be modularly combined to meet different levels of clinical need regarding the detection sensitivity from aM to nM. Finally, a size-coded SBEAA set (SC-SBEAA) is also designed that allows ultrasensitive multi-immunoassay for rare samples in a single tube.
Collapse
Affiliation(s)
- Desheng Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 Shaanxi Province P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
| | - Xiaobo Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 Shaanxi Province P. R. China
| | - Liping Zhu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 Shaanxi Province P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 Shaanxi Province P. R. China
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University Xi'an 710119 Shaanxi Province P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
| |
Collapse
|
26
|
Adam T, Gopinath SC. Nanosensors: Recent Perspectives on Attainments and Future Promise of Downstream Applications. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
27
|
Michelhaugh SA, Januzzi JL. Using Artificial Intelligence to Better Predict and Develop Biomarkers. Heart Fail Clin 2022; 18:275-285. [PMID: 35341540 DOI: 10.1016/j.hfc.2021.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.
Collapse
|
28
|
Multi-Omics Characterization of a Human Stem Cell-Based Model of Cardiac Hypertrophy. Life (Basel) 2022; 12:life12020293. [PMID: 35207580 PMCID: PMC8875317 DOI: 10.3390/life12020293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 12/13/2022] Open
Abstract
Cardiac hypertrophy is an important and independent risk factor for the development of cardiac myopathy that may lead to heart failure. The mechanisms underlying the development of cardiac hypertrophy are yet not well understood. To increase the knowledge about mechanisms and regulatory pathways involved in the progression of cardiac hypertrophy, we have developed a human induced pluripotent stem cell (hiPSC)-based in vitro model of cardiac hypertrophy and performed extensive characterization using a multi-omics approach. In a series of experiments, hiPSC-derived cardiomyocytes were stimulated with Endothelin-1 for 8, 24, 48, and 72 h, and their transcriptome and secreted proteome were analyzed. The transcriptomic data show many enriched canonical pathways related to cardiac hypertrophy already at the earliest time point, e.g., cardiac hypertrophy signaling. An integrated transcriptome–secretome analysis enabled the identification of multimodal biomarkers that may prove highly relevant for monitoring early cardiac hypertrophy progression. Taken together, the results from this study demonstrate that our in vitro model displays a hypertrophic response on both transcriptomic- and secreted-proteomic levels. The results also shed novel insights into the underlying mechanisms of cardiac hypertrophy, and novel putative early cardiac hypertrophy biomarkers have been identified that warrant further investigation to assess their potential clinical relevance.
Collapse
|
29
|
Ebihara T, Matsumoto H, Matsubara T, Togami Y, Nakao S, Matsuura H, Kojima T, Sugihara F, Okuzaki D, Hirata H, Yamamura H, Ogura H. Cytokine Elevation in Severe COVID-19 From Longitudinal Proteomics Analysis: Comparison With Sepsis. Front Immunol 2022; 12:798338. [PMID: 35095877 PMCID: PMC8790049 DOI: 10.3389/fimmu.2021.798338] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/21/2021] [Indexed: 12/29/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) is a new viral disease. Uncontrolled inflammation called “cytokine storm” is reported to contribute to disease pathogenesis as well as sepsis. We aimed to identify cytokines related to the pathogenesis of COVID-19 through a proteomics analysis of 1463 plasma proteins, validate these cytokines, and compare them with sepsis. Materials and Methods In a derivation cohort of 306 patients with COVID-19, 1463 unique plasma proteins were measured on days 1, 4, and 8. Cytokines associated with disease severity and prognosis were derived. In a validation cohort of 62 COVID-19 patients and 38 sepsis patients treated in the intensive care unit [ICU], these derived cytokines were measured on days 1 (day of ICU admission), 2-3, and 6-8 (maximum: 3 time points/patient). Derived cytokines were compared with healthy controls and between COVID-19 and sepsis patients, and the associations with prognosis were evaluated. The time to wean off mechanical ventilation (MV) was evaluated only for COVID-19. Results IL-6, amphiregulin, and growth differentiation factor (GDF)-15 were associated with disease severity and prognosis in the derivation cohort. In the validation cohort, IL-6 and GDF-15 were elevated in COVID-19 and sepsis on day 1, and the levels of these cytokines were higher in sepsis than in COVID-19. IL-6 and GDF-15 were associated with prognosis in sepsis. Cox proportional hazards model with time as a dependent covariate showed a significant relationship between plasma GDF-15 level and time to wean off MV (hazard ratio, 0.549 [95% confidence level, 0.382–0.789]). The GDF-15 level at ICU admission predicted late recovery. Conclusion GDF-15 and IL-6 derived from proteomics analysis were related with disease severity of COVID-19. Their values were higher in sepsis than in COVID-19 and were associated with prognosis in sepsis. In COVID-19 patients treated in the ICU, GDF-15 was associated with the time to wean off MV and better predicted late recovery.
Collapse
Affiliation(s)
- Takeshi Ebihara
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tsunehiro Matsubara
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shunichiro Nakao
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hiroshi Matsuura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Osaka Prefectural Nakakawachi Emergency and Critical Care Center, Higashiosaka, Japan
| | - Takashi Kojima
- Laboratory for Clinical Investigation, Osaka University Hospital, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hitoshi Yamamura
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, Higashiosaka, Japan
| | - Hiroshi Ogura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| |
Collapse
|
30
|
Roy AL, Wilder EL, Anderson JM. Validation of antibodies: Lessons learned from the Common Fund Protein Capture Reagents Program. SCIENCE ADVANCES 2021; 7:eabl7148. [PMID: 34757791 PMCID: PMC8580312 DOI: 10.1126/sciadv.abl7148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Large-scale generation of protein capture reagents remains a technical challenge, but their generation is just the beginning. Validation is a critical, iterative process that yields different results for different uses. Independent, community-based validation offers the possibility of transparent data sharing, with use case–specific results made broadly available. This type of resource, which can grow as new validation data are obtained for an expanding group of reagents, provides a community resource that should accompany future reagent-generating efforts. To address a pressing need for antibodies or other reagents that recognize human proteins, the National Institutes of Health Common Fund launched the Protein Capture Reagents Program in 2010 as a pilot to target human transcription factors. Here, we describe lessons learned from this program concerning generation and validation of research reagents, which we believe are generally applicable for future research endeavors working in a similar space.
Collapse
Affiliation(s)
- Ananda L. Roy
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA
- Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth L. Wilder
- Office of Strategic Coordination, National Institutes of Health, Bethesda, MD 20892, USA
- Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| | - James M. Anderson
- Division of Program Coordination, Planning and Strategic Initiatives, Office of the Director, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
31
|
Xiao Q, Zhang F, Xu L, Yue L, Kon OL, Zhu Y, Guo T. High-throughput proteomics and AI for cancer biomarker discovery. Adv Drug Deliv Rev 2021; 176:113844. [PMID: 34182017 DOI: 10.1016/j.addr.2021.113844] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023]
Abstract
Biomarkers are assayed to assess biological and pathological status. Recent advances in high-throughput proteomic technology provide opportunities for developing next generation biomarkers for clinical practice aided by artificial intelligence (AI) based techniques. We summarize the advances and limitations of cancer biomarkers based on genomic and transcriptomic analysis, as well as classical antibody-based methodologies. Then we review recent progresses in mass spectrometry (MS)-based proteomics in terms of sample preparation, peptide fractionation by liquid chromatography (LC) and mass spectrometric data acquisition. We highlight applications of AI techniques in high-throughput clinical studies as compared with clinical decisions based on singular features. This review sets out our approach for discovering clinical biomarkers in studies using proteomic big data technology conjoined with computational and statistical methods.
Collapse
|
32
|
Ősz Á, Lánczky A, Győrffy B. Survival analysis in breast cancer using proteomic data from four independent datasets. Sci Rep 2021; 11:16787. [PMID: 34408238 PMCID: PMC8373859 DOI: 10.1038/s41598-021-96340-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/28/2021] [Indexed: 11/18/2022] Open
Abstract
Breast cancer clinical treatment selection is based on the immunohistochemical determination of four protein biomarkers: ESR1, PGR, HER2, and MKI67. Our aim was to correlate immunohistochemical results to proteome-level technologies in measuring the expression of these markers. We also aimed to integrate available proteome-level breast cancer datasets to identify and validate new prognostic biomarker candidates. We searched studies involving breast cancer patient cohorts with published survival and proteomic information. Immunohistochemistry and proteomic technologies were compared using the Mann-Whitney test. Receiver operating characteristics (ROC) curves were generated to validate discriminative power. Cox regression and Kaplan-Meier survival analysis were calculated to assess prognostic power. False Discovery Rate was computed to correct for multiple hypothesis testing. We established a database integrating protein expression data and survival information from four independent cohorts for 1229 breast cancer patients. In all four studies combined, a total of 7342 unique proteins were identified, and 1417 of these were identified in at least three datasets. ESR1, PGR, and HER2 protein expression levels determined by RPPA or LC-MS/MS methods showed a significant correlation with the levels determined by immunohistochemistry (p < 0.0001). PGR and ESR1 levels showed a moderate correlation (correlation coefficient = 0.17, p = 0.0399). An additional panel of candidate proteins, including apoptosis-related proteins (BCL2,), adhesion markers (CDH1, CLDN3, CLDN7) and basal markers (cytokeratins), were validated as prognostic biomarkers. Finally, we expanded our previously established web tool designed to validate survival-associated biomarkers by including the proteomic datasets analyzed in this study ( https://kmplot.com/ ). In summary, large proteomic studies now provide sufficient data enabling the validation and ranking of potential protein biomarkers.
Collapse
Affiliation(s)
- Ágnes Ősz
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary
| | - András Lánczky
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7-9, 1094, Budapest, Hungary.
- TTK Momentum Cancer Biomarker Research Group, Institute of Enzymology, 1117, Budapest, Hungary.
- 2nd Department of Pediatrics, Semmelweis University, 1094, Budapest, Hungary.
| |
Collapse
|
33
|
Okada H, Mimura M, Tomita S, Kurita R. Affinity Diversification of a Polymer Probe for Pattern-recognition-based Biosensing Using Chemical Additives. ANAL SCI 2021; 37:713-719. [PMID: 33518589 DOI: 10.2116/analsci.20scp23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pattern-recognition-based sensing has attracted attention as a promising alternative to conventional sensing methods that rely on selective recognition. Here, we report on novel strategy using chemical additives with the ability to modulate probe/analyte interactions to more easily construct pattern-recognition-based sensing systems for proteins and cells. The fluorescence of dansyl-modified cationic poly-L-lysine (PLL-Dnc) is enhanced upon binding to proteins in aqueous solution, while the addition of salts, inert polymers, or alcohols modulates the protein/PLL-Dnc interactions via a variety of mechanisms. Subsequent readout of the fluorescence changes produces response patterns that reflect the characteristics of the analytes. Multivariate analysis of the response patterns allowed for accurate identification of not only eight structurally similar albumin homologues, but also four mammalian cells. This strategy, which uses inexpensive and common additives, significantly improves the accessibility of pattern-recognition-based sensing, which will offer new opportunities for the detection of various bioanalytes.
Collapse
Affiliation(s)
- Hiroki Okada
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology.,Faculty of Pure and Applied Sciences, University of Tsukuba
| | - Masahiro Mimura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology.,Faculty of Pure and Applied Sciences, University of Tsukuba
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology
| | - Ryoji Kurita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology.,Faculty of Pure and Applied Sciences, University of Tsukuba.,DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology
| |
Collapse
|
34
|
Bouwens E, Schuurman AS, Akkerhuis KM, Manintveld OC, Caliskan K, van Ramshorst J, Germans T, Umans VA, Boersma E, Kardys I. Associations of serially measured PCSK9, LDLR and MPO with clinical outcomes in heart failure. Biomark Med 2021; 15:247-255. [PMID: 33590771 DOI: 10.2217/bmm-2020-0585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate the temporal evolution of plasma proprotein convertase subtilisin/kexin type 9 (PCSK9), low-density lipoprotein receptor (LDLR) and myeloperoxidase (MPO) in relation to clinical outcome in chronic heart failure (CHF). Methodology & results: Trimonthly blood sampling was performed during a median follow-up of 2.2 (IQR 1.4-2.5) years in 263 CHF patients. Seventy patients reached the primary end point (PE) (cardiovascular death, heart transplantation, left ventricular assist device implantation or HF-hospitalization). MPO level was independently associated with the PE; the adjusted (for clinical factors) hazard ratio (aHR) per standard deviation difference in MPO was 1.71 (95% CI: 1.23-2.43) at any time during follow-up. PCSK9 level (HR: 1.45 [1.04-2.06]) and LDLR (HR: 0.66 [0.49-0.87]) were statistical significantly associated with the PE but only in unadjusted analyses. Slope of temporal MPO evolution (aHR: 1.34 [1.12-1.76] per 0.1 standard deviation/year difference in slope) and LDLR (aHR: 0.78 [0.61-0.90]) however, were associated with PE. Conclusion: Temporal patterns of MPO and LDLR are independently associated with clinical outcome in CHF, which illustrates the importance of assessing temporal evolutions. Clinical trial registration information: registered in ClinicalTrials.gov, number NCT01851538. https://clinicaltrials.gov/ct2/show/NCT01851538.
Collapse
Affiliation(s)
- Elke Bouwens
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | - Kadir Caliskan
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| | - Jan van Ramshorst
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Tjeerd Germans
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Victor Awm Umans
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Eric Boersma
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| | - Isabella Kardys
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands
| |
Collapse
|
35
|
Sonnenschein K, Fiedler J, de Gonzalo-Calvo D, Xiao K, Pfanne A, Just A, Zwadlo C, Soltani S, Bavendiek U, Kraft T, Dos Remedios C, Cebotari S, Bauersachs J, Thum T. Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy. Sci Rep 2021; 11:1755. [PMID: 33469076 PMCID: PMC7815737 DOI: 10.1038/s41598-020-80868-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/28/2020] [Indexed: 01/02/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is one of the most common hereditary heart diseases and can be classified into an obstructive (HOCM) and non-obstructive (HNCM) form. Major characteristics for HCM are the hypertrophy of cardiomyocytes and development of cardiac fibrosis. Patients with HCM have a higher risk for sudden cardiac death compared to a healthy population. In the present study, we investigated the abundancy of selected proteins as potential biomarkers in patients with HCM. We included 60 patients with HCM and 28 healthy controls and quantitatively measured the rate of a set of 92 proteins already known to be associated with cardiometabolic processes via protein screening using the proximity extension assay technology in a subgroup of these patients (20 HCM and 10 healthy controls). After validation of four hits in the whole cohort of patients consisting of 88 individuals (60 HCM patients, 28 healthy controls) we found only one candidate, c-KIT, which was regulated significantly different between HCM patients and healthy controls and thus was chosen for further analyses. c-KIT is a tyrosine-protein kinase acting as receptor for the stem cell factor and activating several pathways essential for cell proliferation and survival, hematopoiesis, gametogenesis and melanogenesis. Serum protein levels of c-KIT were significantly lower in patients with HCM than in healthy controls, even after adjusting for confounding factors age and sex. In addition, c-KIT levels in human cardiac tissue of patients with HOCM were significant higher compared to controls indicating high levels of c-KIT in fibrotic myocardium. Furthermore, c-KIT concentration in serum significantly correlated with left ventricular end-diastolic diameter in HOCM, but not HCM patients. The present data suggest c-KIT as a novel biomarker differentiating between patients with HCM and healthy population and might provide further functional insights into fibrosis-related processes of HOCM.
Collapse
Affiliation(s)
- Kristina Sonnenschein
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.,Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - David de Gonzalo-Calvo
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Av. de Monforte de Lemos, 28029, Madrid, Spain.,Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Av. Alcalde Rovira Roure 80, 25198, Lleida, Spain
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Angelika Pfanne
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Carolin Zwadlo
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Samira Soltani
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Udo Bavendiek
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Theresia Kraft
- Institute of Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Cristobal Dos Remedios
- Anatomy and Histology, School of Medical Sciences, Bosch Institute, University of Sydney, Camperdown, Australia
| | - Serghei Cebotari
- Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany. .,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany. .,Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany.
| |
Collapse
|
36
|
Tarhoni I, Wakefield CJ, Kollipara R, Fidler MJ, Batus M, Bonomi P, Borgia JA. Relationship between circulating tumor-associated autoantibodies and clinical outcomes in advanced-stage NSCLC patients receiving PD-1/-L1 directed immune checkpoint inhibition. J Immunol Methods 2021; 490:112956. [PMID: 33434603 DOI: 10.1016/j.jim.2021.112956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/20/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Durable tumor regressions are observed in a subset of advanced-stage non-small cell lung cancer (NSCLC) patients receiving PD-1/-L1 targeted immune checkpoint inhibitors (or 'immunotherapy') alone or in combination with chemotherapy. However, the majority of advanced NSCLC patients receiving these agents do not experience long-term disease control. Existing methods to identify patients most likely to gain clinical benefit from PD-1/-L1 immunotherapy have limitations, creating a need for improved methods to guide treatment selection, particularly for those likely to benefit from single-agent immunotherapy. Here, we describe the development of a series of novel assays for tumor-associated autoantibodies as part of an exploratory study intended to determine if these biomarkers have potential prognostic value in this setting. METHOD A selection of recombinant tumor autoantigens previously characterized for their diagnostic utility were developed and preliminarily evaluated by this study. These include: Fumarate Dehydrogenase (FH), Hydroxysteroid 17-Beta Dehydrogenase 10 (HSD17B10), Inosine Monophosphate Dehydrogenase 2 (IMPDH2), New York Esophageal Squamous Cell Carcinoma-1 (NY ESO-1), Phosphoglycerate Mutase 1 (PGAM1), and Vimentin. Custom Luminex immunobead assays were developed for these targets to quantitatively assess autoantibody levels in individual patient sera. Assays were erected as indirect immunoassays on MagPlex® Microspheres using standard carbodiimide/NHS-based chemistries, utilizing a biotin-conjugated secondary (i.e. anti-human IgG) antibody and R-phycoerythrin-conjugated streptavidin reporter system. Standard curves were created for quantitative purposes using commercially-available anti-antigen antibodies and permitted analytical performance characteristics to be calculated. These assays were used to preliminarily evaluate a series of pretreatment serum samples from stage IV NSCLC patients receiving anti PD-1/-L1 therapy after failure of at least one prior line of therapy (n = 40) and their classification efficiency calculated based on 12 months overall survival (OS) threshold. RESULTS Six assays were developed that each showed dynamic ranges of four orders of magnitude and provided more than 90% classification accuracy based on the observed clinical outcome data. Inter- and intra-assay precision was assessed within these standards and overall %CVs of ≤7% and ≤ 10%, respectively, were calculated. Generally, the baseline level of autoantibodies were significantly (p < 0.05) lower in the ≥12 months survival group relative to the <12 months survival groups. Serum titers of FH, HSD170B, NY-ESO-1, and vimentin were significantly correlated with ≥12 month survival (p-value 0.0038, 0.0061, 0.0073, and 0.022, respectively). IMPDH2 and PGAM1 were found to have marginal significance (p-value 0.08 and 0.076, respectively). CONCLUSION This study demonstrates an efficient and promising means for assessing circulating autoantibody titers that could be useful in selecting advanced NSCLC patients for PD-1/-L1 directed immunotherapy. Further exploration and validation of this paradigm is warranted to further refine current treatment selection methods for this therapeutic strategy.
Collapse
Affiliation(s)
- Imad Tarhoni
- Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Connor J Wakefield
- Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Revathi Kollipara
- Department of Medical Oncology, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Mary Jo Fidler
- Department of Medical Oncology, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Marta Batus
- Department of Medical Oncology, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Philip Bonomi
- Department of Medical Oncology, Rush University Medical Center, Chicago, IL 606012, United States of America
| | - Jeffrey A Borgia
- Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, IL 606012, United States of America; Department of Pathology, Rush University Medical Center, Chicago, IL 606012, United States of America.
| |
Collapse
|
37
|
Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
Collapse
Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| |
Collapse
|
38
|
Production of a polyclonal antibody against inosine-uridine preferring nucleoside hydrolase of Acanthamoeba castellanii and its access to diagnosis of Acanthamoeba keratitis. PLoS One 2020; 15:e0239867. [PMID: 32997695 PMCID: PMC7526901 DOI: 10.1371/journal.pone.0239867] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Acanthamoeba keratitis (AK) is a rare disease but its prevalence throughout the globe continues to grow, primarily due to increased contact lens usage. Since early-stage symptoms associated with AK closely resemble those from other corneal infections, accurate diagnosis is difficult and this often results in delayed treatment and exacerbation of the disease, which can lead to permanent visual impairment. Accordingly, developing a rapid Acanthamoeba–specific diagnostic method is highly desired. In the present study, a rapid and differential method for AK diagnosis was developed using the secretory proteins derived from the pathogenic Acanthamoeba. Among the vast quantities of proteins secreted by the pathogenic Acanthamoeba, an open reading frame of the inosine-uridine preferring nucleoside hydrolase (IPNH) gene was obtained. After expressing and purifying the IPNH protein using the pGEX 4T-3 vector system, mice were immunized with the purified proteins for polyclonal antibody generation. Western blot was performed using protein lysates of the human corneal cell, non-pathogenic amoeba, pathogenic amoeba, and clinical amoeba isolate along with lysates from other causes of keratitis such as Staphylococcus aureus, Pseudomonas aeruginosa, and Fusarium solani to confirm Acanthamoeba-specificity. Western blot using the polyclonal IPNH antibody revealed that IPNH was Acanthamoeba-specific since these proteins were only observed in lysates of Acanthamoeba origin or its culture media. Our findings indicate that the IPNH antibody of Acanthamoeba may serve as a potential agent for rapid and differential AK diagnosis.
Collapse
|
39
|
A Multichannel Pattern-Recognition-Based Protein Sensor with a Fluorophore-Conjugated Single-Stranded DNA Set. SENSORS 2020; 20:s20185110. [PMID: 32911729 PMCID: PMC7570997 DOI: 10.3390/s20185110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/16/2022]
Abstract
Recently, pattern-recognition-based protein sensing has received considerable attention because it offers unique opportunities that complement more conventional antibody-based detection methods. Here, we report a multichannel pattern-recognition-based sensor using a set of fluorophore-conjugated single-stranded DNAs (ssDNAs), which can detect various proteins. Three different fluorophore-conjugated ssDNAs were placed into a single microplate well together with a target protein, and the generated optical response pattern that corresponds to each environment-sensitive fluorophore was read via multiple detection channels. Multivariate analysis of the resulting optical response patterns allowed an accurate detection of eight different proteases, indicating that fluorescence signal acquisition from a single compartment containing a mixture of ssDNAs is an effective strategy for the characterization of the target proteins. Additionally, the sensor could identify proteins, which are potential targets for disease diagnosis, in a protease and inhibitor mixture of different composition ratios. As our sensor benefits from simple construction and measurement procedures, and uses accessible materials, it offers a rapid and simple platform for the detection of proteins.
Collapse
|
40
|
Migisha Ntwali P, Heo CE, Han JY, Chae SY, Kim M, Vu HM, Kim MS, Kim HI. Mass spectrometry-based proteomics of single cells and organoids: The new generation of cancer research. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
41
|
Wang Z, Fang X, Sun N, Deng C. A rational route to hybrid aptamer-molecularly imprinted magnetic nanoprobe for recognition of protein biomarkers in human serum. Anal Chim Acta 2020; 1128:1-10. [PMID: 32825893 DOI: 10.1016/j.aca.2020.06.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 01/20/2023]
Abstract
Although antibody has played a great role in highly specific recognition of protein biomarkers, it faces poor stability, reproducibility, high-cost and time-consuming preparation, etc. Here, aptamer and molecularly imprinted polymers (MIPs), both as promising substitutes of antibody, were integrated onto magnetic nanoparticles by Au-S bonds and SiO2 as imprinted layer for preparing a new nanoprobe. Highly specific and sensitive recognition of different protein biomarkers, such as insulin for diabetes and alpha-fetoprotein (AFP) for hepatic carcinoma, were achieved respectively by the system of combining hybrid aptamer-molecularly imprinted magnetic nanoprobe and mass spectrometry. With the double affinities offered by aptamer-MIPs, insulin can be detected at 0.5 ng mL-1 in human serum dilution, the equlibrium dissociation constant between nanoprobe and insulin is measured as 23.61 ± 2.27 μM. Likewise, AFP can be sufficiently detected in human saliva dilution from 1000 ng mL-1 to 20 ng mL-1, and two patients with hepatic carcinoma are discriminated from healthy person due to the abnormally high expression of AFP in serum.
Collapse
Affiliation(s)
- Zidan Wang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, And Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaowei Fang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, And Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, And Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Chunhui Deng
- Institutes of Biomedical Sciences, And Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
42
|
Sugai H, Tomita S, Kurita R. Pattern-recognition-based Sensor Arrays for Cell Characterization: From Materials and Data Analyses to Biomedical Applications. ANAL SCI 2020; 36:923-934. [PMID: 32249248 DOI: 10.2116/analsci.20r002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To capture a broader scope of complex biological phenomena, alternatives to conventional sensing based on specificity for cell detection and characterization are needed. Pattern-recognition-based sensing is an analytical method designed to mimic mammalian sensory systems for analyte identification based on the pattern recognition of multivariate data, which are generated using an array of multiple probes that cross-reactively interact with analytes. This sensing approach is significantly different from conventional specific cell sensing based on highly specific probes, including antibodies against biomarkers. Encouraged by the advantages of this technique, such as the simplicity, rapidity, and tunability of the systems without requiring a priori knowledge of biomarkers, numerous sensor arrays have been developed over the past decade and used in a variety of cell sensing applications; these include disease diagnosis, drug discovery, and fundamental research. This review summarizes recent progress in pattern-recognition-based cell sensing, with a particular focus on guidelines for designing materials and arrays, techniques for analyzing response patterns, and applications of sensor systems that are focused primarily for the biomedical field.
Collapse
Affiliation(s)
- Hiroka Sugai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST)
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST).,Faculty of Pure and Applied Sciences, University of Tsukuba
| |
Collapse
|
43
|
Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections. PLoS One 2020; 15:e0235328. [PMID: 32628701 PMCID: PMC7337308 DOI: 10.1371/journal.pone.0235328] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/14/2020] [Indexed: 12/25/2022] Open
Abstract
Objective Current urinary tract infection (UTI) diagnostic strategies that rely on leukocyte esterase have limited accuracy. We performed an aptamer-based proteomics pilot study to identify urine protein levels that could differentiate a culture proven UTI from culture negative samples, regardless of pyuria status. Methods We analyzed urine from 16 children with UTIs, 8 children with culture negative pyuria and 8 children with negative urine culture and no pyuria. The urine levels of 1,310 proteins were quantified using the Somascan™ platform and normalized to urine creatinine. Machine learning with support vector machine (SVM)-based feature selection was performed to determine the combination of urine biomarkers that optimized diagnostic accuracy. Results Eight candidate urine protein biomarkers met filtering criteria. B-cell lymphoma protein, C-X-C motif chemokine 6, C-X-C motif chemokine 13, cathepsin S, heat shock 70kDA protein 1A, mitogen activated protein kinase, protein E7 HPV18 and transgelin. AUCs ranged from 0.91 to 0.95. The best prediction was achieved by the SVMs with radial basis function kernel. Conclusions Biomarkers panel can be identified by the emerging technologies of aptamer-based proteomics and machine learning that offer the potential to increase UTI diagnostic accuracy, thereby limiting unneeded antibiotics.
Collapse
|
44
|
Uzdensky AB. Apoptosis regulation in the penumbra after ischemic stroke: expression of pro- and antiapoptotic proteins. Apoptosis 2020; 24:687-702. [PMID: 31256300 DOI: 10.1007/s10495-019-01556-6] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ischemic stroke is the leading cause of human disability and mortality in the world. The main problem in stroke therapy is the search of efficient neuroprotector capable to rescue neurons in the potentially salvageable transition zone (penumbra), which is expanding after brain damage. The data on molecular mechanisms of penumbra formation and expression of diverse signaling proteins in the penumbra during first 24 h after ischemic stroke are discussed. Two basic features of cell death regulation in the ischemic penumbra were observed: (1) both apoptotic and anti-apoptotic proteins are simultaneously over-expressed in the penumbra, so that the fate of individual cells is determined by the balance between these opposite tendencies. (2) Similtaneous and concerted up-regulation in the ischemic penumbra of proteins that execute apoptosis (caspases 3, 6, 7; Bcl-10, SMAC/DIABLO, AIF, PSR), signaling proteins that regulate different apoptosis pathways (p38, JNK, DYRK1A, neurotrophin receptor p75); transcription factors that control expression of various apoptosis regulation proteins (E2F1, p53, c-Myc, GADD153); and proteins, which are normally involved in diverse cellular functions, but stimulate apoptosis in specific situations (NMDAR2a, Par4, GAD65/67, caspase 11). Hence, diverse apoptosis initiation and regulation pathways are induced simultaneously in penumbra from very different initial positions. Similarly, various anti-apoptotic proteins (Bcl-x, p21/WAF-1, MDM2, p63, PKBα, ERK1, RAF1, ERK5, MAKAPK2, protein phosphatases 1α and MKP-1, estrogen and EGF receptors, calmodulin, CaMKII, CaMKIV) are upregulated. These data provide an integral view of neurodegeneration and neuroprotection in penumbra. Some discussed proteins may serve as potential targets for anti-stroke therapy.
Collapse
Affiliation(s)
- Anatoly B Uzdensky
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, 194/1 Stachky Prospect, Rostov-on-Don, Russia, 344090.
| |
Collapse
|
45
|
Bonnet M, Soulat J, Bons J, Léger S, De Koning L, Carapito C, Picard B. Quantification of biomarkers for beef meat qualities using a combination of Parallel Reaction Monitoring- and antibody-based proteomics. Food Chem 2020; 317:126376. [DOI: 10.1016/j.foodchem.2020.126376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/31/2020] [Accepted: 02/08/2020] [Indexed: 12/24/2022]
|
46
|
Klimczak-Tomaniak D, Bouwens E, Schuurman AS, Akkerhuis KM, Constantinescu A, Brugts J, Westenbrink BD, van Ramshorst J, Germans T, Pączek L, Umans V, Boersma E, Kardys I. Temporal patterns of macrophage- and neutrophil-related markers are associated with clinical outcome in heart failure patients. ESC Heart Fail 2020; 7:1190-1200. [PMID: 32196993 PMCID: PMC7261550 DOI: 10.1002/ehf2.12678] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/17/2020] [Accepted: 02/22/2020] [Indexed: 12/18/2022] Open
Abstract
AIMS Evidence on the association of macrophage- and neutrophil-related blood biomarkers with clinical outcome in heart failure patients is limited, and, with the exception of C-reactive protein, no data exist on their temporal evolution. We aimed to investigate whether temporal patterns of these biomarkers are related to clinical outcome in patients with stable chronic heart failure (CHF). METHODS AND RESULTS In 263 patients with CHF, we performed serial plasma measurements of scavenger receptor cysteine-rich type 1 protein M130 (CD163), tartrate-resistant acid phosphatase type 5 (TRAP), granulins (GRN), spondin-1 (SPON1), peptidoglycan recognition protein 1 (PGLYRP1), and tissue factor pathway inhibitor (TFPI). The Cardiovascular Panel III (Olink Proteomics AB, Uppsala, Sweden) was used. During 2.2 years of follow-up, we collected 1984 samples before the occurrence of the composite primary endpoint (PE) or censoring. For efficiency, we selected 567 samples for the measurements (all baseline samples, the last two samples preceding the PE, and the last sample before censoring in event-free patients). The relationship between repeatedly measured biomarker levels and the PE was evaluated by joint models. Mean (±standard deviation) age was 67 ± 13 years; 189 (72%) were men; left ventricular ejection fraction (%) was 32 ± 11. During follow-up, 70 (27%) patients experienced the PE. Serially measured biomarkers predicted the PE in a multivariable model adjusted for baseline clinical characteristics [hazard ratio (95% confidence interval) per 1-standard deviation change in biomarker]: CD163 [2.07(1.47-2.98), P < 0.001], TRAP [0.62 (0.43-0.90), P = 0.009], GRN [2.46 (1.64-3.84), P < 0.001], SPON1 [3.94 (2.50-6.50), P < 0.001], and PGLYRP1 [1.62 (1.14-2.31), P = 0.006]. CONCLUSIONS Changes in plasma levels of CD163, TRAP, GRN, SPON1, and PGLYRP1 precede adverse cardiovascular events in patients with CHF.
Collapse
Affiliation(s)
- Dominika Klimczak-Tomaniak
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Immunology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Division of Heart Failure and Cardiac Rehabilitation, Medical University of Warsaw, Warsaw, Poland
| | - Elke Bouwens
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne-Sophie Schuurman
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - K Martijn Akkerhuis
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alina Constantinescu
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jasper Brugts
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - B Daan Westenbrink
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan van Ramshorst
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Tjeerd Germans
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Leszek Pączek
- Department of Immunology, Transplantation and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Victor Umans
- Department of Cardiology, Northwest Clinics, Alkmaar, The Netherlands
| | - Eric Boersma
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Isabella Kardys
- Department of Cardiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
47
|
Bouwens E, Brankovic M, Mouthaan H, Baart S, Rizopoulos D, van Boven N, Caliskan K, Manintveld O, Germans T, van Ramshorst J, Umans V, Akkerhuis KM, Kardys I. Temporal Patterns of 14 Blood Biomarker candidates of Cardiac Remodeling in Relation to Prognosis of Patients With Chronic Heart Failure-The Bio- SH i FT Study. J Am Heart Assoc 2020; 8:e009555. [PMID: 30760105 PMCID: PMC6405680 DOI: 10.1161/jaha.118.009555] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background Remodeling biomarkers carry high potential for predicting adverse events in chronic heart failure (CHF) patients. However, temporal patterns during the course of CHF, and especially the trajectory before an adverse event, are unknown. We studied the prognostic value of temporal patterns of 14 cardiac remodeling biomarker candidates in stable patients with CHF from the Bio‐SHiFT (Serial Biomarker Measurements and New Echocardiographic Techniques in Chronic Heart Failure Patients Result in Tailored Prediction of Prognosis) study. Methods and Results In 263 CHF patients, we performed trimonthly blood sampling during a median follow‐up of 2.2 years. For the analysis, we selected all baseline samples, the 2 samples closest to the primary end point (PE), or the last sample available for end point–free patients. Thus, in 567 samples, we measured suppression of tumorigenicity‐2, galectin‐3, galectin‐4, growth differentiation factor‐15, matrix metalloproteinase‐2, 3, and 9, tissue inhibitor metalloproteinase‐4, perlecan, aminopeptidase‐N, caspase‐3, cathepsin‐D, cathepsin‐Z, and cystatin‐B. The PE was a composite of cardiovascular mortality, heart transplantation, left ventricular assist device implantation, and HF hospitalization. Associations between repeatedly measured biomarker candidates and the PE were investigated by joint modeling. Median age was 68 (interquartile range: 59–76) years with 72% men; 70 patients reached the PE. Repeatedly measured suppression of tumorigenicity‐2, galectin‐3, galectin‐4, growth differentiation factor‐15, matrix metalloproteinase‐2 and 9, tissue inhibitor metalloproteinase‐4, perlecan, cathepsin‐D, and cystatin‐B levels were significantly associated with the PE, and increased as the PE approached. The slopes of biomarker trajectories were also predictors of clinical outcome, independent of their absolute level. Associations persisted after adjustment for clinical characteristics and pharmacological treatment. Suppression of tumorigenicity‐2 was the strongest predictor (hazard ratio: 7.55 per SD difference, 95% CI: 5.53–10.30), followed by growth differentiation factor‐15 (4.06, 2.98–5.54) and matrix metalloproteinase‐2 (3.59, 2.55–5.05). Conclusions Temporal patterns of remodeling biomarker candidates predict adverse clinical outcomes in CHF. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT01851538.
Collapse
Affiliation(s)
- Elke Bouwens
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| | - Milos Brankovic
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| | | | - Sara Baart
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| | | | - Nick van Boven
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| | - Kadir Caliskan
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| | | | - Tjeerd Germans
- 4 Department of Cardiology Northwest Clinics Alkmaar the Netherlands
| | - Jan van Ramshorst
- 4 Department of Cardiology Northwest Clinics Alkmaar the Netherlands
| | - Victor Umans
- 4 Department of Cardiology Northwest Clinics Alkmaar the Netherlands
| | | | - Isabella Kardys
- 1 Department of Cardiology Erasmus MC Rotterdam the Netherlands
| |
Collapse
|
48
|
Bouwens E, van den Berg VJ, Akkerhuis KM, Baart SJ, Caliskan K, Brugts JJ, Mouthaan H, van Ramshorst J, Germans T, Umans VAWM, Boersma E, Kardys I. Circulating Biomarkers of Cell Adhesion Predict Clinical Outcome in Patients with Chronic Heart Failure. J Clin Med 2020; 9:E195. [PMID: 31936828 PMCID: PMC7020068 DOI: 10.3390/jcm9010195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/31/2022] Open
Abstract
Cardiovascular inflammation and vascular endothelial dysfunction are involved in chronic heart failure (CHF), and cellular adhesion molecules are considered to play a key role in these mechanisms. We evaluated temporal patterns of 12 blood biomarkers of cell adhesion in patients with CHF. In 263 ambulant patients, serial, tri-monthly blood samples were collected during a median follow-up of 2.2 (1.4-2.5) years. The primary endpoint (PE) was a composite of cardiovascular mortality, HF hospitalization, heart transplantation and implantation of a left ventricular assist device and was reached in 70 patients. We selected the baseline blood samples in all patients, the two samples closest to a PE, or, for event-free patients, the last sample available. In these 567 samples, associations between biomarkers and PE were investigated by joint modelling. The median age was 68 (59-76) years, with 72% men and 74% New York Heart Association class I-II. Repeatedly measured levels of Complement component C1q receptor (C1qR), Cadherin 5 (CDH5), Chitinase-3-like protein 1 (CHI3L1), Ephrin type-B receptor 4 (EPHB4), Intercellular adhesion molecule-2 (ICAM-2) and Junctional adhesion molecule A (JAM-A) were independently associated with the PE. Their rates of change also predicted clinical outcome. Level of CHI3L1 was numerically the strongest predictor with a hazard ratio (HR) (95% confidence interval) of 2.27 (1.66-3.16) per SD difference in level, followed by JAM-A (2.10, 1.42-3.23) and C1qR (1.90, 1.36-2.72), adjusted for clinical characteristics. In conclusion, temporal patterns of C1qR, CDH5, CHI3L1, EPHB4, ICAM2 and JAM-A are strongly and independently associated with clinical outcome in CHF patients.
Collapse
|
49
|
Abstract
OBJECTIVE To use plasma neuron-derived exosomes (NDEs) to detect proteins that diagnose HIV-associated neurocognitive disorders (HAND). To compare NDE cargo from HAND with Alzheimer's disease. DESIGN Eighty plasma samples were assayed including men (n = 29) and women (n = 51) with and without HAND. METHODS Plasma NDEs were isolated by immunoadsorption with neuron specific L1 cell adhesion molecule antibody. NDE proteins were quantified by ELISA and proximity extension assays for 184 targets. RESULTS Neuronal enrichment of NDE was confirmed with elevated synaptophysin and normalized to the exosomal marker, apoptosis-linked gene-2-interacting protein X (ALIX). NDE from men and women had significant divergent results. High mobility group box 1 and neurofilament light were significantly increased in NDE from cognitively impaired men and were unchanged in women. NDE from HIV+ men had decreased p-T181-tau, a marker increased in Alzheimer's disease, compared with no difference in women. NDE amyloid beta was not increased in cognitive impairment. Proximity extension assays analysis showed 25 proteins were differentially expressed in HIV infection alone. Seven proteins identified asymptomatic and mild cognitive impairment in HIV+ women. NDE from women had significantly decreased cathepsin S, total tau, neuronal cell adhesion molecule and contactin 5 in mild impairment. Twelve proteins were increased in NDE from cognitively impaired men, including carboxypeptidase M, cadherin 3, colony stimulating factor 2 receptor alpha subunit and mesencephalic astrocyte-derived neurotropic factor. CONCLUSION NDE proteins differ in HIV infection alone and cognitive impairment between men and women suggesting mechanistic sex differences associated with HAND. Several NDE targets are different from that reported for Alzheimer's disease.
Collapse
|
50
|
Jing W, Wang Y, Yang Y, Wang Y, Ma G, Wang S, Tao N. Time-Resolved Digital Immunoassay for Rapid and Sensitive Quantitation of Procalcitonin with Plasmonic Imaging. ACS NANO 2019; 13:8609-8617. [PMID: 31276361 PMCID: PMC7008466 DOI: 10.1021/acsnano.9b02771] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Timely diagnosis of acute diseases improves treatment outcomes and saves lives, but it requires fast and precision quantification of biomarkers. Here, we report a time-resolved digital immunoassay based on plasmonic imaging of binding of single nanoparticles to biomarkers captured on a sensor surface. The real-time and high contrast of plasmonic imaging lead to fast and precise counting of the individual biomarkers over a wide dynamic range. We demonstrated the detection principle, evaluated the performance of the method using procalcitonin (PCT) as an example, and achieved a limit of detection of ∼2.8 pg/mL, dynamic range of 4.2-12500 pg/mL, for a total detection time of ∼25 min.
Collapse
Affiliation(s)
- Wenwen Jing
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
| | - Yan Wang
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
| | - Yunze Yang
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
| | - Yi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Guangzhong Ma
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| |
Collapse
|