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Wang S, Xie S, Zheng Q, Zhang Z, Wang T, Zhang G. Biofluid biomarkers for Alzheimer's disease. Front Aging Neurosci 2024; 16:1380237. [PMID: 38659704 PMCID: PMC11039951 DOI: 10.3389/fnagi.2024.1380237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease, with a complex pathogenesis and an irreversible course. Therefore, the early diagnosis of AD is particularly important for the intervention, prevention, and treatment of the disease. Based on the different pathophysiological mechanisms of AD, the research progress of biofluid biomarkers are classified and reviewed. In the end, the challenges and perspectives of future research are proposed.
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Affiliation(s)
- Sensen Wang
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong, China
| | - Sitan Xie
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
| | - Qinpin Zheng
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong, China
| | - Zhihui Zhang
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
| | - Tian Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong, China
| | - Guirong Zhang
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, Shandong, China
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Takis PG, Aggelidou VA, Sands CJ, Louka A. Mapping of 1 H NMR chemical shifts relationship with chemical similarities for the acceleration of metabolic profiling: Application on blood products. Magn Reson Chem 2023; 61:759-769. [PMID: 37666776 PMCID: PMC10946494 DOI: 10.1002/mrc.5392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
One-dimensional (1D) proton-nuclear magnetic resonance (1 H-NMR) spectroscopy is an established technique for the deconvolution of complex biological sample types via the identification/quantification of small molecules. It is highly reproducible and could be easily automated for small to large-scale bioanalytical, epidemiological, and in general metabolomics studies. However, chemical shift variability is a serious issue that must still be solved in order to fully automate metabolite identification. Herein, we demonstrate a strategy to increase the confidence in assignments and effectively predict the chemical shifts of various NMR signals based upon the simplest form of statistical models (i.e., linear regression). To build these models, we were guided by chemical homology in serum/plasma metabolites classes (i.e., amino acids and carboxylic acids) and similarity between chemical groups such as methyl protons. Our models, built on 940 serum samples and validated in an independent cohort of 1,052 plasma-EDTA spectra, were able to successfully predict the 1 H NMR chemical shifts of 15 metabolites within ~1.5 linewidths (Δv1/2 ) error range on average. This pilot study demonstrates the potential of developing an algorithm for the accurate assignment of 1 H NMR chemical shifts based solely on chemically defined constraints.
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Affiliation(s)
- Panteleimon G. Takis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Varvara A. Aggelidou
- Department of Biological Applications and TechnologiesUniversity of IoanninaIoanninaGreece
| | - Caroline J. Sands
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Alexandra Louka
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of NeurologyUniversity College LondonLondonUK
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Palevich N, Maclean PH, Cao M. Non-targeted multimodal metabolomics data from ovine rumen fluid fractions. Microbiol Resour Announc 2023; 12:e0039223. [PMID: 37466335 PMCID: PMC10508094 DOI: 10.1128/mra.00392-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
From an animal health perspective, our understanding of the metabolites in rumen fluid across different host species is poorly understood. Here, we present a metabolomic data set generated using hydrophilic interaction liquid chromatography and semi-polar (C18) chromatography methods coupled to high-resolution mass spectrometry of fractionated ovine rumen samples.
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Affiliation(s)
- Nikola Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Mingshu Cao
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
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Pucchio A, Krance S, Pur DR, Bassi A, Miranda R, Felfeli T. The role of artificial intelligence in analysis of biofluid markers for diagnosis and management of glaucoma: A systematic review. Eur J Ophthalmol 2023; 33:1816-1833. [PMID: 36426575 PMCID: PMC10469503 DOI: 10.1177/11206721221140948] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/01/2022] [Indexed: 08/31/2023]
Abstract
PURPOSE This review focuses on utility of artificial intelligence (AI) in analysis of biofluid markers in glaucoma. We detail the accuracy and validity of AI in the exploration of biomarkers to provide insight into glaucoma pathogenesis. METHODS A comprehensive search was conducted across five electronic databases including Embase, Medline, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science. Studies pertaining to biofluid marker analysis using AI or bioinformatics in glaucoma were included. Identified studies were critically appraised and assessed for risk of bias using the Joanna Briggs Institute Critical Appraisal tools. RESULTS A total of 10,258 studies were screened and 39 studies met the inclusion criteria, including 23 cross-sectional studies (59%), nine prospective cohort studies (23%), six retrospective cohort studies (15%), and one case-control study (3%). Primary open angle glaucoma (POAG) was the most commonly studied subtype (55% of included studies). Twenty-four studies examined disease characteristics, 10 explored treatment decisions, and 5 provided diagnostic clarification. While studies examined at entire metabolomic or proteomic profiles to determine changes in POAG, there was heterogeneity in the data with over 175 unique, differentially expressed biomarkers reported. Discriminant analysis and artificial neural network predictive models displayed strong differentiating ability between glaucoma patients and controls, although these tools were untested in a clinical context. CONCLUSION The use of AI models could inform glaucoma diagnosis with high sensitivity and specificity. While insight into differentially expressed biomarkers is valuable in pathogenic exploration, no clear pathogenic mechanism in glaucoma has emerged.
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Affiliation(s)
- Aidan Pucchio
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Saffire Krance
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Daiana R Pur
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Arshpreet Bassi
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rafael Miranda
- Toronto Health Economics and Technology Assessment Collaborative, University of Toronto, Toronto, Ontario, Canada
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Tina Felfeli
- Toronto Health Economics and Technology Assessment Collaborative, University of Toronto, Toronto, Ontario, Canada
- Department of Ophthalmology and Visual Sciences, University of Toronto, Toronto, Ontario, Canada
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
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5
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Maiti KS. Non-Invasive Disease Specific Biomarker Detection Using Infrared Spectroscopy: A Review. Molecules 2023; 28:2320. [PMID: 36903576 PMCID: PMC10005715 DOI: 10.3390/molecules28052320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Many life-threatening diseases remain obscure in their early disease stages. Symptoms appear only at the advanced stage when the survival rate is poor. A non-invasive diagnostic tool may be able to identify disease even at the asymptotic stage and save lives. Volatile metabolites-based diagnostics hold a lot of promise to fulfil this demand. Many experimental techniques are being developed to establish a reliable non-invasive diagnostic tool; however, none of them are yet able to fulfil clinicians' demands. Infrared spectroscopy-based gaseous biofluid analysis demonstrated promising results to fulfil clinicians' expectations. The recent development of the standard operating procedure (SOP), sample measurement, and data analysis techniques for infrared spectroscopy are summarized in this review article. It has also outlined the applicability of infrared spectroscopy to identify the specific biomarkers for diseases such as diabetes, acute gastritis caused by bacterial infection, cerebral palsy, and prostate cancer.
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Affiliation(s)
- Kiran Sankar Maiti
- Max–Planck–Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-289-14054
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
- Laser-Forschungslabor, Klinikum der Universität München, Fraunhoferstrasse 20, 82152 Planegg, Germany
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Cordts I, Wachinger A, Scialo C, Lingor P, Polymenidou M, Buratti E, Feneberg E. TDP-43 Proteinopathy Specific Biomarker Development. Cells 2023; 12. [PMID: 36831264 DOI: 10.3390/cells12040597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
TDP-43 is the primary or secondary pathological hallmark of neurodegenerative diseases, such as amyotrophic lateral sclerosis, half of frontotemporal dementia cases, and limbic age-related TDP-43 encephalopathy, which clinically resembles Alzheimer's dementia. In such diseases, a biomarker that can detect TDP-43 proteinopathy in life would help to stratify patients according to their definite diagnosis of pathology, rather than in clinical subgroups of uncertain pathology. For therapies developed to target pathological proteins that cause the disease a biomarker to detect and track the underlying pathology would greatly enhance such undertakings. This article reviews the latest developments and outlooks of deriving TDP-43-specific biomarkers from the pathophysiological processes involved in the development of TDP-43 proteinopathy and studies using biosamples from clinical entities associated with TDP-43 pathology to investigate biomarker candidates.
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Upasham S, Pali M, Jagannath B, Lin KC, Prasad S. Electrochemical Aptasensing for Lifestyle and Chronic Disease Management. Curr Med Chem 2023; 30:895-909. [PMID: 35619314 DOI: 10.2174/0929867329666220520111715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/21/2022] [Accepted: 03/10/2022] [Indexed: 11/22/2022]
Abstract
Over the past decade, researchers have investigated electrochemical sensing for the purpose of fabricating wearable point-of-use platforms. These wearable platforms have the ability to non-invasively track biomarkers that are clinically relevant and provide a comprehensive evaluation of the user's health. Due to many significant operational advantages, aptamer-based sensing is gaining traction.Aptamer-based sensors have properties like long-term stability, resistance to denaturation, and high sensitivity. Using electrochemical sensing with aptamer-based biorecognition is advantageous because it provides significant benefits like lower detection limits, a wider range of operations, and, most importantly, the ability to detect using a label-free approach. This paper provides an outlook into the current state of electrochemical aptasensing. This review looks into the significance of the detection of biomarkers like glucose, cortisol etc., for the purpose of lifestyle and chronic disease monitoring. Moreover, this review will also provide a comprehensive evaluation of the current challenges and prospects in this field.
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Affiliation(s)
- Sayali Upasham
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Madhavi Pali
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Badrinath Jagannath
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Kai-Chun Lin
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
| | - Shalini Prasad
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas-75080, USA
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Ahmad F, Tanguy S, Dubreuil A, Magnin A, Faucheron JL, de Loubens C. Flow simulations of rectal evacuation: towards a quantitative evaluation from video defaecography. Interface Focus 2022; 12:20220033. [PMID: 36330321 PMCID: PMC9560784 DOI: 10.1098/rsfs.2022.0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/24/2022] [Indexed: 10/16/2023] Open
Abstract
Mechanistic understanding of anorectal (patho)physiology is missing to improve the medical care of patients suffering from defaecation disorders. Our objective is to show that complex fluid dynamics modelling of video defaecography may open new perspectives in the diagnosis of defaecation disorders. Based on standard X-ray video defaecographies, we developed a bi-dimensional patient-specific simulation of the expulsion of soft materials, the faeces, by the rectum. The model quantified velocity, pressure and stress fields during the defaecation of a neostool with soft stool-like rheology for patients showing normal and pathological defaecatory function. In normal defaecation, the proximal-distal pressure gradient resulted from both the anorectal junction which formed a converging channel and the anal canal. The flow of the neostool through these anatomical parts was dominated by its shear-thinning viscous properties, rather than its yield stress. Consequently, the evacuation flow rate was significantly affected by variations in pressure applied by the rectum, and much less by the geometry of the anorectal junction. Lastly, we simulated impaired defaecations in the absence of obvious obstructive phenomena. Comparison with normal defaecation allowed us to discuss critical elements which should lead to effective medical management.
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Affiliation(s)
- Faisal Ahmad
- University Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
| | - Stéphane Tanguy
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC, Grenoble, France
| | | | - Albert Magnin
- University Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
| | - Jean-Luc Faucheron
- University Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC, Grenoble, France
- Department of Surgery, Colorectal Unit, CHU Grenoble Alpes, University Grenoble Alpes, Grenoble, France
| | - Clément de Loubens
- University Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
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Iwamoto H, Okihara M, Akashi I, Kihara Y, Konno O, Kawachi S, Sunamura M, Sugimoto M. Metabolomic Profiling of Plasma, Urine, and Saliva of Kidney Transplantation Recipients. Int J Mol Sci 2022; 23. [PMID: 36430414 DOI: 10.3390/ijms232213938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Kidney biopsy is commonly used to diagnose kidney transplant dysfunction after transplantation. Therefore, the development of minimally invasive and quantitative methods to evaluate kidney function in transplant recipients is necessary. Here, we used capillary electrophoresis-mass spectrometry to analyze the biofluids collected from transplant recipients with impaired (Group I, n = 31) and stable (Group S, n = 19) kidney function and from donors (Group D, n = 9). Metabolomics analyses identified and quantified 97 metabolites in plasma, 133 metabolites in urine, and 108 metabolites in saliva. Multivariate analyses revealed apparent differences in the metabolomic profiles of the three groups. In plasma samples, arginine biosynthesis and purine metabolism between the I and S Groups differed. In addition, considerable differences in metabolomic profiles were observed between samples collected from participants with T cell-mediated rejection (TCR), antibody-mediated rejection, and other kidney disorders (KD). The metabolomic profiles in the three types of biofluids showed different patterns between TCR and KD, wherein 3-indoxyl sulfate showed a significant increase in TCR consistently in both plasma and urine samples. These results suggest that each biofluid has different metabolite features to evaluate kidney function after transplantation and that 3-indoxyl sulfate could predict acute rejection.
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Azimzadeh O, Moertl S, Ramadan R, Baselet B, Laiakis EC, Sebastian S, Beaton D, Hartikainen JM, Kaiser JC, Beheshti A, Salomaa S, Chauhan V, Hamada N. Application of radiation omics in the development of adverse outcome pathway networks: an example of radiation-induced cardiovascular disease. Int J Radiat Biol 2022; 98:1722-1751. [PMID: 35976069 DOI: 10.1080/09553002.2022.2110325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Epidemiological studies have indicated that exposure of the heart to doses of ionizing radiation as low as 0.5 Gy increases the risk of cardiac morbidity and mortality with a latency period of decades. The damaging effects of radiation to myocardial and endothelial structures and functions have been confirmed radiobiologically at high dose, but much less is known at low dose. Integration of radiation biology and epidemiology data is a recommended approach to improve the radiation risk assessment process. The adverse outcome pathway (AOP) framework offers a comprehensive tool to compile and translate mechanistic information into pathological endpoints which may be relevant for risk assessment at the different levels of a biological system. Omics technologies enable the generation of large volumes of biological data at various levels of complexity, from molecular pathways to functional organisms. Given the quality and quantity of available data across levels of biology, omics data can be attractive sources of information for use within the AOP framework. It is anticipated that radiation omics studies could improve our understanding of the molecular mechanisms behind the adverse effects of radiation on the cardiovascular system. In this review, we explored the available omics studies on radiation-induced cardiovascular disease (CVD) and their applicability to the proposed AOP for CVD. RESULTS The results of 80 omics studies published on radiation-induced CVD over the past 20 years have been discussed in the context of the AOP of CVD proposed by Chauhan et al. Most of the available omics data on radiation-induced CVD are from proteomics, transcriptomics, and metabolomics, whereas few datasets were available from epigenomics and multi-omics. The omics data presented here show great promise in providing information for several key events of the proposed AOP of CVD, particularly oxidative stress, alterations of energy metabolism, extracellular matrix and vascular remodeling. CONCLUSIONS The omics data presented here shows promise to inform the various levels of the proposed AOP of CVD. However, the data highlight the urgent need of designing omics studies to address the knowledge gap concerning different radiation scenarios, time after exposure and experimental models. This review presents the evidence to build a qualitative omics-informed AOP and provides views on the potential benefits and challenges in using omics data to assess risk-related outcomes.
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Affiliation(s)
- Omid Azimzadeh
- Federal Office for Radiation Protection (BfS), Section Radiation Biology, 85764 Neuherberg, Germany
| | - Simone Moertl
- Federal Office for Radiation Protection (BfS), Section Radiation Biology, 85764 Neuherberg, Germany
| | - Raghda Ramadan
- Institute for Environment, Health and Safety, Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Bjorn Baselet
- Institute for Environment, Health and Safety, Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Evagelia C Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | | | | | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Jan Christian Kaiser
- Helmholtz Zentrum München, Institute of Radiation Medicine (HMGU-IRM), 85764 Neuherberg, Germany
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sisko Salomaa
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vinita Chauhan
- Environmental Health Science Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Nobuyuki Hamada
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Komae, Tokyo 201-8511, Japan
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Aitekenov S, Sultangaziyev A, Abdirova P, Yussupova L, Gaipov A, Utegulov Z, Bukasov R. Raman, Infrared and Brillouin Spectroscopies of Biofluids for Medical Diagnostics and for Detection of Biomarkers. Crit Rev Anal Chem 2022; 53:1561-1590. [PMID: 35157535 DOI: 10.1080/10408347.2022.2036941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
This review surveys Infrared, Raman/SERS and Brillouin spectroscopies for medical diagnostics and detection of biomarkers in biofluids, that include urine, blood, saliva and other biofluids. These optical sensing techniques are non-contact, noninvasive and relatively rapid, accurate, label-free and affordable. However, those techniques still have to overcome some challenges to be widely adopted in routine clinical diagnostics. This review summarizes and provides insights on recent advancements in research within the field of vibrational spectroscopy for medical diagnostics and its use in detection of many health conditions such as kidney injury, cancers, cardiovascular and infectious diseases. The six comprehensive tables in the review and four tables in supplementary information summarize a few dozen experimental papers in terms of such analytical parameters as limit of detection, range, diagnostic sensitivity and specificity, and other figures of merits. Critical comparison between SERS and FTIR methods of analysis reveals that on average the reported sensitivity for biomarkers in biofluids for SERS vs FTIR is about 103 to 105 times higher, since LOD SERS are lower than LOD FTIR by about this factor. High sensitivity gives SERS an edge in detection of many biomarkers present in biofluids at low concentration (nM and sub nM), which can be particularly advantageous for example in early diagnostics of cancer or viral infections.HighlightsRaman, Infrared spectroscopies use low volume of biofluidic samples, little sample preparation, fast time of analysis and relatively inexpensive instrumentation.Applications of SERS may be a bit more complicated than applications of FTIR (e.g., limited shelf life for nanoparticles and substrates, etc.), but this can be generously compensated by much higher (by several order of magnitude) sensitivity in comparison to FTIR.High sensitivity makes SERS a noninvasive analytical method of choice for detection, quantification and diagnostics of many health conditions, metabolites, and drugs, particularly in diagnostics of cancer, including diagnostics of its early stages.FTIR, particularly ATR-FTIR can be a method of choice for efficient sensing of many biomarkers, present in urine, blood and other biofluids at sufficiently high concentrations (mM and even a few µM)Brillouin scattering spectroscopy detecting visco-elastic properties of probed liquid medium, may also find application in clinical analysis of some biofluids, such as cerebrospinal fluid and urine.
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Affiliation(s)
- Sultan Aitekenov
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Alisher Sultangaziyev
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Perizat Abdirova
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Yussupova
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Zhandos Utegulov
- Department of Physics, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Rostislav Bukasov
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
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Santos-Rivera M, Woolums AR, Thoresen M, Meyer F, Vance CK. Bovine Respiratory Syncytial Virus (BRSV) Infection Detected in Exhaled Breath Condensate of Dairy Calves by Near-Infrared Aquaphotomics. Molecules 2022; 27:549. [PMID: 35056864 PMCID: PMC8779643 DOI: 10.3390/molecules27020549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Bovine respiratory syncytial virus (BRSV) is a major contributor to respiratory disease in cattle worldwide. Traditionally, BRSV infection is detected based on non-specific clinical signs, followed by reverse transcriptase-polymerase chain reaction (RT-PCR), the results of which can take days to obtain. Near-infrared aquaphotomics evaluation based on biochemical information from biofluids has the potential to support the rapid identification of BRSV infection in the field. This study evaluated NIR spectra (n = 240) of exhaled breath condensate (EBC) from dairy calves (n = 5) undergoing a controlled infection with BRSV. Changes in the organization of the aqueous phase of EBC during the baseline (pre-infection) and infected (post-infection and clinically abnormal) stages were found in the WAMACS (water matrix coordinates) C1, C5, C9, and C11, likely associated with volatile and non-volatile compounds in EBC. The discrimination of these chemical profiles by PCA-LDA models differentiated samples collected during the baseline and infected stages with an accuracy, sensitivity, and specificity >93% in both the calibration and validation. Thus, biochemical changes occurring during BRSV infection can be detected and evaluated with NIR-aquaphotomics in EBC. These findings form the foundation for developing an innovative, non-invasive, and in-field diagnostic tool to identify BRSV infection in cattle.
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Affiliation(s)
- Mariana Santos-Rivera
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA; (M.S.-R.); (F.M.)
| | - Amelia R. Woolums
- College of Veterinary Medicine, Pathobiology & Population Medicine, Mississippi State University, Starkville, MS 39762, USA; (A.R.W.); (M.T.)
| | - Merrilee Thoresen
- College of Veterinary Medicine, Pathobiology & Population Medicine, Mississippi State University, Starkville, MS 39762, USA; (A.R.W.); (M.T.)
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA; (M.S.-R.); (F.M.)
| | - Carrie K. Vance
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA; (M.S.-R.); (F.M.)
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13
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Yan M, Gao F, Chen M, Hu Q, Yang Y, Chen K, Wang P, Lei H, Ma Q. Synergistic Combination of Facile Thiol-Maleimide Derivatization and Supramolecular Solvent-Based Microextraction for UHPLC-HRMS Analysis of Glutathione in Biofluids. Front Chem 2021; 9:786627. [PMID: 34957048 PMCID: PMC8695729 DOI: 10.3389/fchem.2021.786627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Glutathione (GSH) is the most abundant non-protein thiol in biofluids, enabling diverse physiological functions. Among the proposed methods for GSH detection, ultra-high-performance liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS) has the advantages of high sensitivity and efficiency. In this study, a novel analytical method was developed for the determination of GSH using supramolecular solvent (SUPRAS)-based dispersive liquid–liquid microextraction (DLLME) and UHPLC–HRMS. N-Laurylmaleimide was dissolved in tetrahydrofuran, which served three functions: 1) precipitate the proteins present in the biofluid sample, 2) provide a reaction environment for derivatization, and 3) enable the use of SUPRAS as the dispersing agent. Critical parameters were optimized based on single factor testing and response surface methodology. The established method was validated in terms of linearity, accuracy, precision, and successful quantitative analysis of GSH in saliva, urine, and plasma samples. Experimental results showed that SUPRAS as an extraction solvent was particularly suitable for the extraction of GSH from complex matrices. The current study provides a useful tool for accurate measurements of GSH concentrations, which could potentially be used for clinical diagnostics.
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Affiliation(s)
- Mengmeng Yan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.,Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Feng Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Meng Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Hu
- Chinese Academy of Inspection and Quarantine, Beijing, China.,School of Chemical Engineering, Dalian University of Technology, Dalian, China
| | - Yuqin Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Kedian Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Penglong Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Haimin Lei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Qiang Ma
- Chinese Academy of Inspection and Quarantine, Beijing, China
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14
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Vacchiano V, Mastrangelo A, Zenesini C, Masullo M, Quadalti C, Avoni P, Polischi B, Cherici A, Capellari S, Salvi F, Liguori R, Parchi P. Plasma and CSF Neurofilament Light Chain in Amyotrophic Lateral Sclerosis: A Cross-Sectional and Longitudinal Study. Front Aging Neurosci 2021; 13:753242. [PMID: 34744694 PMCID: PMC8569186 DOI: 10.3389/fnagi.2021.753242] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Neurofilament light chain (NfL) is a validated biofluid marker of neuroaxonal damage with great potential for monitoring patients with neurodegenerative diseases. We aimed to further validate the clinical utility of plasma (p) vs. CSF (c) NfL for distinguishing patients with Amyotrophic Lateral Sclerosis (ALS) from ALS mimics. We also assessed the association of biomarker values with clinical variables and survival and established the longitudinal changes of pNfL during the disease course. Methods: We studied 231 prospectively enrolled patients with suspected ALS who underwent a standardized protocol including neurological examination, electromyography, brain MRI, and lumbar puncture. Patients who received an alternative clinical diagnosis were considered ALS mimics. We classified the patients based on the disease progression rate (DPR) into fast (DPR > 1), intermediate (DPR 0.5–1), and slow progressors (DPR < 0.5). All patients were screened for the most frequent ALS-associated genes. Plasma and CSF samples were retrospectively analyzed; NfL concentrations were measured with the SIMOA platform using a commercial kit. Results: ALS patients (n = 171) showed significantly higher pNfL (p < 0.0001) and cNfL (p < 0.0001) values compared to ALS mimics (n = 60). Both cNfL and pNfL demonstrated a good diagnostic value in discriminating the two groups, although cNfL performed slightly better (cNfL: AUC 0.924 ± 0.022, sensitivity 86.8%, specificity 92.4; pNfL: AUC 0.873 ± 0.036, sensitivity 84.7%, specificity 83.3%). Fast progressors showed higher cNfL and pNfL as compared to intermediate (p = 0.026 and p = 0.001) and slow progressors (both p < 0.001). Accordingly, ALS patients with higher baseline cNfL and pNfL levels had a shorter survival (highest tertile of cNfL vs. lowest tertile, HR 4.58, p = 0.005; highest tertile of pNfL vs. lowest tertile, HR 2.59, p = 0.015). Moreover, there were positive associations between cNfL and pNfL levels and the number of body regions displaying UMN signs (rho = 0.325, p < 0.0001; rho = 0.308, p = 0.001). Finally, longitudinal analyses in 57 patients showed stable levels of pNfL during the disease course. Conclusion: Both cNfL and pNfL have excellent diagnostic and prognostic performance for symptomatic patients with ALS. The stable longitudinal trajectory of pNfL supports its use as a marker of drug effect in clinical trials.
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Affiliation(s)
- Veria Vacchiano
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Andrea Mastrangelo
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Marco Masullo
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Corinne Quadalti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Patrizia Avoni
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Barbara Polischi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Arianna Cherici
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Sabina Capellari
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Fabrizio Salvi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Rocco Liguori
- Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Piero Parchi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Experimental Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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15
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Parkin GM, McCarthy MJ, Thein SH, Piccerillo HL, Warikoo N, Granger DA, Thomas EA. Saliva testing as a means to monitor therapeutic lithium levels in patients with psychiatric disorders: Identification of clinical and environmental covariates, and their incorporation into a prediction model. Bipolar Disord 2021; 23:679-688. [PMID: 34536974 PMCID: PMC9291088 DOI: 10.1111/bdi.13128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The narrow therapeutic window of lithium medications necessitates frequent serum monitoring, which can be expensive and inconvenient for the patient. Compared to blood, saliva collection is easier, non-invasive, requires less processing, and can be done without the need for trained personnel. This study investigated the utility of longitudinal salivary lithium level monitoring. METHODS We measured salivary lithium levels using ICP-OES in n = 169 passive drool samples, collected both as single observations and longitudinally for up to 18 months, from a multi-center cohort of n = 75 patients with bipolar disorder or other psychiatric conditions. RESULTS Saliva and serum lithium levels were highly correlated. Adjustment for daily lithium dose, diabetes, and smoking improved this relationship (r = 0.77). Using the adjusted intersubject equation and a patient's salivary lithium value, we observed a strong correlation between the predicted vs. observed serum lithium levels (r = 0.70). Most patients had highly stable saliva/serum ratios across multiple visits, with longitudinal variability significantly greater with age. Use of the intrasubject saliva/serum ratio from a single prior observation had similar predictive power to the use of the adjusted intersubject equation. However, the use of the mean intrasubject ratio from three prior observations could robustly predict serum lithium levels (predicted vs. observed r = 0.90). CONCLUSIONS These findings strongly suggest that saliva could be used for lithium monitoring, and open the door for the development and implementation of a point-of-care salivary lithium device for use at home or the clinic. We propose that the use of saliva will dramatically improve treatment opportunities for patients with mood disorders.
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Affiliation(s)
- Georgia M. Parkin
- Department of EpidemiologyUniversity of California IrvineIrvineCaliforniaUSA,Institute for Interdisciplinary Salivary Bioscience ResearchUniversity of California IrvineIrvineCaliforniaUSA
| | - Michael J. McCarthy
- Department of PsychiatryUniversity of California San DiegoSan DiegoCaliforniaUSA,VA San Diego Healthcare SystemSan DiegoCaliforniaUSA
| | - Soe H. Thein
- Department of Psychiatry and Behavioral SciencesUC Davis Health SystemSacramentoCaliforniaUSA
| | - Hillary L. Piccerillo
- Institute for Interdisciplinary Salivary Bioscience ResearchUniversity of California IrvineIrvineCaliforniaUSA
| | | | - Douglas A. Granger
- Institute for Interdisciplinary Salivary Bioscience ResearchUniversity of California IrvineIrvineCaliforniaUSA,Johns Hopkins University School of NursingBloomberg School of Public Health, and School of MedicineBaltimoreMarylandUSA
| | - Elizabeth A. Thomas
- Department of EpidemiologyUniversity of California IrvineIrvineCaliforniaUSA,Institute for Interdisciplinary Salivary Bioscience ResearchUniversity of California IrvineIrvineCaliforniaUSA
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16
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Abstract
Bacterial biofilms, which can be found wherever there is water and a substrate, can cause chronic infections and clogging of industrial flow systems. Despite intensive investigation of the dynamics and rheological properties of biofilms, the impact of their rheological properties on streamer growth remains unknown. We numerically simulated biofilm growth in a pillar-flow and investigated the effects of rheological properties of a filamentous flow-shaped biofilm, called a 'streamer', on its formation by varying the viscoelasticity. The flow-field is assumed to be a Stokes flow and is solved by a boundary element method. A Maxwell model is used for extracellular matrix-mediated streamer growth to express the fluidity of streamer formations. Both high elastic modulus and viscosity are needed for streamer formation, and high viscosity promotes streamer growth at low cell concentrations. Our findings are consistent with experimental observations and can explain the relationship between the cell concentrations and viscosity at which streamers form.
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Affiliation(s)
- Hiroki Kitamura
- Department of Finemechanics, Tohoku University, Aoba 6-6-01, Sendai, Miyagi, Japan
| | - Toshihiro Omori
- Department of Finemechanics, Tohoku University, Aoba 6-6-01, Sendai, Miyagi, Japan
| | - Takuji Ishikawa
- Department of Finemechanics, Tohoku University, Aoba 6-6-01, Sendai, Miyagi, Japan.,Department of Biomedical Engineering, Tohoku University, Aoba 6-6-01, Sendai, Miyagi, Japan
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17
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Li AL, Chou CY, Chen CL, Wu KL, Lin SC, Chen HC, Wang MC, Chang CC, Hsu BG, Wu MS, Ma N, Huang CC. The MicroRNA Prediction Models as Ancillary Diagnosis Biomarkers for Urothelial Carcinoma in Patients With Chronic Kidney Disease. Front Med (Lausanne) 2021; 8:726214. [PMID: 34660637 PMCID: PMC8517232 DOI: 10.3389/fmed.2021.726214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 12/24/2022] Open
Abstract
Urothelial carcinoma is a common urological cancer in chronic kidney disease patients. Cystoscopy and urine cytology are the clinical diagnostic tools for UC. However, cystoscopy is an invasive procedure, while urine cytology showed low sensitivity for low-grade urothelial tumors. High accuracy with non-invasive tools for UC is needed for CKD patients. Our study collected a total of 272 urine and 138 plasma samples to detect the miRNA expression levels for establishing UC signatures from CKD patients. Seventeen candidate miRNAs of biofluids were selected and confirmed by qRT-PCR. Our results showed that urinary miR-1274a and miR-30a-5p expression levels were significantly lower but miR-19a-5p expression levels were higher in UC when compared with CKD. In plasma samples, miR-155-5p, miR-19b-1-5p, miR-378, and miR-636 showed significantly lower expression in UC compared to those with CKD. The Kaplan-Meier curve showed that lower expression of miR-19a, miR-19b, miR-636 and miR-378, and higher expression of miR-708-5p were associated with poor prognosis in patients with bladder cancer. In addition, we produced classifiers for predicting UC by multiple logistic regression. The urine signature was developed with four miRNAs, and the AUC was 0.8211. Eight miRNA expression levels from both urine and plasma samples were examined, and the AUC was 0.8595. Two miRNA classifiers and the nomograms could improve the drawbacks of current UC biomarker screenings for patients with CKD.
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Affiliation(s)
- An-Lun Li
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Department of Internal Medicine, Asia University Hospital, Taichung, Taiwan
| | - Chien-Lung Chen
- Department of Nephrology, Landseed International Hospital, Taoyuan, Taiwan
| | - Kun-Lin Wu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.,Division of Nephrology, Department of Internal Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Chun Chen
- Division of Nephrology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Cheng Kung University Hospital, Tainan, Taiwan
| | - Chia-Chu Chang
- Division of Nephrology, Department of Internal Medicine, Kuang Tien General Hospital, Taichung, Taiwan.,Department of Nutrition, Hungkuang University, Taichung, Taiwan
| | - Bang-Gee Hsu
- Division of Nephrology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Taipei Medical University and Hospitals, Taipei, Taiwan
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and The Kidney Institute, China Medical University and Hospitals, Taichung, Taiwan
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18
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Morlion A, Everaert C, Nuytens J, Hulstaert E, Vandesompele J, Mestdagh P. Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA Biol 2021; 18:215-222. [PMID: 34470578 PMCID: PMC8682977 DOI: 10.1080/15476286.2021.1971438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.
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Affiliation(s)
- Annelien Morlion
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Celine Everaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Justine Nuytens
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Hulstaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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19
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Wang WX, Springer JE, Hatton KW. MicroRNAs as Biomarkers for Predicting Complications following Aneurysmal Subarachnoid Hemorrhage. Int J Mol Sci 2021; 22:ijms22179492. [PMID: 34502401 PMCID: PMC8431281 DOI: 10.3390/ijms22179492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/14/2022] Open
Abstract
Aneurysmal subarachnoid hemorrhage (aSAH) is a high mortality hemorrhagic stroke that affects nearly 30,000 patients annually in the United States. Approximately 30% of aSAH patients die during initial hospitalization and those who survive often carry poor prognosis with one in five having permanent physical and/or cognitive disabilities. The poor outcome of aSAH can be the result of the initial catastrophic event or due to the many acute or delayed neurological complications, such as cerebral ischemia, hydrocephalus, and re-bleeding. Unfortunately, no effective biomarker exists to predict or diagnose these complications at a clinically relevant time point when neurologic injury can be effectively treated and managed. Recently, a number of studies have demonstrated that microRNAs (miRNAs) in extracellular biofluids are highly associated with aSAH and complications. Here we provide an overview of the current research on relevant human studies examining the correlation between miRNAs and aSAH complications and discuss the potential application of using miRNAs as biomarkers in aSAH management.
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Affiliation(s)
- Wang-Xia Wang
- Sanders-Brown Center on Aging, Spinal Cord and Brain Injury Research Center, and the Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA
- Correspondence: ; Tel.: +1-859-218-3886
| | - Joe E. Springer
- Spinal Cord and Brain Injury Research Center, and the Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA;
| | - Kevin W. Hatton
- Department of Anesthesiology Critical Care Medicine, University of Kentucky, Lexington, KY 40536, USA;
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20
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Sun R, Cui C, Zhou Y, Cui Q. Comprehensive Analysis of RNA Expression Correlations between Biofluids and Human Tissues. Genes (Basel) 2021; 12:935. [PMID: 34207420 PMCID: PMC8234006 DOI: 10.3390/genes12060935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, biofluid has been considered a promising source of non-invasive biomarkers for health monitoring and disease diagnosis. However, the expression consistency between biofluid and human tissue, which is fundamental to RNA biomarker development, has not been fully evaluated. In this study, we collected expression profiles across 53 human tissues and five main biofluid types. Utilizing the above dataset, we uncovered a globally positive correlation pattern between various biofluids (including blood, urine, bile, saliva and stool) and human tissues. However, significantly varied biofluid-tissue similarity levels and tendencies were observed between mRNA and lncRNA. Moreover, a higher correlation was found between biofluid types and their functionally related and anatomically closer tissues. In particular, a highly specific correlation was discovered between urine and the prostate. The biological sex of the donor was also proved to be an important influencing factor in biofluid-tissue correlation. Moreover, genes enriched in basic biological processes were found to display low variability across biofluid types, while genes enriched in catabolism-associated pathways were identified as highly variable.
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Affiliation(s)
| | | | | | - Qinghua Cui
- Key Laboratory of Molecular Cardiovascular Sciences of the Ministry of Education, Center for Non-Coding RNA Medicine, Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; (R.S.); (C.C.); (Y.Z.)
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21
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Hildebrandt A, Kirchner B, Nolte-'t Hoen ENM, Pfaffl MW. miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples. J Mol Biol 2021; 433:167070. [PMID: 34052284 DOI: 10.1016/j.jmb.2021.167070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized, membrane-enclosed vesicles released by cells for intercellular communication. EVs are involved in pathological processes and miRNAs in EVs have gained interest as easily accessible biomolecules in liquid biopsies for diagnostic purposes. To validate potential miRNA biomarker, transcriptome analyses must be carried out to detect suitable reference miRNAs. miREV is a database with over 400 miRNA sequencing data sets and helps the researcher to find suitable reference miRNAs for their individual experimental setup. The researcher can put together a specific sample set in miREV, which is similar to his own experimental concept in order to find the most suitable references. This allows to run validation experiments without having to carry out a complex and costly transcriptome analysis priorly. Additional read count tables of each generated sample set are downloadable for further analysis. miREV is freely available at https://www.physio.wzw.tum.de/mirev/.
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22
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Abstract
Saliva has become an attractive body fluid for on-site, remote, and real-time monitoring of oral and systemic health. At the same time, the scientific community needs a saliva-centered information platform that keeps pace with the rapid accumulation of new data and knowledge by annotating, refining, and updating the salivary proteome catalog. We developed the Human Salivary Proteome (HSP) Wiki as a public data platform for researching and retrieving custom-curated data and knowledge on the saliva proteome. The HSP Wiki is dynamically compiled and updated based on published saliva proteome studies and up-to-date protein reference records. It integrates a wide range of available information by funneling in data from established external protein, genome, transcriptome, and glycome databases. In addition, the HSP Wiki incorporates data from human disease-related studies. Users can explore the proteome of saliva simply by browsing the database, querying the available data, performing comparisons of data sets, and annotating existing protein entries using a simple, intuitive interface. The annotation process includes both user feedback and curator committee review to ensure the quality and validity of each entry. Here, we present the first overview of features and functions the HSP Wiki offers. As a saliva proteome-centric, publicly accessible database, the HSP Wiki will advance the knowledge of saliva composition and function in health and disease for users across a wide range of disciplines. As a community-based data- and knowledgebase, the HSP Wiki will serve as a worldwide platform to exchange salivary proteome information, inspire novel research ideas, and foster cross-discipline collaborations. The HSP Wiki will pave the way for harnessing the full potential of the salivary proteome for diagnosis, risk prediction, therapy of oral and systemic diseases, and preparedness for emerging infectious diseases.Database URL: https://salivaryproteome.nidcr.nih.gov/.
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Affiliation(s)
- W W Lau
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - M Hardt
- Forsyth Center for Salivary Diagnostics, Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA.,Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Y H Zhang
- Department of Bioscience Research, College of Dentistry, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - M Freire
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Infectious Diseases and Global Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - S Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, USA
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23
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Jose M, Oudebrouckx G, Bormans S, Veske P, Thoelen R, Deferme W. Monitoring Body Fluids in Textiles: Combining Impedance and Thermal Principles in a Printed, Wearable, and Washable Sensor. ACS Sens 2021; 6:896-907. [PMID: 33499590 DOI: 10.1021/acssensors.0c02037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This work explores the feasibility of coupling two different techniques, the impedance and the transient plane source (TPS) principle, to quantify the moisture content and its compositional parameters simultaneously. The sensor is realized directly on textiles with the use of printing and coating technology. Impedance measurements use the fluid's electrical properties, while the TPS measurements are based on the thermal effusivity of the liquid. Impedance and TPS measurements show equal competency in measuring the fluid volume with a lowest measurable quantity of 0.5 μL, enabling ultralow volume passive measurements for sweat analysis. Both sensor principles were tested by monitoring the drying of a wet cloth and the measurements show perfect repeatability and accuracy. Nevertheless, when the biofluid property changes, the TPS sensor does not reflect this information on its readings, whereas, on the other hand, impedance can provide information on compositional changes. However, since the volume of the fluid changes simultaneously, one cannot differentiate between a volume change and a compositional change from impedance measurements alone. Therefore, we show in this work that we can apply impedance to measure the compositional properties; meanwhile, the TPS measurements accurately carry out volume measurements irrespective of the interferences from its compositional variations. To prove this, both of these techniques are applied for the quantification and composition monitoring of sweat, showing the capability to measure moisture content and compositional parameters simultaneously. TPS measurements can also be an indicator of the local temperature of the medium confined by the sensor, and it does not influence the fluid parameters. Compiling both impedance and thermal sensors in a single platform triggers smart wearable prospects of metering the liquid volume and simultaneously analyzing other compositional changes and body temperature. Finally, the repeatability and stability of the sensor readings and the washability of the device are tested. This device could be a potential sensing tool in real-life applications, such as wound monitoring and sweat analysis, and could be a promising addition toward future smart wearable sensors.
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Affiliation(s)
- Manoj Jose
- Hasselt University, Institute for Materials Research (IMO-IMOMEC) 1, 3590 Diepenbeek, Belgium
- IMEC, Division IMOMEC, Wetenschapspark 1, B-3590 Diepenbeek, Belgium
| | - Gilles Oudebrouckx
- Hasselt University, Institute for Materials Research (IMO-IMOMEC) 1, 3590 Diepenbeek, Belgium
- IMEC, Division IMOMEC, Wetenschapspark 1, B-3590 Diepenbeek, Belgium
| | - Seppe Bormans
- Hasselt University, Institute for Materials Research (IMO-IMOMEC) 1, 3590 Diepenbeek, Belgium
- IMEC, Division IMOMEC, Wetenschapspark 1, B-3590 Diepenbeek, Belgium
| | - Paula Veske
- Centre for Microsystems Technology (CMST), IMEC and Ghent University, Technologiepark 126, 9052 Gent, Belgium
| | - Ronald Thoelen
- Hasselt University, Institute for Materials Research (IMO-IMOMEC) 1, 3590 Diepenbeek, Belgium
- IMEC, Division IMOMEC, Wetenschapspark 1, B-3590 Diepenbeek, Belgium
| | - Wim Deferme
- Hasselt University, Institute for Materials Research (IMO-IMOMEC) 1, 3590 Diepenbeek, Belgium
- IMEC, Division IMOMEC, Wetenschapspark 1, B-3590 Diepenbeek, Belgium
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24
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Akhunov S, Ashurov K, Axmedov S, Kasimov B, Rotshteyn V, Radjabov A, Usmanov D. Development of surface ionization mass spectrometry for detection of stimulants in human urine. Eur J Mass Spectrom (Chichester) 2021; 27:29-38. [PMID: 33745338 DOI: 10.1177/14690667211002777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This paper demonstrates direct detection of stimulants such as amphetamine, methamphetamine and cocaine spiked with untreated urine and a real world sample using surface ionization mass spectrometry. Spiked samples were analyzed without preliminary chromatographic separation and extraction procedure using the developed method. Moreover, in order to check the analytical capabilities of the method non-extracted real world sample was analyzed. After liquid-liquid extraction, the same sample was analyzed using the method for comparative study. Limit of detection of spiked samples was in the range of 10 pg (10 ng/ml) to 100 pg (100 ng/ml). Linear ranges of samples were two orders of magnitude or more than two orders of magnitude. It was revealed these spiked samples and real world sample can be analyzed without preliminary chromatographic separation and preliminary extraction procedure due to high selectivity of the method and the presence of the indicator lines of studied analytes in the mass spectra. The surface ionization mass spectrometry data was attested by the GC/MS analysis of these samples.
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Affiliation(s)
- Shovkatjon Akhunov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Khatam Ashurov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Sherzod Axmedov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Beknazar Kasimov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Vladimir Rotshteyn
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Azim Radjabov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
| | - Dilshadbek Usmanov
- Laboratory of Adsorption and Emission Phenomenon, Institute of Ion-Plasma and Laser Technologies, Tashkent, Uzbekistan
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25
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Hackshaw KV, Miller JS, Aykas DP, Rodriguez-Saona L. Vibrational Spectroscopy for Identification of Metabolites in Biologic Samples. Molecules 2020; 25:E4725. [PMID: 33076318 PMCID: PMC7587585 DOI: 10.3390/molecules25204725] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Vibrational spectroscopy (mid-infrared (IR) and Raman) and its fingerprinting capabilities offer rapid, high-throughput, and non-destructive analysis of a wide range of sample types producing a characteristic chemical "fingerprint" with a unique signature profile. Nuclear magnetic resonance (NMR) spectroscopy and an array of mass spectrometry (MS) techniques provide selectivity and specificity for screening metabolites, but demand costly instrumentation, complex sample pretreatment, are labor-intensive, require well-trained technicians to operate the instrumentation, and are less amenable for implementation in clinics. The potential for vibration spectroscopy techniques to be brought to the bedside gives hope for huge cost savings and potential revolutionary advances in diagnostics in the clinic. We discuss the utilization of current vibrational spectroscopy methodologies on biologic samples as an avenue towards rapid cost saving diagnostics.
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Affiliation(s)
- Kevin V. Hackshaw
- Department of Internal Medicine, Division of Rheumatology, Dell Medical School, The University of Texas, 1601 Trinity St, Austin, TX 78712, USA
| | - Joseph S. Miller
- Department of Medicine, Ohio University Heritage College of Osteopathic Medicine, Dublin, OH 43016, USA;
| | - Didem P. Aykas
- Department of Food Science and Technology, Ohio State University, Columbus, OH 43210, USA; (D.P.A.); (L.R.-S.)
- Department of Food Engineering, Faculty of Engineering, Adnan Menderes University, Aydin 09100, Turkey
| | - Luis Rodriguez-Saona
- Department of Food Science and Technology, Ohio State University, Columbus, OH 43210, USA; (D.P.A.); (L.R.-S.)
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26
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Corey-Bloom J, Fischer RS, Kim A, Snell C, Parkin GM, Granger DA, Granger SW, Thomas EA. Levels of Interleukin-6 in Saliva, but Not Plasma, Correlate with Clinical Metrics in Huntington's Disease Patients and Healthy Control Subjects. Int J Mol Sci 2020; 21:ijms21176363. [PMID: 32887270 PMCID: PMC7503233 DOI: 10.3390/ijms21176363] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
Growing evidence suggests that inflammatory responses, in both the brain and peripheral tissues, contribute to disease pathology in Huntington's disease (HD), an inherited, progressive neurodegenerative disorder typically affecting adults in their 30-40 s. Hence, studies of inflammation-related markers in peripheral fluids might be useful to better characterize disease features. In this study, we measured levels of C-reactive protein (CRP), Interleukin-6 (IL-6), interleukin 1 beta (IL-1B), and alpha-amylase (AA) in saliva and plasma from n = 125 subjects, including n = 37 manifest HD patients, n = 36 premanifest patients, and n = 52 healthy controls, using immunoassays. We found increases in salivary levels of IL-6, IL-1B and CRP across different disease groups and increased levels of IL-6 in the plasma of HD patients as compared to premanifest patients and controls. The levels of salivary IL-6 were significantly correlated with each of the other salivary markers, as well as with IL-6 levels measured in plasma. Further, salivary IL-6 and IL-1B levels were significantly positively correlated with Total Motor Score (TMS) and chorea scores and negatively correlated with Total Functional Capacity (TFC) in HD patients, whereby in healthy control subjects, IL-6 was significantly negatively correlated with Montreal Cognitive Assessment (MoCA) and the Symbol Digit Modalities test (SDM). Interestingly, the plasma levels of IL-6 did not show similar correlations to any clinical measures in either HD or control subjects. These findings suggest that salivary IL-6 is particularly relevant as a potential non-invasive biomarker for HD symptoms. The advent of an effective, dependable salivary biomarker would meet the urgent need for a less invasive means of identifying and monitoring HD disease progression.
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Affiliation(s)
- Jody Corey-Bloom
- Department of Neurosciences, University of California, San Diego, CA 92037, USA; (J.C.-B.); (C.S.)
| | - Ryan S. Fischer
- Salimetrics, LLC, Carlsbad, CA 92008, USA; (R.S.F.); (S.W.G.)
| | - Aeri Kim
- Department of Neurosciences, University of California, San Diego, CA 92037, USA; (J.C.-B.); (C.S.)
| | - Chase Snell
- Department of Neurosciences, University of California, San Diego, CA 92037, USA; (J.C.-B.); (C.S.)
| | - Georgia M. Parkin
- Institute for Interdisciplinary Salivary Bioscience Research, University of California Irvine, Irvine, CA 92697, USA; (G.M.P.); (D.A.G.)
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | - Douglas A. Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California Irvine, Irvine, CA 92697, USA; (G.M.P.); (D.A.G.)
- Bloomberg School of Public Health, and School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Elizabeth A. Thomas
- Institute for Interdisciplinary Salivary Bioscience Research, University of California Irvine, Irvine, CA 92697, USA; (G.M.P.); (D.A.G.)
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
- Correspondence:
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27
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Foroutan A, Fitzsimmons C, Mandal R, Piri-Moghadam H, Zheng J, Guo A, Li C, Guan LL, Wishart DS. The Bovine Metabolome. Metabolites 2020; 10:metabo10060233. [PMID: 32517015 PMCID: PMC7345087 DOI: 10.3390/metabo10060233] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/17/2023] Open
Abstract
From an animal health perspective, relatively little is known about the typical or healthy ranges of concentrations for many metabolites in bovine biofluids and tissues. Here, we describe the results of a comprehensive, quantitative metabolomic characterization of six bovine biofluids and tissues, including serum, ruminal fluid, liver, Longissimus thoracis (LT) muscle, semimembranosus (SM) muscle, and testis tissues. Using nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography–tandem mass spectrometry (LC–MS/MS), and inductively coupled plasma–mass spectrometry (ICP–MS), we were able to identify and quantify more than 145 metabolites in each of these biofluids/tissues. Combining these results with previous work done by our team on other bovine biofluids, as well as previously published literature values for other bovine tissues and biofluids, we were able to generate quantitative reference concentration data for 2100 unique metabolites across five different bovine biofluids and seven different tissues. These experimental data were combined with computer-aided, genome-scale metabolite inference techniques to add another 48,628 unique metabolites that are biochemically expected to be in bovine tissues or biofluids. Altogether, 51,801 unique metabolites were identified in this study. Detailed information on these 51,801 unique metabolites has been placed in a publicly available database called the Bovine Metabolome Database.
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Affiliation(s)
- Aidin Foroutan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (A.F.); (C.F.); (L.L.G.)
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (A.F.); (C.F.); (L.L.G.)
- Agriculture and Agri-Food Canada, Edmonton, AB T6G 2P5, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - Hamed Piri-Moghadam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - AnChi Guo
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - Carin Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (A.F.); (C.F.); (L.L.G.)
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (R.M.); (H.P.-M.); (J.Z.); (A.G.); (C.L.)
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
- Correspondence:
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28
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Kumar S, Fritz Z, Sulakhiya K, Theis T, Berthiaume F. Transcriptional Factors and Protein Biomarkers as Target Therapeutics in Traumatic Spinal Cord and Brain Injury. Curr Neuropharmacol 2020; 18:1092-1105. [PMID: 32442086 PMCID: PMC7709155 DOI: 10.2174/1570159x18666200522203542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/19/2020] [Accepted: 05/07/2020] [Indexed: 12/04/2022] Open
Abstract
Traumatic injury to the spinal cord (SCI) and brain (TBI) are serious health problems and affect many people every year throughout the world. These devastating injuries are affecting not only patients but also their families socially as well as financially. SCI and TBI lead to neurological dysfunction besides continuous inflammation, ischemia, and necrosis followed by progressive neurodegeneration. There are well-established changes in several other processes such as gene expression as well as protein levels that are the important key factors to control the progression of these diseases. We are not yet able to collect enough knowledge on the underlying mechanisms leading to the altered gene expression profiles and protein levels in SCI and TBI. Cell loss is hastened by the induction or imbalance of pro- or anti-inflammatory expression profiles and transcription factors for cell survival after or during trauma. There is a sequence of events of dysregulation of these factors from early to late stages of trauma that opens a therapeutic window for new interventions to prevent/restrict the progression of these diseases. There has been increasing interest in the modulation of these factors for improving the patient’s quality of life by targeting both SCI and TBI. Here, we review some of the recent transcriptional factors and protein biomarkers that have been developed and discovered in the last decade in the context of targeted therapeutics for SCI and TBI patients.
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Affiliation(s)
- Suneel Kumar
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Zachary Fritz
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Kunjbihari Sulakhiya
- Department of Pharmacy, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Thomas Theis
- W. M. Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers, The
State University of New Jersey, Piscataway, New Jersey, USA
| | - Francois Berthiaume
- Department of Biomedical Engineering, The State University of New Jersey, Piscataway, New Jersey, USA
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29
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Corey-Bloom J, Haque A, Aboufadel S, Snell C, Fischer RS, Granger SW, Granger DA, Thomas EA. Uric Acid as a Potential Peripheral Biomarker for Disease Features in Huntington's Patients. Front Neurosci 2020; 14:73. [PMID: 32194366 PMCID: PMC7065265 DOI: 10.3389/fnins.2020.00073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022] Open
Abstract
Oxidative stress has long been implicated in the pathophysiology and progression of Huntington's disease (HD). Uric acid (UA) is a naturally occurring antioxidant that is present in the brain and periphery. Growing evidence has implicated UA as a molecular biomarker for several neurodegenerative diseases, most notably Parkinson's disease (PD). In this study, we investigated UA levels in clinical samples from HD patients and normal controls (NCs) and assessed potential relationships between UA levels and disease and clinical data. UA levels were measured in plasma (n = 107) and saliva (n = 178) samples from premanifest (pre-HD) and manifest HD patients and control subjects. Gender effects of UA levels were observed in both biofluids, with male patients showing higher UA levels compared to female patients. Comparisons of UA levels across diagnostic groups, separated by gender, revealed that both plasma and salivary UA levels were significantly lower in female pre-HD and manifest HD patients compared to NCs. Salivary levels of UA were also significantly lower in male manifest HD patients versus controls, but not in plasma. Correlations of peripheral UA levels to clinical data also showed differences according to gender. In male HD patients, both plasma and salivary UA levels were significantly negatively correlated with total functional capacity (TFC), while positive correlations were observed with total motor score (TMS). Female HD patients showed a significant positive correlation between plasma UA levels and TMS, while salivary UA levels from female patients were significantly correlated to disease burden. Finally, in a separate cohort, we show that UA levels are decreased in postmortem prefrontal cortical samples (n = 20) from HD subjects compared to matched controls. These findings suggest that decreased levels of UA in the brains of HD patients can be reflected in peripheral fluids, with salivary measures of UA particularly offering significant promise as a potentially relevant, non-invasive biomarker of disease symptoms and burden. Our findings further highlight the impact of sexual dimorphism in HD pathophysiology.
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Affiliation(s)
- Jody Corey-Bloom
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Ameera Haque
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Sameer Aboufadel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Chase Snell
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | | | | | - Douglas A Granger
- Salimetrics, LLC, Carlsbad, CA, United States.,Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, Irvine, CA, United States.,School of Medicine, Johns Hopkins University, Baltimore, MD, United States.,Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,School of Nursing, Johns Hopkins University, Baltimore, MD, United States
| | - Elizabeth A Thomas
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, Irvine, CA, United States.,Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, United States
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30
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Edman MC, Janga SR, Kakan SS, Okamoto CT, Freire D, Feigenbaum D, Lew M, Hamm-Alvarez SF. Tears - more to them than meets the eye: why tears are a good source of biomarkers in Parkinson's disease. Biomark Med 2020; 14:151-163. [PMID: 32064896 DOI: 10.2217/bmm-2019-0364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tears are a known source of biomarkers for both ocular and systemic diseases with particular advantages; specifically, the noninvasiveness of sample collection and a unique and increasingly better-defined protein composition. Here, we discuss our rationale for use of tears for discovery of biomarkers for Parkinson's disease (PD). These reasons include literature supporting changes in tear flow and composition in PD, and the interconnections between the ocular surface system and neurons affected in PD. We highlight recent data on the identification of tear biomarkers including oligomeric α-synuclein, associated with neuronal degeneration in PD, in tears of PD patients and discuss possible sources for its release into tears. Challenges and next steps for advancing such biomarkers to clinical usage are highlighted.
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Affiliation(s)
- Maria C Edman
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Srikanth R Janga
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Shruti Singh Kakan
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Curtis T Okamoto
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Daniel Freire
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Danielle Feigenbaum
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mark Lew
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sarah F Hamm-Alvarez
- Department of Ophthalmology and Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
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31
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Ramaswamy P, Yadav R, Pal PK, Christopher R. Clinical Application of Circulating MicroRNAs in Parkinson's Disease: The Challenges and Opportunities as Diagnostic Biomarker. Ann Indian Acad Neurol 2020; 23:84-97. [PMID: 32055127 PMCID: PMC7001448 DOI: 10.4103/aian.aian_440_19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Discovery of evolutionarily conserved, nonprotein-coding, endogenous microRNAs has induced a paradigm shift in the overall understanding of gene regulation. Now, microRNAs are considered and classified as master regulators of gene expression as they regulate a wide range of processes – gene regulation, splicing, translation and posttranscriptional modifications. Besides, dysregulated microRNAs have been related to many diseases, including Parkinson's and related disorders. Several studies proposed that differentially expressed microRNAs as a potential biomarker. So far, there is no accepted clinical diagnostic test for Parkinson's disease based on biochemical analysis of biological fluids. However, circulating microRNAs possess many vital features typical of reliable biomarkers and discriminates Parkinson's patients from healthy control with much higher sensitivity and specificity. Though they show tremendous promise as a putative biomarker, translating these research findings to clinical application is often met with many obstacles. Most of the candidate microRNAs reported as a diagnostic biomarker is not organ-specific, and their overlap is low between studies. Therefore this review aimed to highlight the challenges in the application of microRNA in guiding disease discrimination decisions and its future prospects as a diagnostic biomarker in Parkinson's Disease.
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Affiliation(s)
- Palaniswamy Ramaswamy
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, Karnataka, India
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32
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Li J, He X, Deng Y, Yang C. An Update on Isolation Methods for Proteomic Studies of Extracellular Vesicles in Biofluids. Molecules 2019; 24:E3516. [PMID: 31569778 DOI: 10.3390/molecules24193516] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are lipid bilayer enclosed particles which present in almost all types of biofluids and contain specific proteins, lipids, and RNA. Increasing evidence has demonstrated the tremendous clinical potential of EVs as diagnostic and therapeutic tools, especially in biofluids, since they can be detected without invasive surgery. With the advanced mass spectrometry (MS), it is possible to decipher the protein content of EVs under different physiological and pathological conditions. Therefore, MS-based EV proteomic studies have grown rapidly in the past decade for biomarker discovery. This review focuses on the studies that isolate EVs from different biofluids and contain MS-based proteomic analysis. Literature published in the past decade (2009.1-2019.7) were selected and summarized with emphasis on isolation methods of EVs and MS analysis strategies, with the aim to give an overview of MS-based EV proteomic studies and provide a reference for future research.
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33
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Zhang J, Luo H, Xiong Z, Wan K, Liao Q, He H. High-throughput sequencing reveals biofluid exosomal miRNAs associated with immunity in pigs. Biosci Biotechnol Biochem 2019; 84:53-62. [PMID: 31483222 DOI: 10.1080/09168451.2019.1661767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Large numbers of miRNAs are found in biofluid exosomes. We isolated ~50-200 nm diameter exosomes from four types of porcine biofluid (urine, plasma, semen, and bile) using serial centrifugation and ultracentrifugation procedures. A total of 42.15 M raw data were generated from four small RNA libraries. This produced 40.17 M map-able sequences, of which we identified 204 conserved miRNAs, and 190 novel candidate miRNAs. Furthermore, we identified 34 miRNAs specifically expressed in only one library, all with well-characterized immune-related functions. A set of five universally abundant miRNAs (miR-148a-3p, miR-21-5p, let-7f-5p, let-7i-5p, and miR-99a-5p) across all four biofluids was also found. Function enrichment analysis revealed that the target genes of the five ubiquitous miRNAs are primarily involved in immune and RNA metabolic processes. In summary, our findings suggest that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system.
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Affiliation(s)
- Jie Zhang
- College of Animal Science, Southwest University, Chongqing, China
| | - Hui Luo
- College of Animal Science, Southwest University, Chongqing, China
| | - Zibiao Xiong
- College of Animal Science, Southwest University, Chongqing, China
| | - Kun Wan
- College of Animal Science, Southwest University, Chongqing, China
| | - Qinfeng Liao
- College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing, China
| | - Hang He
- College of Animal Science and Technology, Chongqing Three Gorges Vocational College, Chongqing, China
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34
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Hamm-Alvarez SF, Okamoto CT, Janga SR, Feigenbaum D, Edman MC, Freire D, Shah M, Ghanshani R, Mack WJ, Lew MF. Oligomeric α-synuclein is increased in basal tears of Parkinson's patients. Biomark Med 2019; 13:941-952. [PMID: 31262201 DOI: 10.2217/bmm-2019-0167] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: Secretion of proteins into basal tears of Parkinson's disease (PD) patients may be altered by changes in nerve function. Materials & methods: Oligomeric α-SynOligo and total α-SynTotal, CCL-2, DJ-1, LF and MMP-9 were measured in basal tears from 93 PD patients and 82 age- and sex-equivalent healthy controls. Results: α-SynTotal was decreased (p = 0.0043), whereas α-SynOligo (p < 0.0001) and the ratio of α-SynOligo/α-SynTotal (p < 0.0001) were increased in basal tears from PD patients compared with healthy controls. Area under receiver-operating curves of α-SynOligo and α-SynOligo/α-SynTotal contents were 0.70 (95% confidence limits: 0.621-0.774) and 0.72 (95% confidence limits: 0.642-0.792). Conclusion: PD patient basal tears may contain biomarkers that can be assayed noninvasively and inexpensively.
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Affiliation(s)
- Sarah F Hamm-Alvarez
- Department of Ophthalmology & Roski Eye Institute, Keck School of Medicine, Los Angeles, CA 90033-6103, USA.,Department of Pharmacology & Pharmaceutical Sciences, School of Pharmacy, Los Angeles, CA 90033-6103, USA
| | - Curtis T Okamoto
- Department of Pharmacology & Pharmaceutical Sciences, School of Pharmacy, Los Angeles, CA 90033-6103, USA
| | - Srikanth R Janga
- Department of Ophthalmology & Roski Eye Institute, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Danielle Feigenbaum
- Department of Neurology, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Maria C Edman
- Department of Ophthalmology & Roski Eye Institute, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Daniel Freire
- Department of Neurology, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Mihir Shah
- Department of Ophthalmology & Roski Eye Institute, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Raveena Ghanshani
- Department of Ophthalmology & Roski Eye Institute, Keck School of Medicine, Los Angeles, CA 90033-6103, USA.,Department of Neurology, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
| | - Wendy J Mack
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033-6103, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine, Los Angeles, CA 90033-6103, USA
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Verber NS, Shepheard SR, Sassani M, McDonough HE, Moore SA, Alix JJP, Wilkinson ID, Jenkins TM, Shaw PJ. Biomarkers in Motor Neuron Disease: A State of the Art Review. Front Neurol 2019; 10:291. [PMID: 31001186 PMCID: PMC6456669 DOI: 10.3389/fneur.2019.00291] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/06/2019] [Indexed: 12/17/2022] Open
Abstract
Motor neuron disease can be viewed as an umbrella term describing a heterogeneous group of conditions, all of which are relentlessly progressive and ultimately fatal. The average life expectancy is 2 years, but with a broad range of months to decades. Biomarker research deepens disease understanding through exploration of pathophysiological mechanisms which, in turn, highlights targets for novel therapies. It also allows differentiation of the disease population into sub-groups, which serves two general purposes: (a) provides clinicians with information to better guide their patients in terms of disease progression, and (b) guides clinical trial design so that an intervention may be shown to be effective if population variation is controlled for. Biomarkers also have the potential to provide monitoring during clinical trials to ensure target engagement. This review highlights biomarkers that have emerged from the fields of systemic measurements including biochemistry (blood, cerebrospinal fluid, and urine analysis); imaging and electrophysiology, and gives examples of how a combinatorial approach may yield the best results. We emphasize the importance of systematic sample collection and analysis, and the need to correlate biomarker findings with detailed phenotype and genotype data.
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Affiliation(s)
- Nick S Verber
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Stephanie R Shepheard
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Matilde Sassani
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Harry E McDonough
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Sophie A Moore
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - James J P Alix
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Iain D Wilkinson
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Tom M Jenkins
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Pamela J Shaw
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
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Fernando T, Sawala A, Bailey AP, Gould AP, Driscoll PC. An Improved Method for Measuring Absolute Metabolite Concentrations in Small Biofluid or Tissue Samples. J Proteome Res 2019; 18:1503-1512. [PMID: 30757904 PMCID: PMC6456871 DOI: 10.1021/acs.jproteome.8b00773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The
measurement of absolute metabolite concentrations in small
samples remains a significant analytical challenge. This is particularly
the case when the sample volume is only a few microliters or less
and cannot be determined accurately via direct measurement. We previously
developed volume determination with two standards (VDTS) as a method
to address this challenge for biofluids. As a proof-of-principle,
we applied VDTS to NMR spectra of polar metabolites in the hemolymph
(blood) of the tiny yet powerful genetic model Drosophila
melanogaster. This showed that VDTS calculation of absolute
metabolite concentrations in fed versus starved Drosophila larvae is more accurate than methods utilizing normalization to
total spectral signal. Here, we introduce paired VDTS (pVDTS), an
improved VDTS method for biofluids and solid tissues that implements
the statistical power of paired control and experimental replicates.
pVDTS utilizes new equations that also include a correction for dilution
errors introduced by the variable surface wetness of solid samples.
We then show that metabolite concentrations in Drosophila larvae are more precisely determined and logically consistent using
pVDTS than using the original VDTS method. The refined pVDTS workflow
described in this study is applicable to a wide range of different
tissues and biofluids.
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Affiliation(s)
- Tharindu Fernando
- Physiology and Metabolism Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
| | - Annick Sawala
- Physiology and Metabolism Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
| | - Andrew P Bailey
- Physiology and Metabolism Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
| | - Alex P Gould
- Physiology and Metabolism Laboratory , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
| | - Paul C Driscoll
- Metabolomics Science Technology Platform , The Francis Crick Institute , 1 Midland Road , London NW1 1AT , U.K
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Ilea A, Andrei V, Feurdean CN, Băbțan AM, Petrescu NB, Câmpian RS, Boșca AB, Ciui B, Tertiș M, Săndulescu R, Cristea C. Saliva, a Magic Biofluid Available for Multilevel Assessment and a Mirror of General Health-A Systematic Review. Biosensors (Basel) 2019; 9:bios9010027. [PMID: 30769890 PMCID: PMC6468816 DOI: 10.3390/bios9010027] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/01/2019] [Accepted: 02/09/2019] [Indexed: 02/07/2023]
Abstract
Background: Saliva has been recently proposed as an alternative to classic biofluid analyses due to both availability and reliability regarding the evaluation of various biomarkers. Biosensors have been designed for the assessment of a wide spectrum of compounds, aiding in the screening, diagnosis, and monitoring of pathologies and treatment efficiency. This literature review aims to present the development in the biosensors research and their utility using salivary assessment. Methods: a comprehensive literature search has been conducted in the PubMed database, using the keywords “saliva” and “sensor”. A two-step paper selection algorithm was devised and applied. Results: The 49 papers selected for the present review focused on assessing the salivary biomarkers used in general diseases, oral pathologies, and pharmacology. The biosensors proved to be reliable tools for measuring the salivary levels of biochemical metabolic compounds such as glucose, proteinases and proteins, heavy metals and various chemical compounds, microorganisms, oncology markers, drugs, and neurotransmitters. Conclusions: Saliva is a biofluid with a significant clinical applicability for the evaluation and monitoring of a patient’s general health. Biosensors designed for assessing a wide range of salivary biomarkers are emerging as promising diagnostic or screening tools for improving the patients’ quality of life.
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Affiliation(s)
- Aranka Ilea
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Oral Rehabilitation, Oral Health and Dental Office Management, Faculty of Dentistry, 400012 Cluj-Napoca, Romania.
| | - Vlad Andrei
- DMD, Rezident doctor in Periodontology, Clinical County Hospital, 540136 Târgu Mureș, Romania.
| | - Claudia Nicoleta Feurdean
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Oral Rehabilitation, Oral Health and Dental Office Management, Faculty of Dentistry, 400012 Cluj-Napoca, Romania.
| | - Anida-Maria Băbțan
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Oral Rehabilitation, Oral Health and Dental Office Management, Faculty of Dentistry, 400012 Cluj-Napoca, Romania.
| | - Nausica Bianca Petrescu
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Oral Rehabilitation, Oral Health and Dental Office Management, Faculty of Dentistry, 400012 Cluj-Napoca, Romania.
| | - Radu Septimiu Câmpian
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Oral Rehabilitation, Oral Health and Dental Office Management, Faculty of Dentistry, 400012 Cluj-Napoca, Romania.
| | - Adina Bianca Boșca
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Histology, Faculty of Medicine, 400349 Cluj, Romania.
| | - Bianca Ciui
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Analytical Chemistry, Faculty of Pharmacy, 400349 Cluj, Romania.
| | - Mihaela Tertiș
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Analytical Chemistry, Faculty of Pharmacy, 400349 Cluj, Romania.
| | - Robert Săndulescu
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Analytical Chemistry, Faculty of Pharmacy, 400349 Cluj, Romania.
| | - Cecilia Cristea
- Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, Department of Analytical Chemistry, Faculty of Pharmacy, 400349 Cluj, Romania.
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Wang Q, Zhang Y, Zheng N, Guo L, Song X, Zhao S, Wang J. Biological System Responses of Dairy Cows to Aflatoxin B1 Exposure Revealed with Metabolomic Changes in Multiple Biofluids. Toxins (Basel) 2019; 11:toxins11020077. [PMID: 30717092 PMCID: PMC6410036 DOI: 10.3390/toxins11020077] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 01/20/2019] [Indexed: 01/28/2023] Open
Abstract
Research on mycotoxins now requires a systematic study of post-exposure organisms. In this study, the effects of aflatoxin B1 (AFB1) on biofluids biomarkers were examined with metabolomics and biochemical tests. The results showed that milk concentration of aflatoxin M1 changed with the addition or removal of AFB1. AFB1 significantly affected serum concentrations of superoxide dismutase (SOD) and malon dialdehyde (MDA), SOD/MDA, and the total antioxidant capacity. Significant differences of volatile fatty acids and NH3-N were detected in the rumen fluid. Eighteen rumen fluid metabolites, 11 plasma metabolites, and 9 milk metabolites were significantly affected by the AFB1. These metabolites are mainly involved in the pathway of amino acids metabolism. Our results suggest that not only is the study of macro-indicators (milk composition and production) important, but that more attention should be paid to micro-indicators (biomarkers) when assessing the risks posed by mycotoxins to dairy cows.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liya Guo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiaoming Song
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Salari A, Dalton C. Simultaneous Pumping and Mixing of Biological Fluids in a Double-Array Electrothermal Microfluidic Device. Micromachines (Basel) 2019; 10:mi10020092. [PMID: 30696037 PMCID: PMC6413218 DOI: 10.3390/mi10020092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/18/2019] [Accepted: 01/25/2019] [Indexed: 11/29/2022]
Abstract
Transport and mixing of minute amounts of biological fluids are significantly important in lab-on-a-chip devices. It has been shown that the electrothermal technique is a suitable candidate for applications involving high-conductivity biofluids, such as blood, saliva, and urine. Here, we introduce a double-array AC electrothermal (ACET) device consisting of two opposing microelectrode arrays, which can be used for simultaneous mixing and pumping. First, in a 2D simulation, an optimum electrode-pair configuration capable of achieving fast transverse mixing at a microfluidic channel cross-section is identified by comparing different electrode geometries. The results show that by adjusting the applied voltage pattern and position of the asymmetrical microelectrodes in the two arrays, due to the resultant circular flow streamlines, the time it takes for the analytes to be convected across the channel cross-section is reduced by 95% compared to a diffusion-only-based transport regime, and by 80% compared to a conventional two-layer ACET device. Using a 3D simulation, the fluid transport (pumping and mixing) capabilities of such an electrode pair placed at different angles longitudinally relative to the channel was studied. It was found that an asymmetrical electrode configuration placed at an angle in the range of 30°≤θ≤45° can significantly increase transversal mixing efficiency while generating strong longitudinal net flow. These findings are of interest for lab-on-a-chip applications, especially for biosensors and immunoassays, where mixing analyte solutions while simultaneously moving them through a microchannel can greatly enhance the sensing efficiency.
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Affiliation(s)
- Alinaghi Salari
- Biomedical Engineering Graduate Program, Ryerson University, Toronto, ON M5B 2K3, Canada.
- Institute for Biomedical Engineering, Science and Technology (iBEST), St. Michael's Hospital, Toronto, ON M5B 1T8, Canada.
- Keenan Research Centre, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada.
| | - Colin Dalton
- Electrical and Computer Engineering Department, University of Calgary, Calgary, AB T2N 1N4, Canada.
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB T2N 1N4, Canada.
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Halvaei S, Daryani S, Eslami-S Z, Samadi T, Jafarbeik-Iravani N, Bakhshayesh TO, Majidzadeh-A K, Esmaeili R. Exosomes in Cancer Liquid Biopsy: A Focus on Breast Cancer. Mol Ther Nucleic Acids 2018; 10:131-141. [PMID: 29499928 PMCID: PMC5862028 DOI: 10.1016/j.omtn.2017.11.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/04/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023]
Abstract
The important challenge about cancer is diagnosis in primary stages and proper treatment. Although classical clinico-pathological features of the tumor have major prognostic value, the advances in diagnosis and treatment are indebted to discovery of molecular biomarkers and control of cancer in the pre-invasive state. Moreover, the efficiency of available therapeutic options is highly diminished, and chemotherapy is still the main treatment due to lack of enough specific targets. Accordingly, finding the new noninvasive biomarkers for cancer is still an important clinical challenge that is not achieved yet. There are current technologies to screen, diagnose, prognose, and treat cancer, but the limitations of these implements and procedures are undeniable. Liquid biopsy as a noninvasive method has a promising future in the field of cancer, and exosomes as one of the recent areas have drawn much attention. In this review, the potential capability of exosomes is summarized in cancer with the special focus on breast cancer as the second cause of cancer mortality in women all around the world. It discusses reasons to choose exosomes for liquid biopsy and the studies related to different potential biomarkers found in the exosomes. Moreover, exosome studies on milk as a specific biofluid are also discussed. At last, because choosing the method for exosome studies is very challenging, a summary of different techniques is provided.
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Affiliation(s)
- Sina Halvaei
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Shiva Daryani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Zahra Eslami-S
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Tannaz Samadi
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Narges Jafarbeik-Iravani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | | | - Keivan Majidzadeh-A
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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Abstract
Background: A 2017 study reported that “Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi”. Analysis of two human blood plasma sequencing datasets was said to provide evidence for uptake of plant miRNAs into human plasma. The results were also purportedly inconsistent with contamination. Methods: Sequences from public datasets and miRNA databases were compared with results downloaded from the website of the reporting journal. Results: Only one putative plant miRNA (“peu-MIR2910) mapped consistently above background, and this sequence is found with 100% identity in a human rRNA. Several other rarer but consistently mapped putative plant miRNAs also have 100% or near 100% matches to human transcripts or genomic sequences, and some do not appear to map to plant genomes at all. Conclusions: Reanalysis of public data suggests that dietary plant xenomiR uptake is not supported, but instead confirms previous findings that detection of rare plant miRNAs in mammalian sequencing datasets is artifactual. Some putative plant miRNAs, including MIR2910 and MIR2911, may represent human sequence contamination or other artifacts in plant studies, emphasizing the need for rigorous controls and data filtering strategies when assessing possible xenomiRNAs.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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Habartová L, Logerová H, Tomaník L, Marešová A, Setnička V. Electronic circular dichroism for the detection of microalbuminuria. Chirality 2018; 30:576-580. [PMID: 29443429 DOI: 10.1002/chir.22832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
Over the past decades, chiroptical spectroscopy has proved its incomparable ability to elucidate the structure and spatial arrangement of chiral molecules. Systematic analysis of biomolecules in the natural environment of biofluids, however, remains challenging. In this study, we used chiroptical spectroscopy to monitor urinary levels of human serum albumin. Not only severe proteinuria but even just a slightly increased urinary excretion of albumin (microalbuminuria) may indicate serious health complications, especially for diabetic individuals. Given the chiral nature of albumin and its typical spectral pattern, it may be easily observable by chiroptical spectroscopy, particularly electronic circular dichroism. The performed chiroptical analysis of urine not only allowed the detection of clinically confirmed microalbuminuria but was also able to reveal this pathological condition in cases beyond the diagnostic capability of common clinical procedures. Thus, our approach suggests that electronic circular dichroism is a useful tool for the fast and reliable qualitative monitoring of microalbuminuria with the potential for a quantitative analysis in the future.
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Affiliation(s)
- Lucie Habartová
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Hana Logerová
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague 6, Czech Republic.,Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague 10, Czech Republic
| | - Lukáš Tomaník
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Aneta Marešová
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Vladimír Setnička
- Department of Analytical Chemistry, University of Chemistry and Technology Prague, Prague 6, Czech Republic
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NEMKOV T, HANSEN KC, D’ALESSANDRO A. A three-minute method for high-throughput quantitative metabolomics and quantitative tracing experiments of central carbon and nitrogen pathways. Rapid Commun Mass Spectrom 2017; 31:663-673. [PMID: 28195377 PMCID: PMC5364945 DOI: 10.1002/rcm.7834] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 05/07/2023]
Abstract
RATIONALE The implementation of mass spectrometry (MS)-based metabolomics is advancing many areas of biomedical research. The time associated with traditional chromatographic methods for resolving metabolites prior to mass analysis has limited the potential to perform large-scale, highly powered metabolomics studies and clinical applications. METHODS Here we describe a three-minute method for the rapid profiling of central metabolic pathways through UHPLC/MS, tracing experiments in vitro and in vivo, and targeted quantification of compounds of interest using spiked in heavy labeled standards. RESULTS This method has shown to be linear, reproducible, selective, sensitive, and robust for the semi-targeted analysis of central carbon and nitrogen metabolism. Isotopically labeled internal standards are used for absolute quantitation of steady-state metabolite levels and de novo synthesized metabolites in tracing studies. We further propose exploratory applications to biofluids, cell and tissue extracts derived from relevant biomedical/clinical samples. CONCLUSIONS While limited to the analysis of central carbon and nitrogen metabolism, this method enables the analysis of hundreds of samples per day derived from diverse biological matrices. This approach makes it possible to analyze samples from large patient populations for translational research, personalized medicine, and clinical metabolomics applications. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Travis NEMKOV
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
| | - Kirk C. HANSEN
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
| | - Angelo D’ALESSANDRO
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
- Corresponding author: Angelo D’Alessandro, PhD, Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, 12801 East 17th Ave., 80045 Aurora, CO, Phone # 303 724-8495,
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Lee CW, Su H, Cai YD, Wu MT, Wu DC, Shiea J. Rapid Identification of Psychoactive Drugs in Drained Gastric Lavage Fluid and Whole Blood Specimens of Drug Overdose Patients Using Ambient Mass Spectrometry. ACTA ACUST UNITED AC 2017; 6:S0056. [PMID: 28573080 DOI: 10.5702/massspectrometry.s0056] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 11/23/2022]
Abstract
Psychoactive drug overdoses are life-threatening and require prompt and proper treatment in the emergency room to minimize morbidity and mortality. Prompt identification of the ingested psychoactive drugs is challenging, since witness recall is unreliable and patients' symptoms do not necessarily explain their loss of consciousness. Gas and liquid chromatography mass spectrometric analyses have been the traditionally employed methods to detect and identify abused substances; however, these techniques are time-consuming and labor-intensive. In this study, thermal desorption electrospray ionization mass spectrometry, an ambient mass spectrometric technique, was applied to rapidly characterize flunitrazepam, lysergic acid diethylamide, and 3,4-methylenedioxy-methamphetamine in drained gastric lavage fluid, and ketamine, cocaine, amphetamine and norketamine in whole blood samples. No pretreatment of the gastric lavage fluid specimens was required and the entire analytical process took less than 30 s per specimen. Liquid-liquid extraction, followed by centrifugation, was performed on the whole blood samples. The corresponding compounds were identified through matching the obtained mass spectrometric data with those provided by commercial databases. The limits-of-detection of the tested drugs in both drained gastric lavage fluid and whole blood samples are at sub ppm levels. This is sensitive enough for emergency medical application, since the quantities of medications ingested by overdosed abusers are much higher than the amounts that were tested.
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Affiliation(s)
- Chi-Wei Lee
- Graduate Institute of Medicine, Kaohsiung Medical University.,Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University
| | - Hung Su
- Department of Chemistry, National Sun Yat-Sen University
| | - You-Da Cai
- Department of Chemistry, National Sun Yat-Sen University
| | - Ming-Tsang Wu
- Department of Public Health, College of Health Sciences, Kaohsiung Medical University
| | - Den-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-Sen University.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University
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Iftikhar H, Carney GE. Evidence and potential in vivo functions for biofluid miRNAs: From expression profiling to functional testing: Potential roles of extracellular miRNAs as indicators of physiological change and as agents of intercellular information exchange. Bioessays 2016; 38:367-78. [PMID: 26934338 DOI: 10.1002/bies.201500130] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A controversial hypothesis in RNA biology is that extracellular microRNAs (miRNAs), including those in biofluids, have non-cell-autonomous activities. Several studies have characterized biofluid miRNA profiles in healthy or diseased individuals but generally have failed to identify distinct disease signatures. It remains unclear whether alterations in fluid miRNA levels are simply indicators of physiological change or whether miRNAs are taken up by new cells at concentrations sufficient to affect gene expression. There are limitations to biofluid miRNA studies performed to date: methodology for isolating and quantifying biofluid miRNAs is not standardized across studies; mechanistic details of miRNA release and uptake are incomplete; and efforts to assess non-cell-autonomous effects of extracellular miRNAs have employed predominantly in vitro strategies. We describe controversies and questions that need to be addressed to test possible in vivo roles of extracellular miRNAs and propose model organisms with rich genetic toolkits for carrying out in vivo functional analyses.
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Affiliation(s)
- Hina Iftikhar
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Ginger E Carney
- Department of Biology, Texas A&M University, College Station, TX, USA
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46
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Galasko D. Expanding the Repertoire of Biomarkers for Alzheimer's Disease: Targeted and Non-targeted Approaches. Front Neurol 2015; 6:256. [PMID: 26733934 PMCID: PMC4680926 DOI: 10.3389/fneur.2015.00256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 01/12/2023] Open
Abstract
The first biofluid markers developed for Alzheimer’s disease (AD) used targeted approaches for discovery. These initial biomarkers were directed at key protein constituents of the hallmark brain lesions in AD. Biomarkers for plaques targeted the amyloid beta protein (Aβ) and for tangles, the microtubule-associated protein tau. Cerebrospinal fluid levels of Aβ and tau have excellent diagnostic utility and can be used to monitor aspects of therapeutic development. Recent research has extended our current concepts of AD, which now include a slow buildup of pathology during a long pre-symptomatic period, a complex cascade of pathological pathways in the brain that may accelerate once symptoms develop, the potential of aggregated proteins to spread across brain pathways, and interactions with vascular and other age-associated brain pathologies. There are many potential roles for biomarkers within this landscape. A more diverse set of biomarkers would provide a better picture of the staging and state of pathological events in the brain across the stages of AD. The aim of this review is to focus on methods of biomarker discovery that may help to expand the currently accepted biomarkers. Opportunities and approaches for targeted and non-targeted (or −omic) biomarker discovery are highlighted, with examples from recent studies. How biomarker discoveries can be developed and integrated to become useful tools in diagnostic and therapeutic efforts is discussed.
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Affiliation(s)
- Douglas Galasko
- Department of Neurosciences, Shiley-Marcos Alzheimer's Disease Research Center, University of California, San Diego , La Jolla, CA , USA
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47
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Affiliation(s)
- Victor Levenson
- CatholicHealth Initiatives Center for Translational Research, 801 West Baltimore Street, Ste 302, Baltimore, MD 21201, USA
| | - Yuriko Mori
- CatholicHealth Initiatives Center for Translational Research, 801 West Baltimore Street, Ste 302, Baltimore, MD 21201, USA
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48
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Mitchell AL, Gajjar KB, Theophilou G, Martin FL, Martin-Hirsch PL. Vibrational spectroscopy of biofluids for disease screening or diagnosis: translation from the laboratory to a clinical setting. J Biophotonics 2014; 7:153-165. [PMID: 24648213 DOI: 10.1002/jbio.201400018] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 06/03/2023]
Abstract
There remains a need for objective and cost-effective approaches capable of diagnosing early-stage disease in point-of-care clinical settings. Given an increasingly ageing population resulting in a rising prevalence of chronic diseases, the need for screening to facilitate the personalising of therapies to prevent or slow down pathology development will increase. Such a tool needs to be robust but simple enough to be implemented into clinical practice. There is interest in extracting biomarkers from biofluids (e.g., plasma or serum); techniques based on vibrational spectroscopy provide an option. Sample preparation is minimal, techniques involved are relatively low-cost, and data frameworks are available. This review explores the evidence supporting the applicability of vibrational spectroscopy to generate spectral biomarkers of disease in biofluids. We extend the inter-disciplinary nature of this approach to hypothesise a microfluidic platform that could allow such measurements. With an appropriate lightsource, such engineering could revolutionize screening in the 21(st) century.
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Affiliation(s)
- Alana L Mitchell
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
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Tzirakis K, Papaharilaou Y, Giordano D, Ekaterinaris J. Numerical investigation of biomagnetic fluids in circular ducts. Int J Numer Method Biomed Eng 2014; 30:297-317. [PMID: 24123947 DOI: 10.1002/cnm.2603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 06/17/2013] [Accepted: 07/19/2013] [Indexed: 06/02/2023]
Abstract
A mathematical model for the description of biomagnetic fluid flow exposed to a magnetic field that accounts for both electric and magnetic properties of the biofluid is presented. This is achieved by adding the Lorentz and magnetization forces in the Navier-Stokes equations. To demonstrate the effects of magnetic fields, we consider the case of laminar, incompressible, viscous, the steady flow of a Newtonian biomagnetic fluid (i) between two parallel plates; and (ii) through a straight rigid tube with a 60% in diameter, 84% on area, axisymmetric stenosis. Two external magnetic fields were investigated: one produced by an infinite wire carrying constant current, and a dipole-like field. We show, numerically and analytically, that the wire produces an irrotational force that, independent of its intensity, only alters the pressure leaving the velocity field unaffected. In contrast, when the fluid is exposed to the dipole-like field, which generates a rotational force, then both pressure and velocity can be strongly influenced even at moderate field strengths. Similar trends were obtained when a time varying flow is simulated through the axisymmetric stenosis in the presence of the dipole-like rotational magnetic field. It is expected that our findings could have important applications in blood flow control.
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Affiliation(s)
- K Tzirakis
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
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50
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McAlexander MA, Phillips MJ, Witwer KW. Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid. Front Genet 2013; 4:83. [PMID: 23720669 PMCID: PMC3655275 DOI: 10.3389/fgene.2013.00083] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 04/24/2013] [Indexed: 11/30/2022] Open
Abstract
Interest in extracellular RNA (exRNA) has intensified as evidence accumulates that these molecules may be useful as indicators of a wide variety of biological conditions. To establish specific exRNA molecules as clinically relevant biomarkers, reproducible recovery from biological samples and reliable measurements of the isolated RNA are paramount. Toward these ends, careful and rigorous comparisons of technical procedures are needed at all steps from sample handling to RNA isolation to RNA measurement protocols. In the investigations described in this methods paper, RT-qPCR was used to examine the apparent recovery of specific endogenous miRNAs and a spiked-in synthetic RNA from blood plasma samples. RNA was isolated using several widely used RNA isolation kits, with or without the addition of glycogen as a carrier. Kits examined included total RNA isolation systems that have been commercially available for several years and commonly adapted for extraction of biofluid RNA, as well as more recently introduced biofluids-specific RNA methods. Our conclusions include the following: some RNA isolation methods appear to be superior to others for the recovery of RNA from biological fluids; addition of a carrier molecule seems to be beneficial for some but not all isolation methods; and quantitative recovery of RNA is observed from increasing volumes of cerebrospinal fluid.
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Affiliation(s)
- Melissa A McAlexander
- Retrovirus Laboratory, Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine Baltimore, MD, USA
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