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del Valle E, Rubio-Sardón N, Menéndez-Pérez C, Martínez-Pinilla E, Navarro A. Apolipoprotein D as a Potential Biomarker in Neuropsychiatric Disorders. Int J Mol Sci 2023; 24:15631. [PMID: 37958618 PMCID: PMC10650001 DOI: 10.3390/ijms242115631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Neuropsychiatric disorders (NDs) are a diverse group of pathologies, including schizophrenia or bipolar disorders, that directly affect the mental and physical health of those who suffer from them, with an incidence that is increasing worldwide. Most NDs result from a complex interaction of multiple genes and environmental factors such as stress or traumatic events, including the recent Coronavirus Disease (COVID-19) pandemic. In addition to diverse clinical presentations, these diseases are heterogeneous in their pathogenesis, brain regions affected, and clinical symptoms, making diagnosis difficult. Therefore, finding new biomarkers is essential for the detection, prognosis, response prediction, and development of new treatments for NDs. Among the most promising candidates is the apolipoprotein D (Apo D), a component of lipoproteins implicated in lipid metabolism. Evidence suggests an increase in Apo D expression in association with aging and in the presence of neuropathological processes. As a part of the cellular neuroprotective defense machinery against oxidative stress and inflammation, changes in Apo D levels have been demonstrated in neuropsychiatric conditions like schizophrenia (SZ) or bipolar disorders (BPD), not only in some brain areas but in corporal fluids, i.e., blood or serum of patients. What is not clear is whether variation in Apo D quantity could be used as an indicator to detect NDs and their progression. This review aims to provide an updated view of the clinical potential of Apo D as a possible biomarker for NDs.
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Affiliation(s)
- Eva del Valle
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Nuria Rubio-Sardón
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Carlota Menéndez-Pérez
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Eva Martínez-Pinilla
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
| | - Ana Navarro
- Department of Morphology and Cell Biology, University of Oviedo, 33006 Oviedo, Spain; (E.d.V.); (N.R.-S.); (C.M.-P.); (A.N.)
- Instituto de Neurociencias del Principado de Asturias (INEUROPA), 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Spain
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2
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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Del-Pozo J, Headon DJ, Glover JD, Azar A, Schuepbach-Mallepell S, Bhutta MF, Riddell J, Maxwell S, Milne E, Schneider P, Cheeseman M. The EDA deficient mouse has Zymbal's gland hypoplasia and acute otitis externa. Dis Model Mech 2022; 15:274882. [PMID: 35107126 PMCID: PMC8990926 DOI: 10.1242/dmm.049034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 01/21/2022] [Indexed: 12/05/2022] Open
Abstract
In mice, rats, dogs and humans, the growth and function of sebaceous glands and eyelid Meibomian glands depend on the ectodysplasin signalling pathway. Mutation of genes encoding the ligand EDA, its transmembrane receptor EDAR and the intracellular signal transducer EDARADD leads to hypohidrotic ectodermal dysplasia, characterised by impaired development of teeth and hair, as well as cutaneous glands. The rodent ear canal has a large auditory sebaceous gland, the Zymbal’s gland, the function of which in the health of the ear canal has not been determined. We report that EDA-deficient mice, EDAR-deficient mice and EDARADD-deficient rats have Zymbal’s gland hypoplasia. EdaTa mice have 25% prevalence of otitis externa at postnatal day 21 and treatment with agonist anti-EDAR antibodies rescues Zymbal’s glands. The aetiopathogenesis of otitis externa involves infection with Gram-positive cocci, and dosing pregnant and lactating EdaTa females and pups with enrofloxacin reduces the prevalence of otitis externa. We infer that the deficit of sebum is the principal factor in predisposition to bacterial infection, and the EdaTa mouse is a potentially useful microbial challenge model for human acute otitis externa. Summary: Ectodysplasin-deficient mice have growth retardation of the auditory sebaceous Zymbal's gland and are predisposed to spontaneous bacterial infection of the outer ear canal by opportunistic pathogens.
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Affiliation(s)
- Jorge Del-Pozo
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Denis J Headon
- Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - James D Glover
- Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Ali Azar
- Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | | | - Mahmood F Bhutta
- Department of ENT, Royal Sussex County Hospital, Brighton BN2 5BE, UK.,Brighton and Sussex Medical School, Falmer Brighton BN1 9PX, UK
| | - Jon Riddell
- Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Scott Maxwell
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Elspeth Milne
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Michael Cheeseman
- Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK.,Division of Pathology, University of Edinburgh, Institute of Genetics & Molecular Medicine, Crewe Road, Edinburgh, EH4 2XR, Scotland, UK.,Centre for Comparative Pathology, Division of Pathology, University of Edinburgh, Institute of Genetics & Molecular Medicine, Crewe Road, Edinburgh, EH4 2XR, Scotland, UK
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4
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Ferrara F, Zoupanou S, Primiceri E, Ali Z, Chiriacò MS. Beyond liquid biopsy: Toward non-invasive assays for distanced cancer diagnostics in pandemics. Biosens Bioelectron 2021; 196:113698. [PMID: 34688113 PMCID: PMC8527216 DOI: 10.1016/j.bios.2021.113698] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/01/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022]
Abstract
Liquid biopsy technologies have seen a significant improvement in the last decade, offering the possibility of reliable analysis and diagnosis from several biological fluids. The use of these technologies can overcome the limits of standard clinical methods, related to invasiveness and poor patient compliance. Along with this there are now mature examples of lab-on-chips (LOC) which are available and could be an emerging and breakthrough technology for the present and near-future clinical demands that provide sample treatment, reagent addition and analysis in a sample-in/answer-out approach. The possibility of combining non-invasive liquid biopsy and LOC technologies could greatly assist in the current need for minimizing exposure and transmission risks. The recent and ongoing pandemic outbreak of SARS-CoV-2, indeed, has heavily influenced all aspects of life worldwide. Ordinary tasks have been forced to switch from “in presence” to “distanced”, limiting the possibilities for a large number of activities in all fields of life outside of the home. Unfortunately, one of the settings in which physical distancing has assumed noteworthy consequences is the screening, diagnosis and follow-up of diseases. In this review, we analyse biological fluids that are easily collected without the intervention of specialized personnel and the possibility that they may be used -or not-for innovative diagnostic assays. We consider their advantages and limitations, mainly due to stability and storage and their integration into Point-of-Care diagnostics, demonstrating that technologies in some cases are mature enough to meet current clinical needs.
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Affiliation(s)
- Francesco Ferrara
- STMicroelectronics s.r.l., via per Monteroni, 73100, Lecce, Italy; CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy.
| | - Sofia Zoupanou
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy; University of Salento, Dept. of Mathematics & Physics E. de Giorgi, Via Arnesano, 73100, Lecce, Italy
| | - Elisabetta Primiceri
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
| | - Zulfiqur Ali
- University of Teesside, School of Health & Life Sciences, Healthcare Innovation Centre, Middlesbrough, TS1 3BX, Tees Valley, England, UK
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5
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An apocrine mechanism delivers a fully immunocompetent exocrine secretion. Sci Rep 2021; 11:15915. [PMID: 34354130 PMCID: PMC8342421 DOI: 10.1038/s41598-021-95309-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Apocrine secretion is a recently discovered widespread non-canonical and non-vesicular secretory mechanism whose regulation and purpose is only partly defined. Here, we demonstrate that apocrine secretion in the prepupal salivary glands (SGs) of Drosophila provides the sole source of immune-competent and defense-response proteins to the exuvial fluid that lies between the metamorphosing pupae and its pupal case. Genetic ablation of its delivery from the prepupal SGs to the exuvial fluid decreases the survival of pupae to microbial challenges, and the isolated apocrine secretion has strong antimicrobial effects in "agar-plate" tests. Thus, apocrine secretion provides an essential first line of defense against exogenously born infection and represents a highly specialized cellular mechanism for delivering components of innate immunity at the interface between an organism and its external environment.
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Lecchi C, Zamarian V, Borriello G, Galiero G, Grilli G, Caniatti M, D'Urso ES, Roccabianca P, Perego R, Minero M, Legnani S, Calogero R, Arigoni M, Ceciliani F. Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa. Front Immunol 2020; 11:914. [PMID: 32547539 PMCID: PMC7273745 DOI: 10.3389/fimmu.2020.00914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Otitis externa is one of the most common diseases in dogs. It is associated with bacteria and yeast, which are regarded as secondary causes. Cerumen is a biological substance playing an important role in the protection of ear skin. The involvement of cerumen in immune defense is poorly understood. MicroRNAs can modulate the host immune response and can provide promising biomarkers for several inflammatory and infectious disorder diagnosis. The aims of this study were to profile the cerumen miRNA signature associated with otitis externa in dogs, integrate miRNAs to their target genes related to immune functions, and investigate their potential use as biomarkers. Cerumen was collected from healthy and otitis affected dogs and the expression of miRNAs was profiled by Next Generation Sequencing; the validation of the altered miRNAs was performed using RT-qPCR. The potential ability of miRNAs to modulate immune-related genes was investigated using bioinformatics tools. The results pointed out that 32 miRNAs, of which 14 were up- and 18 down-regulated, were differentially expressed in healthy vs. otitis-affected dogs. These results were verified by RT-qPCR. To assess the diagnostic value of miRNAs, ROC analysis was carried out, highlighting that 4 miRNAs are potential biomarkers to discriminate otitis-affected dogs. Bioinformatics showed that cerumen miRNAs may be involved in the modulation of host immune response. In conclusion, we have demonstrated for the first time that miRNAs can be efficiently extracted and quantified from cerumen, that their profile changes between healthy and otitis affected dogs, and that they may serve as potential biomarkers. Further studies are necessary to confirm their diagnostic value and to investigate their interaction with immune-related genes.
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Affiliation(s)
- Cristina Lecchi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valentina Zamarian
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Giorgia Borriello
- Dipartimento di Sanità Animale, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Giorgio Galiero
- Dipartimento di Sanità Animale, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Guido Grilli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Mario Caniatti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Elisa Silvia D'Urso
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paola Roccabianca
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Roberta Perego
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Michela Minero
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Sara Legnani
- Department of Small Animal Clinical Science, Institute of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Raffaele Calogero
- Department of Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di Torino, Turin, Italy
| | - Maddalena Arigoni
- Department of Biotechnology and Health Sciences, Molecular Biotechnology Center, Università di Torino, Turin, Italy
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
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7
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Shokry E, Filho NRA. Insights into cerumen and application in diagnostics: past, present and future prospective. Biochem Med (Zagreb) 2019; 27:030503. [PMID: 29180914 PMCID: PMC5696747 DOI: 10.11613/bm.2017.030503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/16/2017] [Indexed: 12/11/2022] Open
Abstract
Cerumen or earwax is an emerging bio-fluid in clinical diagnosis that has been very little exploited during the past decades in spite of its high diagnostic potential. It is highly abundant in diagnostic biomarkers such as genetic material, lipids, proteins, chemical elements, internal and external metabolites (e.g. hormones, volatile organic compounds, amino acids, xenobiotics etc.) reaching earwax from the blood circulation. Thus, it is able to reflect not only physiology, pathophysiology of the human body but can also detect recent and long term exposure to environmental pollutants, without the need of invasive blood tests and in the same time overcoming many disadvantages faced by using other diagnostic biological fluids. This review discusses the biology, functions, chemistry of earwax, past and current approaches for the study of its chemical composition, emphasizing how a detected variation in its composition can offer information of high clinical value, which can be useful in diagnosis of many diseases such as metabolic disorders and tumours as well as in forensic applications. It also presents details about techniques of sample collection, storage, and analysis. Moreover, it highlights concerns about the use of earwax for diagnostic purposes, which should be addressed to make earwax diagnostics a reality in the future.
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Affiliation(s)
- Engy Shokry
- Laboratório de Métodos de Extração e Separação, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
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8
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Proteomics and the human microbiome: where we are today and where we would like to be. Emerg Top Life Sci 2017; 1:401-409. [DOI: 10.1042/etls20170051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022]
Abstract
What are all these hundreds of different bacterial species doing in and on us? What interactions occur between the host and the microbes, and between the microbes themselves? By studying proteins, metaproteomics tries to find preliminary answers to these questions. There is daunting complexity around this; in fact, many of these proteins have never been studied before. This article is an introduction to the field of metaproteomics in the context of the human microbiome. It summarizes where we are and what we have learnt so far. The focus will be on faecal proteomics as most metaproteomics research has been conducted on that sample type. Metaproteomics has made major advances in the past decade, but new sample preparation strategies, improved mass spectrometric analysis and, most importantly, data analysis and interpretation have the potential to pave the way for large-cohort metaproteomics.
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9
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Licier R, Miranda E, Serrano H. A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples. Proteomes 2016; 4:proteomes4040031. [PMID: 28248241 PMCID: PMC5260964 DOI: 10.3390/proteomes4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 01/13/2023] Open
Abstract
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.
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Affiliation(s)
- Rígel Licier
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico.
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
| | - Eric Miranda
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
| | - Horacio Serrano
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
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10
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Herbst FA, Lünsmann V, Kjeldal H, Jehmlich N, Tholey A, von Bergen M, Nielsen JL, Hettich RL, Seifert J, Nielsen PH. Enhancing metaproteomics--The value of models and defined environmental microbial systems. Proteomics 2016; 16:783-98. [PMID: 26621789 DOI: 10.1002/pmic.201500305] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/24/2022]
Abstract
Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.
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Affiliation(s)
- Florian-Alexander Herbst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Vanessa Lünsmann
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Henrik Kjeldal
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin von Bergen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.,Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
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11
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Oberbach A, Adams V, Schlichting N, Heinrich M, Kullnick Y, Lehmann S, Lehmann S, Feder S, Correia JC, Mohr FW, Völker U, Jehmlich N. Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins. Clin Chim Acta 2015; 453:114-22. [PMID: 26688386 DOI: 10.1016/j.cca.2015.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 01/29/2023]
Abstract
Besides modulation of reverse cholesterol transport, high density lipoprotein (HDL) is able to modulate vascular function by stimulating endothelial nitric oxide synthase. Recently, it could be documented that this function of HDL was significantly impaired in patients with chronic heart failure (CHF). We investigated alterations in the HDL proteome in CHF patients. Therefore, HDL was isolated from 5 controls (HDLhealthy) and 5 CHF patients of NYHA-class IIIb (HDLCHF). Proteome analysis of HDL particles was performed by two-dimensional liquid chromatography-mass spectrometry (SCX/RP LC-MS/MS). In total, we identified 494 distinct proteins, of which 107 proteins were commonly found in both groups (HDLCHF and HDLhealthy) indicating a high inter-subject variability across HDL particles. Several important proteins (e.g. ITGA2, APBA1 or A2M) varied in level. Functional analysis revealed regulated pathways. A minor proportion of bacteria-derived proteins were also identified in the HDL-particles. The extension of the list of HDL-associated proteins allows besides their mere description new insights into alterations in HDL function in diseases. In addition, the detection of bacterial proteins bound to HDL will broaden our view of HDL not only as a cholesterol carrier but also as a carrier of proteins.
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Affiliation(s)
- Andreas Oberbach
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany; Division of Diagnostics, Experimental Surgery/CardiOMICs, Fraunhofer-Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Volker Adams
- Department of Cardiology, University of Leipzig, Heart Center Leipzig, Germany
| | - Nadine Schlichting
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany; Department of Pediatric Surgery, University of Leipzig, Germany
| | - Marco Heinrich
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | - Yvonne Kullnick
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | - Stefanie Lehmann
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | - Sven Lehmann
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | - Stefan Feder
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | - Joao Carlos Correia
- Department of Cardiac Surgery, University of Leipzig, Heart Center Leipzig, Germany
| | | | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany; DZHK (German Center for Cardiovascular Research) Partner Site Greifswald, Germany
| | - Nico Jehmlich
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany.
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Iadarola P, Fumagalli M, Bardoni AM, Salvini R, Viglio S. Recent applications of CE- and HPLC-MS in the analysis of human fluids. Electrophoresis 2015; 37:212-30. [PMID: 26426542 DOI: 10.1002/elps.201500272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/06/2015] [Accepted: 09/11/2015] [Indexed: 01/08/2023]
Abstract
The present review intends to cover the literature on the use of CE-/LC-MS for the analysis of human fluids, from 2010 until present. It has been planned to provide an overview of the most recent practical applications of these techniques to less extensively used human body fluids, including, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate, tear fluid, breast fluid, amniotic fluid, and cerumen. Potential pitfalls related to fluid collection and sample preparation, with particular attention to sample clean-up procedures, and methods of analysis, from the research laboratory to a clinical setting will also be addressed. While being apparent that proteomics/metabolomics represent the most prominent approaches for global identification/quantification of putative biomarkers for a variety of human diseases, evidence is also provided of the suitability of these sophisticated techniques for the detection of heterogeneous components carried by these fluids.
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Affiliation(s)
- Paolo Iadarola
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L. Spallanzani,", Biochemistry Unit, University of Pavia, Italy
| | - Anna Maria Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
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13
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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14
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Farkaš R. Apocrine secretion: New insights into an old phenomenon. Biochim Biophys Acta Gen Subj 2015; 1850:1740-50. [PMID: 25960390 DOI: 10.1016/j.bbagen.2015.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/21/2015] [Accepted: 05/04/2015] [Indexed: 01/14/2023]
Abstract
BACKGROUND While apocrine secretion was among the earliest secretory mechanisms to be identified, its underlying basis remains poorly understood. SCOPE OF REVIEW This review reappraises our understanding of apocrine secretion using insights about apocrine secretion from the salivary glands of Drosophila, in which molecular genetic analyses have provided a glimmer of hope for elucidating the mechanistic aspects of this fundamental process. MAJOR CONCLUSIONS In contrast to the well-defined process of exocytosis, apocrine secretion is non-vesicular transport and secretory pathway that entails the loss of part of the cytoplasm. It often involves apical protrusions and generates cytoplasmic fragments inside a secretory lumen. In its most intense phase this process is accompanied by the release of large fragments of cellular structures and entire organelles that include mitochondria, Golgi, and portions of the endoplasmic reticulum, among others. Proteomic analyses revealed that the secretion is composed of hundreds to thousands of membranous, cytoskeletal, microsomal, mitochondrial, ribosomal, and even nuclear as well as nucleolar proteins. Strikingly, although many nuclear proteins are released, the nuclear deoxyribonucleic acid itself remains intact. In spite of this complexity, it appears that several protein components of apocrine secretion are identical, regardless of the location of the apocrine gland. GENERAL SIGNIFICANCE This type of secretion appears to be common to many, if not all, barrier epithelial tissues including skin derivatives and the epididymis, and is implicated also in lung/bronchi and intestinal epithelium. Apocrine secretion is a mechanism that provides the en masse delivery of a very complex proteinaceous mixture from polarized epithelial tissues to allow for communication at exterior interfaces.
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Affiliation(s)
- Robert Farkaš
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Slovak Academy of Sciences, Vlárska 3, 83306 Bratislava, Slovakia.
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15
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Blaszykowski C, Sheikh S, Thompson M. A survey of state-of-the-art surface chemistries to minimize fouling from human and animal biofluids. Biomater Sci 2015. [DOI: 10.1039/c5bm00085h] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fouling of artificial surfaces by biofluids is a plague Biotechnology deeply suffers from. Herein, we inventory the state-of-the-art surface chemistries developed to minimize this effect from both human and animal biosamples.
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Affiliation(s)
| | - Sonia Sheikh
- University of Toronto
- Department of Chemistry – St. George campus
- Toronto
- Canada M5S 3H6
| | - Michael Thompson
- Econous Systems Inc
- Toronto
- Canada M5S 3H6
- University of Toronto
- Department of Chemistry – St. George campus
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16
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Stentzel S, Vu HC, Weyrich AM, Jehmlich N, Schmidt F, Salazar MG, Steil L, Völker U, Bröker BM. Altered immune proteome ofStaphylococcus aureusunder iron-restricted growth conditions. Proteomics 2014; 14:1857-67. [DOI: 10.1002/pmic.201300512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/16/2014] [Accepted: 05/22/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Stentzel
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Hai Chi Vu
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Anna Maria Weyrich
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Nico Jehmlich
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Frank Schmidt
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
- ZIK-FunGene Junior Research Group “Applied Proteomics”; University Medicine Greifswald; Greifswald Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Barbara M. Bröker
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
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17
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Pye CC, Singh A, Weese JS. Evaluation of the impact of tromethamine edetate disodium dihydrate on antimicrobial susceptibility ofPseudomonas aeruginosain biofilmin vitro. Vet Dermatol 2014; 25:120-3, e33-4. [DOI: 10.1111/vde.12115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Charlotte C. Pye
- Yu of Guelph Veterinary Dermatology; Guelph Veterinary Specialty Hospital; 1460 Gordon Street South Guelph Ontario N1L 1C8
| | - Ameet Singh
- Department Clinical Studies; Ontario Veterinary College; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - J. Scott Weese
- Department Pathobiology; Ontario Veterinary College; University of Guelph; Guelph Ontario Canada N1G 2W1
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