1
|
Abstract
Exosomes are extracellular vesicles secreted by cells and involved in intercellular communications among close and distant cells. Exosomes encapsulate and carry biomolecules as cargo to the recipient cells. They contain nucleic acids (DNA, RNA, microRNA) proteins and lipids. Each exosomal components may be isolated and be studied by specific techniques. In this chapter, different methods will be described to isolate DNA from exosomes, since it is important in shaping the response of the recipient cells following the exosome uptake in multiple scenarios, including physiological and pathological conditions. Moreover, the exosomal DNA may be a novel biomarker for diagnosis, disease progression and patient's treatment response.
Collapse
Affiliation(s)
- Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, United States.
| |
Collapse
|
2
|
Sánchez-Juanes F, González-Buitrago JM. Sample Treatment for Urine Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:125-135. [PMID: 31236841 DOI: 10.1007/978-3-030-12298-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Urine is a biological fluid that can be collected noninvasively in relatively large quantities which can be used for the search of biomarkers of disease, both diseases of the urological tract and systemic diseases. One of the most important aspects in proteomic studies is sample treatment before further analysis. Methods of preparation of a urine sample depend on the techniques that will be used later for separation and identification of the proteins. Also, urine preparation should be as simple as possible to increase reproducibility. Normal urine has a much diluted protein concentration with a high-salt content, which interferes with proteomic analysis. Thus, an initial step in the handling of urine sample should be to concentrate and eliminate salts. As range of protein concentrations in urine spans several orders of magnitude, effective proteomic analyses require either removal of most abundant protein or enrichment of the less abundant ones. In this chapter, we discuss the aspects related to the collection and treatment of urine for proteomic studies.
Collapse
Affiliation(s)
- Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Salamanca, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - José Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain. .,Servicio de Análisis Clínicos/Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain.
| |
Collapse
|
3
|
Musante L, Tataruch-Weinert D, Kerjaschki D, Henry M, Meleady P, Holthofer H. Residual urinary extracellular vesicles in ultracentrifugation supernatants after hydrostatic filtration dialysis enrichment. J Extracell Vesicles 2016; 6:1267896. [PMID: 28326167 PMCID: PMC5328348 DOI: 10.1080/20013078.2016.1267896] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Indexed: 12/16/2022] Open
Abstract
Urinary extracellular vesicles (UEVs) appear an ideal source of biomarkers for kidney and urogenital diseases. The majority of protocols designed for their isolation are based on differential centrifugation steps. However, little is still known of the type and amount of vesicles left in the supernatant. Here we used an isolation protocol for UEVs which uses hydrostatic filtration dialysis as first pre-enrichment step, followed by differential centrifugation. Transmission electron microscopy (TEM), mass spectrometry (MS), western blot, ELISA assays and tuneable resistive pulse sensing (TRPS) were used to characterise and quantify UEVs in the ultracentrifugation supernatant. TEM showed the presence of a variety of small size vesicles in the supernatant while protein identification by MS matched accurately with the protein list available in Vesiclepedia. Screening and relative quantification for specific vesicle markers showed that the supernatant was preferentially positive for CD9 and TSG101. ELISA tests for quantification of exosome revealed that 14%, was left in the supernatant with a particle diameter of 110 nm and concentration of 1.54 × 1010/ml. Here we show a comprehensive characterisation of exosomes and other small size urinary vesicles which the conventional differential centrifugation protocol may lose.
Collapse
Affiliation(s)
- Luca Musante
- Centre for BioAnalytical Sciences, Dublin City University , Dublin 9 , Ireland
| | | | - Dontscho Kerjaschki
- Clinical Institute of Pathology, Medical University of Vienna , Vienna , Austria
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University , Dublin 9 , Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University , Dublin 9 , Ireland
| | - Harry Holthofer
- Freiburg Institute for Advanced Studies, Albert-Ludwigs University , Freiburg , Germany
| |
Collapse
|
4
|
Grigor’eva AE, Tamkovich SN, Eremina AV, Tupikin AE, Kabilov MR, Chernykh VV, Vlassov VV, Laktionov PP, Ryabchikova EI. Exosomes in tears of healthy individuals: Isolation, identification, and characterization. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2016. [DOI: 10.1134/s1990750816020049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
5
|
Chen Z, Kim J. Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. BMC Urol 2016; 16:11. [PMID: 27000794 PMCID: PMC4802825 DOI: 10.1186/s12894-016-0129-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/10/2016] [Indexed: 12/16/2022] Open
Abstract
Background Assays of molecular biomarkers in urine are non-invasive compared to other body fluids and can be easily repeated. Based on the hypothesis that the secreted markers from the diseased organs may locally release into the body fluid in the vicinity of the injury, urine-based assays have been considered beneficial to monitoring bladder health and urological diseases. The urine proteome is much less complex than the serum and tissues, but nevertheless can contain biomarkers for diagnosis and prognosis of diseases. The urine metabolome has a much higher number and concentration of low-molecular metabolites than the serum or tissues, with a far lower lipid concentration, yet informs directly about dietary and microbial metabolism. Discussion We here discuss the use of mass spectrometry-based proteomics and metabolomics for urine biomarker assays, specifically with respect to the underlying mechanisms that trigger the pathological condition. Conclusion Molecular biomarker profiles, based on proteomics and metabolomics studies, reliably distinguish patients from healthy controls, stratify sub-populations with respect to treatment options, and predict therapeutic response of patients with urological disease.
Collapse
Affiliation(s)
- Zhaohui Chen
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA, 90048, USA. .,Department of Medicine, University of California, Los Angeles, CA, USA.
| |
Collapse
|
6
|
Thomas S, Hao L, Ricke WA, Li L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin Appl 2016; 10:358-70. [PMID: 26703953 DOI: 10.1002/prca.201500102] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/05/2015] [Accepted: 12/21/2015] [Indexed: 01/03/2023]
Abstract
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
Collapse
Affiliation(s)
- Samuel Thomas
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - William A Ricke
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Urology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
7
|
Grigor’eva A, Tamkovich S, Eremina A, Tupikin A, Kabilov M, Chernykh V, Vlassov V, Laktionov P, Ryabchikova E. Characteristics of exosomes andmicroparticles discovered in human tears. ACTA ACUST UNITED AC 2016; 62:99-106. [DOI: 10.18097/pbmc20166201099] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Exosomes represent a sort of extracellular vesicles, which transfer molecular signals in organism and possess markers of producing cells. Our study was aimed at search of exosomes in the tears of healthy humans, confirmation of their nature and examination of exosome morphological and molecular-biological characteristics. The tears (110-340 ml) were collected from 24 healthy donors (aged 46-60 years); individual probes were centrifuged at 20000 g for 15 min to pellet cell debris. The supernatants were examined in electron microscope using negative staining; and they were also used for isolation and purification of the exosomes by filtration (100 nm pore-size) and double ultracentrifugation (90 min at 100000 g, 4°C). The “pellets” were subjected to electron microscopy, immunolabeling. The RNA and DNA were isolated from the samples, and their sizes were evaluated by capillary electrophoresis, the concentration and localization of nucleic acids were determined. Sequencing of DNA was performed using MiSeq (“Illumina”, USA), data were analyzed using CLC GW 7.5 (“Qiagen”, USA). Sequences were mapped on human genome (hg19). Electron microscopy revealed in supernatants of the tears cell debris, spherical microparticles (20-40 nm), membrane vesicles and macromolecular aggregates. The “pellets” obtained after ultracentrifugation, contained microparticles (17%), spherical and cup-shaped EVs (40-100 nm, 83%), which were positive for CD63, CD9 and CD24 receptors (specific markers of exosomes). Our study showed presence of high amount of exosomes in human tears, and relation of the exosomes with RNA (size less than 200 nt) and DNA (size was 3-9 kb). Sequencing of the DNA showed that about 92% of the reads mapped to human genome.
Collapse
Affiliation(s)
- A.E. Grigor’eva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - S.N. Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - A.V. Eremina
- Novosibirsk Branch of FSBI “The Acad. S.N. Fyodorov Eye Microsurgery Complex”, Novosibirsk, Russia
| | - A.E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - M.R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - V.V. Chernykh
- Novosibirsk Branch of FSBI “The Acad. S.N. Fyodorov Eye Microsurgery Complex”, Novosibirsk, Russia
| | - V.V. Vlassov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - P.P. Laktionov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - E.I. Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| |
Collapse
|