1
|
Emerging Roles of Exosomes in Cancer for Possible Clinical Use. Cancers (Basel) 2022; 14:cancers14194603. [PMID: 36230526 PMCID: PMC9559386 DOI: 10.3390/cancers14194603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
|
2
|
Proteomics for comprehensive characterization of extracellular vesicles in neurodegenerative disease. Exp Neurol 2022; 355:114149. [PMID: 35732219 DOI: 10.1016/j.expneurol.2022.114149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/28/2022] [Accepted: 06/15/2022] [Indexed: 11/22/2022]
Abstract
Extracellular vesicles (EVs) are small lipid bilayer particles ubiquitously released by almost every cell type. A specific and selective constituents of EVs loaded with variety of proteins, lipids, small noncoding RNAs, and long non-coding RNAs are reflective of cellular events, type, and physiologic/pathophysiologic status of the cell of origin. Moreover, these molecular contents carry information from the cell of origin to recipient cells, modulating intercellular communication. Recent studies demonstrated that EVs not only play a neuroprotective role by mediating the removal of toxic proteins, but also emerge as an important player in various neurodegenerative disease onset and progression through facilitating of misfolded proteins propagation. For this reason, neurodegenerative disease-associated differences in EV proteome relative to normal EVs can be used to fulfil diagnostic, prognostic, and therapeutic purposes. Nonetheless, characterizing EV proteome obtained from biological samples (brain tissue and body fluids, including urea, blood, saliva, and CSF) is a challenging task. Herein, we review the status of EV proteome profiling and the updated discovery of potential biomarkers for the diagnosis of neurodegenerative disease with an emphasis on the integration of high-throughput advanced mass spectrometry (MS) technologies for both qualitative and quantitative analysis of EVs in different clinical tissue/body fluid samples in past five years.
Collapse
|
3
|
Cohn W, Zhu C, Campagna J, Bilousova T, Spilman P, Teter B, Li F, Guo R, Elashoff D, Cole GM, Avidan A, Faull KF, Whitelegge J, Wong DTW, John V. Integrated Multiomics Analysis of Salivary Exosomes to Identify Biomarkers Associated with Changes in Mood States and Fatigue. Int J Mol Sci 2022; 23:5257. [PMID: 35563647 PMCID: PMC9105576 DOI: 10.3390/ijms23095257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 02/07/2023] Open
Abstract
Fatigue and other deleterious mood alterations resulting from prolonged efforts such as a long work shift can lead to a decrease in vigilance and cognitive performance, increasing the likelihood of errors during the execution of attention-demanding activities such as piloting an aircraft or performing medical procedures. Thus, a method to rapidly and objectively assess the risk for such cognitive fatigue would be of value. The objective of the study was the identification in saliva-borne exosomes of molecular signals associated with changes in mood and fatigue that may increase the risk of reduced cognitive performance. Using integrated multiomics analysis of exosomes from the saliva of medical residents before and after a 12 h work shift, we observed changes in the abundances of several proteins and miRNAs that were associated with various mood states, and specifically fatigue, as determined by a Profile of Mood States questionnaire. The findings herein point to a promising protein biomarker, phosphoglycerate kinase 1 (PGK1), that was associated with fatigue and displayed changes in abundance in saliva, and we suggest a possible biological mechanism whereby the expression of the PGK1 gene is regulated by miR3185 in response to fatigue. Overall, these data suggest that multiomics analysis of salivary exosomes has merit for identifying novel biomarkers associated with changes in mood states and fatigue. The promising biomarker protein presents an opportunity for the development of a rapid saliva-based test for the assessment of these changes.
Collapse
Affiliation(s)
- Whitaker Cohn
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Chunni Zhu
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Jesus Campagna
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Tina Bilousova
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Patricia Spilman
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Bruce Teter
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| | - Feng Li
- Center for Oral/Head & Neck Oncology Research, Laboratory of Salivary Diagnostics, School of Dentistry, 10833 Le Conte Avenue, University of California Los Angeles, Los Angeles, CA 90095, USA; (F.L.); (D.T.W.W.)
| | - Rong Guo
- Department of Medicine Statistics Core, David Geffen School of Medicine, 1100 Glendon Avenue, University of California Los Angeles, Los Angeles, CA 90095, USA; (R.G.); (D.E.)
| | - David Elashoff
- Department of Medicine Statistics Core, David Geffen School of Medicine, 1100 Glendon Avenue, University of California Los Angeles, Los Angeles, CA 90095, USA; (R.G.); (D.E.)
| | - Greg M. Cole
- Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (G.M.C.); (A.A.)
| | - Alon Avidan
- Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (G.M.C.); (A.A.)
| | - Kym Francis Faull
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, 760 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (K.F.F.); (J.W.)
| | - Julian Whitelegge
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, 760 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (K.F.F.); (J.W.)
| | - David T. W. Wong
- Center for Oral/Head & Neck Oncology Research, Laboratory of Salivary Diagnostics, School of Dentistry, 10833 Le Conte Avenue, University of California Los Angeles, Los Angeles, CA 90095, USA; (F.L.); (D.T.W.W.)
| | - Varghese John
- The Drug Discovery Lab, Department of Neurology, David Geffen School of Medicine, 710 Westwood Plaza, University of California Los Angeles, Los Angeles, CA 90095, USA; (W.C.); (C.Z.); (J.C.); (T.B.); (P.S.); (B.T.)
| |
Collapse
|
4
|
Liskova A, Samec M, Koklesova L, Giordano FA, Kubatka P, Golubnitschaja O. Liquid Biopsy is Instrumental for 3PM Dimensional Solutions in Cancer Management. J Clin Med 2020; 9:E2749. [PMID: 32854390 PMCID: PMC7563444 DOI: 10.3390/jcm9092749] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
One in every four deaths is due to cancer in Europe. In view of its increasing incidence, cancer became the leading cause of death and disease burden in Denmark, France, the Netherlands, and the UK. Without essential improvements in cancer prevention, an additional 775,000 cases of annual incidence have been prognosed until 2040. Between 1995 and 2018, the direct costs of cancer doubled from EUR 52 billion to EUR 103 billion in Europe, and per capita health spending on cancer increased by 86% from EUR 105 to EUR 195 in general, whereby Austria, Germany, Switzerland, Benelux, and France spend the most on cancer care compared to other European countries. In view of the consequent severe socio-economic burden on society, the paradigm change from a reactive to a predictive, preventive, and personalized medical approach in the overall cancer management is essential. Concepts of predictive, preventive, and personalized medicine (3PM) demonstrate a great potential to revise the above presented trends and to implement cost-effective healthcare that benefits the patient and society as a whole. At any stage, application of early and predictive diagnostics, targeted prevention, and personalization of medical services are basic pillars making 3PM particularly attractive for the patients as well as ethical and cost-effective healthcare. Optimal 3PM approach requires novel instruments such as well-designed liquid biopsy application. This review article highlights current achievements and details liquid biopsy approaches specifically in cancer management. 3PM-relevant expert recommendations are provided.
Collapse
Affiliation(s)
- Alena Liskova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (A.L.); (M.S.); (L.K.)
| | - Marek Samec
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (A.L.); (M.S.); (L.K.)
| | - Lenka Koklesova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (A.L.); (M.S.); (L.K.)
| | - Frank A. Giordano
- Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany;
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia;
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| |
Collapse
|
5
|
NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis. Nat Commun 2020; 11:2887. [PMID: 32513971 PMCID: PMC7280298 DOI: 10.1038/s41467-020-16691-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z. The histone variant H2A.Z is deposited by the SWR1 complex to replace H2A in Arabidopsis, but the mechanism of H2A.Z removal is unclear. Here, the authors show that NRP proteins can regulate gene expression by counteracting SWR1 and prevent excessive accumulation of H2A.Z.
Collapse
|
6
|
Wongpalee SP, Liu S, Gallego-Bartolomé J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nat Commun 2019; 10:3916. [PMID: 31477705 PMCID: PMC6718625 DOI: 10.1038/s41467-019-11759-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 08/01/2019] [Indexed: 11/17/2022] Open
Abstract
Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment—DR (DMS3-RDM1) and DDR′ (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment. RNA polymerase V transcription in plants, which is needed DNA methylation and transcriptional silencing, requires components of the DDR complex. Here the authors show that all components of the DDR complex co-localize with Pol V and report the cryoEM structures of two complexes associated with Pol V recruitment.
Collapse
Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Shiheng Liu
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.,California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolomé
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland.,Faculty of Science, University of Zürich, 8057, Zürich, Switzerland
| | - Wanlu Liu
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, 310058, Hangzhou, P. R. China
| | - Linda Yen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Maria A Nohales
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peggy Hsuanyu Kuo
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
| | | | - Suhua Feng
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA. .,California NanoSystems Institute (CNSI), UCLA, Los Angeles, CA, 90095, USA.
| | - Steven E Jacobsen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA. .,Howard Hughes Medical Institute (HHMI), UCLA, Los Angeles, CA, 90095, USA.
| |
Collapse
|
7
|
Heinzelman P. Magnetic Particle-Based Immunoprecipitation of Nanoscale Extracellular Vesicles from Biofluids. Methods Mol Biol 2018; 1740:85-107. [PMID: 29388138 DOI: 10.1007/978-1-4939-7652-2_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Analysis of nanoscale extracellular vesicles (nsEVs) present in blood, cell culture media, and other biofluids has shown tremendous promise in enabling the development of noninvasive blood-based clinical diagnostic tests, predicting and monitoring the efficacy of treatment programs, and providing molecular level insights into pathology that can enlighten new drug targets in the contexts of health conditions such as cancer and Alzheimer's Disease (AD). In this chapter, we present methods for using magnetic particle-based immunoprecipitation to enrich highly purified populations of nsEVs directly from plasma, serum, and other biofluids. These methods enable downstream analysis of nsEV protein and nucleic acid constituents in the contexts of both global omics profiling and quantification of individual protein or nucleic acid species of interest. Additionally, these methods allow the researcher to either enrich total nsEV populations or enrich nsEVs derived from a particular tissue type from the overall nsEV population. The methods described here are compatible with parallel processing of dozens of biofluid samples and can be valuable tools for enabling nsEV analyses that have high translational relevance in the development of both novel therapeutics and noninvasive diagnostic assays.
Collapse
Affiliation(s)
- Pete Heinzelman
- Department of Neuroscience, Mayo Clinic-Jacksonville, Jacksonville, FL, USA.
| |
Collapse
|