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Ding S, Dong X, Song X. Tumor educated platelet: the novel BioSource for cancer detection. Cancer Cell Int 2023; 23:91. [PMID: 37170255 PMCID: PMC10176761 DOI: 10.1186/s12935-023-02927-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/15/2023] [Indexed: 05/13/2023] Open
Abstract
Platelets, involved in the whole process of tumorigenesis and development, constantly absorb and enrich tumor-specific substances in the circulation during their life span, thus called "Tumor Educated Platelets" (TEPs). The alterations of platelet mRNA profiles have been identified as tumor markers due to the regulatory mechanism of post-transcriptional splicing. Small nuclear RNAs (SnRNAs), the important spliceosome components in platelets, dominate platelet RNA splicing and regulate the splicing intensity of pre-mRNA. Endogenous variation at the snRNA levels leads to widespread differences in alternative splicing, thereby driving the development and progression of neoplastic diseases. This review systematically expounds the bidirectional tumor-platelets interactions, especially the tumor induced alternative splicing in TEP, and further explores whether molecules related to alternative splicing such as snRNAs can serve as novel biomarkers for cancer diagnostics.
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Affiliation(s)
- Shanshan Ding
- Department of Clinical Laboratory, Shandong Cancer Hospital & Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, PR China
| | - Xiaohan Dong
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital & Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, PR China.
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2
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Zhang Q, Song X, Song X. Contents in tumor-educated platelets as the novel biosource for cancer diagnostics. Front Oncol 2023; 13:1165600. [PMID: 37139159 PMCID: PMC10151018 DOI: 10.3389/fonc.2023.1165600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Liquid biopsy, a powerful non-invasive test, has been widely used in cancer diagnosis and treatment. Platelets, the second most abundant cells in peripheral blood, are becoming one of the richest sources of liquid biopsy with the capacity to systematically and locally respond to the presence of cancer and absorb and store circulating proteins and different types of nucleic acids, thus called "tumor-educated platelets (TEPs)". The contents of TEPs are significantly and specifically altered, empowering them with the potential as cancer biomarkers. The current review focuses on the alternation of TEP content, including coding and non-coding RNA and proteins, and their role in cancer diagnostics.
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Affiliation(s)
- Qianru Zhang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- *Correspondence: Xingguo Song,
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3
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Tyagi T, Jain K, Gu SX, Qiu M, Gu VW, Melchinger H, Rinder H, Martin KA, Gardiner EE, Lee AI, Ho Tang W, Hwa J. A guide to molecular and functional investigations of platelets to bridge basic and clinical sciences. NATURE CARDIOVASCULAR RESEARCH 2022; 1:223-237. [PMID: 37502132 PMCID: PMC10373053 DOI: 10.1038/s44161-022-00021-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/17/2022] [Indexed: 07/29/2023]
Abstract
Platelets have been shown to be associated with pathophysiological process beyond thrombosis, demonstrating critical additional roles in homeostatic processes, such as immune regulation, and vascular remodeling. Platelets themselves can have multiple functional states and can communicate and regulate other cells including immune cells and vascular smooth muscle cells, to serve such diverse functions. Although traditional platelet functional assays are informative and reliable, they are limited in their ability to unravel platelet phenotypic heterogeneity and interactions. Developments in methods such as electron microscopy, flow cytometry, mass spectrometry, and 'omics' studies, have led to new insights. In this Review, we focus on advances in platelet biology and function, with an emphasis on current and promising methodologies. We also discuss technical and biological challenges in platelet investigations. Using coronavirus disease 2019 (COVID-19) as an example, we further describe the translational relevance of these approaches and the possible 'bench-to-bedside' utility in patient diagnosis and care.
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Affiliation(s)
- Tarun Tyagi
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Kanika Jain
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Sean X Gu
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, Yale New Haven Hospital, New Haven, CT, USA
| | - Miaoyun Qiu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Vivian W Gu
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Hannah Melchinger
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Henry Rinder
- Department of Laboratory Medicine, Yale University School of Medicine, Yale New Haven Hospital, New Haven, CT, USA
| | - Kathleen A Martin
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth E Gardiner
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Alfred I Lee
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Wai Ho Tang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - John Hwa
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale University School of Medicine, New Haven, CT, USA
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4
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Zhang T, Yuan K, Wang Y, Xu M, Cai S, Chen C, Ma J. Identification of Candidate Biomarkers and Prognostic Analysis in Colorectal Cancer Liver Metastases. Front Oncol 2021; 11:652354. [PMID: 34422629 PMCID: PMC8371911 DOI: 10.3389/fonc.2021.652354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/19/2021] [Indexed: 02/02/2023] Open
Abstract
Background Colorectal cancer (CRC), one of the most common malignant tumors worldwide, has a high mortality rate, especially for patients with CRC liver metastasis (CLM). However, CLM pathogenesis remains unclear. Methods We integrated multiple cohort datasets and databases to clarify and verify potential key candidate biomarkers and signal transduction pathways in CLM. GEO2R, DAVID 6.8, ImageGP, STRING, UALCAN, ONCOMINE, THE HUMAN PROTEIN ATLAS, GEPIA 2.0, cBioPortal, TIMER 2.0, DRUGSURV, CRN, GSEA 4.0.3, FUNRICH 3.1.3 and R 4.0.3 were utilized in this study. Results Sixty-three pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened from three gene expression profiles (GSE6988, GSE14297 and GSE81558). Thirty-one up-regulated genes and four down-regulated genes were identified from these three gene expression profiles and verified by another gene expression profiles (GSE 49355) and TCGA database. Two pathways (IGFBP-IGF signaling pathway and complement-coagulation cascade), eighteen key differentially expressed genes (DEGs), six hub genes (SPARCL1, CDH2, CP, HP, TF and SERPINA5) and two biomarkers (CDH2 and SPARCL1) with significantly prognostic values were screened by multi-omics data analysis and verified by Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) cohort. Conclusions In this study, we identified a robust set of potential candidate biomarkers in CLM, which would provide potential value for early diagnosis and prognosis, and would promote molecular targeting therapy for CRC and CLM.
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Affiliation(s)
- Tianhao Zhang
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaitao Yuan
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yingzhao Wang
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingze Xu
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shirong Cai
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chuangqi Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinping Ma
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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5
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Mantini G, Meijer LL, Glogovitis I, In ‘t Veld SGJG, Paleckyte R, Capula M, Le Large TYS, Morelli L, Pham TV, Piersma SR, Frampton AE, Jimenez CR, Kazemier G, Koppers-Lalic D, Wurdinger T, Giovannetti E. Omics Analysis of Educated Platelets in Cancer and Benign Disease of the Pancreas. Cancers (Basel) 2020; 13:cancers13010066. [PMID: 33383671 PMCID: PMC7795159 DOI: 10.3390/cancers13010066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is traditionally associated with thrombocytosis/hypercoagulation and novel insights on platelet-PDAC "dangerous liaisons" are warranted. Here we performed an integrative omics study investigating the biological processes of mRNAs and expressed miRNAs, as well as proteins in PDAC blood platelets, using benign disease as a reference for inflammatory noise. Gene ontology mining revealed enrichment of RNA splicing, mRNA processing and translation initiation in miRNAs and proteins but depletion in RNA transcripts. Remarkably, correlation analyses revealed a negative regulation on SPARC transcription by isomiRs involved in cancer signaling, suggesting a specific "education" in PDAC platelets. Platelets of benign patients were enriched for non-templated additions of G nucleotides (#ntaG) miRNAs, while PDAC presented length variation on 3' (lv3p) as the most frequent modification on miRNAs. Additionally, we provided an actionable repertoire of PDAC and benign platelet-ome to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in patients with PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can "educate" the platelet. These novel findings could be further exploited for innovative liquid biopsies platforms as well as possible therapeutic targets.
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Affiliation(s)
- Giulia Mantini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
| | - Laura L. Meijer
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Ilias Glogovitis
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Sjors G. J. G. In ‘t Veld
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
| | - Rosita Paleckyte
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Mjriam Capula
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Tessa Y. S. Le Large
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
| | - Thang V. Pham
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Adam E. Frampton
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, The Leggett Building, University of Surrey, Guildford GU2 7WG, UK;
- Faculty of Health and Medical Sciences, The Leggett Building, University of Surrey, Guildford GU2 7XH, UK
| | - Connie R. Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Geert Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands;
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (I.G.); (S.G.J.G.I.V.); (D.K.-L.)
- Correspondence: (T.W.); (E.G.); Tel.: +31-003-120-444-2633 (E.G.)
| | - Elisa Giovannetti
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands; (G.M.); (L.L.M.); (R.P.); (T.Y.S.L.L.); (T.V.P.); (S.R.P.); (C.R.J.)
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
- Correspondence: (T.W.); (E.G.); Tel.: +31-003-120-444-2633 (E.G.)
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6
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Kraemer BF, Geimer M, Franz-Wachtel M, Lamkemeyer T, Mannell H, Lindemann S. Extracellular Matrix-Specific Platelet Activation Leads to a Differential Translational Response and Protein De Novo Synthesis in Human Platelets. Int J Mol Sci 2020; 21:ijms21218155. [PMID: 33142786 PMCID: PMC7672557 DOI: 10.3390/ijms21218155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 02/08/2023] Open
Abstract
Platelets are exposed to extracellular matrix (ECM) proteins like collagen and laminin and to fibrinogen during acute vascular events. However, beyond hemostasis, platelets have the important capacity to migrate on ECM surfaces, but the translational response of platelets to different extracellular matrix stimuli is still not fully characterized. Using 2D-gel electrophoresis, confocal microscopy, polysome analysis and protein sequencing by mass spectrometry, we demonstrate that platelets show a differential expression profile of newly synthesized proteins on laminin, collagen or fibrinogen. In this context, we observed a characteristic, ECM-dependent translocation phenotype of translation initiation factor eIF4E to the ribosomal site. eIF4E accumulated in polysomes with increased binding of mRNA and co-localization with vinculin, leading to de novo synthesis of important cytoskeletal regulator proteins. As the first study, we included a proteome analysis of laminin-adherent platelets and interestingly identified upregulation of essentially important proteins that mediate cytoskeletal regulation and mobility in platelets, such as filamin A, talin, vinculin, gelsolin, coronin or kindlin-3. In summary, we demonstrate that platelet activation with extracellular matrix proteins results in a distinct stimulus-specific translational response of platelets that will help to improve our understanding of the regulation of platelet mobility and migration.
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Affiliation(s)
- Bjoern F. Kraemer
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Marchioninistrasse 15, 81377 Munich, Germany;
| | - Marc Geimer
- Klinik für Anästhesie, Intensiv- und Notfallmedizin, Westpfalz Klinikum Kaiserslautern, Hellmut-Hartert Str. 1, 67655 Kaiserslautern, Germany;
| | - Mirita Franz-Wachtel
- Proteasome Center Tuebingen, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany;
| | - Tobias Lamkemeyer
- Cluster of Excellence Cologne (CEDAD), Mass Spectrometry Facility at the Institute for Genetics, University of Köln, Josef-Stelzmann-Str. 26, 50931 Köln, Germany;
| | - Hanna Mannell
- Doctoral Programme of Clinical Pharmacy, University Hospital, Ludwig-Maximilians-University, Marchioninistr. 27, 81377 Munich, Germany;
- Institute of Cardiovascular Physiology and Pathophysiology Biomedical Center, Ludwig-Maximilians-University, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Stephan Lindemann
- Philipps Universität Marburg, FB 20-Medizin, Baldingerstraße, 35032 Marburg, Germany
- Klinikum Warburg, Medizinische Klinik II, Hüffertstr. 50, 34414 Warburg, Germany
- Medizinische Klinik und Poliklinik III, Otfried-Muller-Str. 10, Universitätsklinikum Tübingen, 72076 Tübingen, Germany
- Correspondence:
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7
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Akingbade OES, Gibson C, Kalaria RN, Mukaetova-Ladinska EB. Platelets: Peripheral Biomarkers of Dementia? J Alzheimers Dis 2019; 63:1235-1259. [PMID: 29843245 DOI: 10.3233/jad-180181] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dementia continues to be the most burdening neurocognitive disorder, having a negative impact on the lives of millions. The search for biomarkers to improve the clinical diagnosis of dementia is ongoing, with the focus on effective use of readily accessible peripheral markers. In this review, we concentrate on platelets as biomarkers of dementia and analyze their potential as easily-accessible clinical biomarkers for various subtypes of dementia. Current platelet protein biomarkers that have been investigated for their clinical utility in the diagnosis of dementia, in particular Alzheimer's disease, include amyloid-β protein precursor (AβPP), the AβPP secretases (BACE1 and ADAM10), α-synuclein, tau protein, serotonin, cholesterol, phospholipases, clusterin, IgG, surface receptors, MAO-B, and coated platelets. Few of them, i.e., platelet tau, AβPP (particularly with regards to coated platelets) and secreted ADAM10 and BACE1 show the most promise to be taken forward into clinical setting to diagnose dementia. Aside from protein biomarkers, changes in factors such as mean platelet volume have the potential to play a very specific role in both the dementia diagnosis and prognosis. This review raises a number of research questions for consideration before application of the above biomarkers to routine clinical setting. It is without doubt that there is a need for more clarification on the effects of dementia on platelet morphology and protein content before these changes can be clinically applied as dementia biomarkers and explored further in differentiating distinct dementia subtypes.
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Affiliation(s)
- Oluwatomi E S Akingbade
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK.,School of Life Sciences, Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Claire Gibson
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Raj N Kalaria
- Institute of Neuroscience, Newcastle University, Newcastle, UK
| | - Elizabeta B Mukaetova-Ladinska
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK.,Evington Centre, Leicester General Hospital, Leicester, UK
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8
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Junqueira-Neto S, Batista IA, Costa JL, Melo SA. Liquid Biopsy beyond Circulating Tumor Cells and Cell-Free DNA. Acta Cytol 2019; 63:479-488. [PMID: 30783027 DOI: 10.1159/000493969] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 09/24/2018] [Indexed: 12/30/2022]
Abstract
Liquid biopsy represents the analysis of tumor-derived material in the blood and other body fluids of cancer patients. This portrays a minimally invasive detection tool for molecular biomarkers. Liquid biopsy has emerged as a complementary or alternative method to surgical biopsy. This non-invasive detection tool overcomes the recurrent problems in the clinical assessment of tumors that stem from the lack of accessibility to the tumor tissue and its clonal heterogeneity. Moreover, body fluid-derived components have shown to reflect the genetic profile of both primary and metastatic lesions and provide a real-time monitoring of tumor dynamics, representing a great promise for personalized medicine. This review will highlight the latest breakthroughs and the current applications of several tumor-derived biomarkers that can be found in body fluids. The authors will focus on tumor-derived exosomes, tumor-educated platelets, and circulating tumor miRNAs and mRNAs, and how these can be used for tumor detection.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/isolation & purification
- Cell-Free Nucleic Acids/blood
- Cell-Free Nucleic Acids/isolation & purification
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/isolation & purification
- Exosomes/chemistry
- Exosomes/pathology
- Humans
- Liquid Biopsy/methods
- MicroRNAs/blood
- MicroRNAs/isolation & purification
- Monitoring, Physiologic
- Mutation
- Neoplasm Recurrence, Local/blood
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/pathology
- Neoplasms/blood
- Neoplasms/diagnosis
- Neoplasms/drug therapy
- Neoplasms/pathology
- Neoplastic Cells, Circulating/chemistry
- Neoplastic Cells, Circulating/pathology
- Precision Medicine/methods
- Prognosis
- RNA, Messenger/blood
- RNA, Messenger/isolation & purification
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Affiliation(s)
- Susana Junqueira-Neto
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal (i3S), Porto, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Medical Faculty of the University of Porto (FMUP), Porto, Portugal
| | - Inês A Batista
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal (i3S), Porto, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - José Luís Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal (i3S), Porto, Portugal
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Medical Faculty of the University of Porto (FMUP), Porto, Portugal
| | - Sónia A Melo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal (i3S), Porto, Portugal,
- Institute of Molecular Pathology & Immunology of the University of Porto (IPATIMUP), Porto, Portugal,
- Medical Faculty of the University of Porto (FMUP), Porto, Portugal,
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9
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10
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Abstract
SIGNIFICANCE Platelets are anucleate blood cells that are involved in hemostasis and thrombosis. Although no longer able to generate ribonucleic acid (RNA) de novo, platelets contain messenger RNA (mRNA), YRNA fragments, and premature microRNAs (miRNAs) that they inherit from megakaryocytes. Recent Advances: Novel sequencing techniques have helped identify the unexpectedly large number of RNA species present in platelets. Throughout their life time, platelets can process the pre-existing pool of premature miRNA to give the fully functional miRNA that can regulate platelet protein expression and function. CRITICAL ISSUES Platelets make a major contribution to the circulating miRNA pool but platelet activation can have major consequences on Dicer levels and thus miRNA maturation, which has implications for studies that are focused on screening-stored platelets. FUTURE DIRECTIONS It will be important to determine the importance of platelets as donors for miRNA-containing microvesicles that can be taken up and processed by other (particularly vascular) cells, thus contributing to homeostasis as well as disease progression. Antioxid. Redox Signal. 29, 902-921.
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Affiliation(s)
- Amro Elgheznawy
- 1 Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University , Frankfurt am Main, Germany .,2 German Center for Cardiovascular Research (DZHK) , Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Ingrid Fleming
- 1 Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University , Frankfurt am Main, Germany .,2 German Center for Cardiovascular Research (DZHK) , Partner site Rhein-Main, Frankfurt am Main, Germany
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11
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Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications. Sci Rep 2018; 8:498. [PMID: 29323256 PMCID: PMC5765118 DOI: 10.1038/s41598-017-18985-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022] Open
Abstract
Platelet activation triggers thrombus formation in physiological and pathological conditions, such as acute coronary syndromes. Current therapies still fail to prevent thrombotic events in numerous patients, indicating that the mechanisms modulating platelet response during activation need to be clarified. The evidence that platelets are capable of de novo protein synthesis in response to stimuli raised the issue of how megakaryocyte-derived mRNAs are regulated in these anucleate cell fragments. Proteogenomics was applied here to investigate this phenomeon in platelets activated in vitro with Collagen or Thrombin Receptor Activating Peptide. Combining proteomics and transcriptomics allowed in depth platelet proteome characterization, revealing a significant effect of either stimulus on proteome composition. In silico analysis revealed the presence of resident immature RNAs in resting platelets, characterized by retained introns, while unbiased proteogenomics correlated intron removal by RNA splicing with changes on proteome composition upon activation. This allowed identification of a set of transcripts undergoing maturation by intron removal during activation and resulting in accumulation of the corresponding peptides at exon-exon junctions. These results indicate that RNA splicing events occur in platelets during activation and that maturation of specific pre-mRNAs is part of the activation cascade, contributing to a dynamic fine-tuning of the transcriptome.
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Best MG, Vancura A, Wurdinger T. Platelet RNA as a circulating biomarker trove for cancer diagnostics. J Thromb Haemost 2017; 15:1295-1306. [PMID: 28671345 DOI: 10.1111/jth.13720] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Platelets are multifunctional cell fragments, circulating in blood in high abundance. Platelets assist in thrombus formation, sensing of pathogens entering the blood stream, signaling to immune cells, releasing vascular remodeling factors, and, negatively, enhancing cancer metastasis. Platelets are 'educated' by their environment, including in patients with cancer. Cancer cells appear to initiate intraplatelet signaling, resulting in splicing of platelet pre-mRNAs, and enhance secretion of cytokines. Platelets can induce leukocyte and endothelial cell modeling factors, for example, through adenine nucleotides (ATP), thereby facilitating extravasation of cancer cells. Besides releasing factors, platelets can also sequester RNAs and proteins released by cancer cells. Thus, platelets actively respond to queues from local and systemic conditions, thereby altering their transcriptome and molecular content. Platelets contain a rich repertoire of RNA species, including mRNAs, small non-coding RNAs and circular RNAs; although studies regarding the functionality of the various platelet RNA species require more attention. Recent advances in high-throughput characterization of platelet mRNAs revealed 10 to > 1000 altered mRNAs in platelets in the presence of disease. Hence, platelet RNA appears to be dynamically affected by pathological conditions, thus possibly providing opportunities to use platelet RNA as diagnostic, prognostic, predictive, or monitoring biomarkers. In this review, we cover the literature regarding the platelet RNA families, processing of platelet RNAs, and the potential application of platelet RNA as disease biomarkers.
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Affiliation(s)
- M G Best
- Department of Neurosurgery, VU University Medical Center, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - A Vancura
- Department of Neurosurgery, VU University Medical Center, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - T Wurdinger
- Department of Neurosurgery, VU University Medical Center, Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
- Department of Neurology, Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, Boston, MA, USA
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13
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Kanikarla-Marie P, Lam M, Menter DG, Kopetz S. Platelets, circulating tumor cells, and the circulome. Cancer Metastasis Rev 2017; 36:235-248. [DOI: 10.1007/s10555-017-9681-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
Supplemental Digital Content is available in the text. Objectives Clozapine is an atypical antipsychotic primarily prescribed for treatment-resistant schizophrenia. We tested the specific effect of clozapine versus other drug treatments on whole-blood gene expression in a sample of patients with psychosis from the UK. Methods A total of 186 baseline whole-blood samples from individuals receiving treatment for established psychosis were analysed for gene expression on Illumina HumanHT-12.v4 BeadChips. After standard quality-control procedures, 152 samples remained, including 55 from individuals receiving clozapine. In a within-case study design, weighted gene correlation network analysis was used to identify modules of coexpressed genes. The influence of mood stabilizers, lithium carbonate/lithium citrate and sodium valproate was studied to identify their possible roles as confounders. Results Individuals receiving clozapine as their only antipsychotic (clozapine monotherapy) had a nominal association with one gene-expression module, whereas no significant change in gene expression was found for other drugs. Conclusion Overall, this study does not provide evidence that clozapine treatment induces medium to large different gene-expression patterns in human whole blood versus other antipsychotic treatments. This does not rule out the possibility of smaller effects as observed for other common antipsychotic treatments.
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The Emerging Role of miR-223 in Platelet Reactivity: Implications in Antiplatelet Therapy. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26221610 PMCID: PMC4499381 DOI: 10.1155/2015/981841] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Platelets are anuclear cells and are devoid of genomic DNA, but they are capable of de novo protein synthesis from mRNA derived from their progenitor cells, megakaryocytes. There is mounting evidence that microRNA (miRNA) plays an important role in regulating gene expression in platelets. miR-223 is the most abundant miRNAs in megakaryocytes and platelets. One of the miR-223-regulated genes is ADP P2Y12, a key target for current antiplatelet drug therapy. Recent studies showed that a blunted response to P2Y12 antagonist, that is, high on-treatment platelet reactivity (HTPR), is a strong predictor of major cardiovascular events (MACEs) in coronary heart disease (CHD) patients receiving antiplatelet treatment. Recent clinical cohort study showed that the level of circulating miR-223 is inversely associated with MACE in CHD patients. In addition, our recent data demonstrated that the level of both intraplatelet and circulating miR-223 is an independent predictor for HTPR, thus providing a link between miR-223 and MACE. These lines of evidence indicate that miR-223 may serve as a potential regulatory target for HTPR, as well as a diagnostic tool for identification of HTPR in clinical settings.
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Cimmino G, Tarallo R, Nassa G, De Filippo MR, Giurato G, Ravo M, Rizzo F, Conte S, Pellegrino G, Cirillo P, Calabro P, Öhman T, Nyman TA, Weisz A, Golino P. Activating stimuli induce platelet microRNA modulation and proteome reorganisation. Thromb Haemost 2015; 114:96-108. [PMID: 25903651 DOI: 10.1160/th14-09-0726] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/27/2015] [Indexed: 11/05/2022]
Abstract
Platelets carry megakaryocyte-derived mRNAs whose translation efficiency before and during activation is not known, although this can greatly affect platelet functions, both under basal conditions and in response to physiological and pathological stimuli, such as those involved in acute coronary syndromes. Aim of the present study was to determine whether changes in microRNA (miRNA) expression occur in response to activating stimuli and whether this affects activity and composition of platelet transcriptome and proteome. Purified platelet-rich plasmas from healthy volunteers were collected and activated with ADP, collagen, or thrombin receptor activating peptide. Transcriptome analysis by RNA-Seq revealed that platelet transcriptome remained largely unaffected within the first 2 hours of stimulation. In contrast, quantitative proteomics showed that almost half of > 700 proteins quantified were modulated under the same conditions. Global miRNA analysis indicated that reorganisation of platelet proteome occurring during activation reflected changes in mature miRNA expression, which therefore, appears to be the main driver of the observed discrepancy between transcriptome and proteome changes. Platelet functions significantly affected by modulated miRNAs include, among others, the integrin/cytoskeletal, coagulation and inflammatory-immune response pathways. These results demonstrate a significant reprogramming of the platelet miRNome during activation, with consequent significant changes in platelet proteome and provide for the first time substantial evidence that fine-tuning of resident mRNA translation by miRNAs is a key event in platelet pathophysiology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Alessandro Weisz
- Prof. Alessandro Weisz, MD, Laboratory of Molecular Medicine and Genomics, University of Salerno, via S. Allende, 1, 84081 Baronissi (SA), Italy, Tel.: +39 089 965043, Fax: +39 089 969657, E-mail:
| | - Paolo Golino
- Prof. Paolo Golino, MD, Department of Cardiothoracic and Respiratory Sciences, Second University of Naples, Via L. Bianchi, 1, 80131 Naples, Italy, Tel.: +39 0823 306395, Fax: +39 0823 232395, E-mail:
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17
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Yu S, Huang H, Deng G, Xie Z, Ye Y, Guo R, Cai X, Hong J, Qian D, Zhou X, Tao Z, Chen B, Li Q. miR-326 targets antiapoptotic Bcl-xL and mediates apoptosis in human platelets. PLoS One 2015; 10:e0122784. [PMID: 25875481 PMCID: PMC4395162 DOI: 10.1371/journal.pone.0122784] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/15/2015] [Indexed: 12/20/2022] Open
Abstract
Platelets play crucial roles in hemostasis, thrombosis, wound healing, inflammation, angiogenesis, and tumor metastases. Because they are anucleated blood cells, platelets lack nuclear DNA, but they do contain mitochondrial DNA, which plays a key role in regulating apoptosis. Recent evidence has suggested that miRNAs are also involved in regulating gene expression and apoptosis in platelets. Our previous study showed that the expression of miR-326 increased visibly when apheresis platelets were stored in vitro. The antiapoptotic Bcl-2 family regulator Bcl-xL has been identified as a putative target of miR-326. In the present study, dual reporter luciferase assays were used to characterize the function of miR-326 in the regulation of the apoptosis of platelet cells. These assays demonstrated that miR-326 bound to the 3′-translated region of Bcl-xL. To directly assess the functional effects of miR-326 expression, levels of Bcl-xL and the apoptotic status of stored apheresis platelets were measured after transfection of miR-326 mimic or inhibitor. Results indicated that miR-326 inhibited Bcl-xL expression and induced apoptosis in stored platelets. Additionally, miR-326 inhibited Bcl-2 protein expression and enhanced Bak expression, possibly through an indirect mechanism, though there was no effect on the expression of Bax. The effect of miR-326 appeared to be limited to apoptosis, with no significant effect on platelet activation. These results provide new insight into the molecular mechanisms affecting differential platelet gene regulation, which may increase understanding of the role of platelet apoptosis in multiple diseases.
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Affiliation(s)
- Shifang Yu
- The Department of Transfusion Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Huicong Huang
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Gang Deng
- The Ningbo Central Blood Station, Ningbo, China
| | - Zuoting Xie
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Yincai Ye
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Ruide Guo
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Xuejiao Cai
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Junying Hong
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Dingliang Qian
- The Department of Laboratory Medicine, The Third Affiliated Hospital of the Wenzhou Medical University, Ruian, China
| | - Xiangjing Zhou
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Zhihua Tao
- The Department of Transfusion Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- * E-mail: (QL); (ZT)
| | - Bile Chen
- The Department of Transfusion Medicine, The First Affiliated Hospital of the Wenzhou Medical University, Wenzhou, China
| | - Qiang Li
- The Department of Laboratory Medicine, The Third Affiliated Hospital of the Wenzhou Medical University, Ruian, China
- * E-mail: (QL); (ZT)
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De Jong S, Neeleman M, Luykx JJ, ten Berg MJ, Strengman E, Den Breeijen HH, Stijvers LC, Buizer-Voskamp JE, Bakker SC, Kahn RS, Horvath S, Van Solinge WW, Ophoff RA. Seasonal changes in gene expression represent cell-type composition in whole blood. Hum Mol Genet 2014; 23:2721-8. [PMID: 24399446 DOI: 10.1093/hmg/ddt665] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Seasonal patterns in behavior and biological parameters are widespread. Here, we examined seasonal changes in whole blood gene expression profiles of 233 healthy subjects. Using weighted gene co-expression network analysis, we identified three co-expression modules showing circannual patterns. Enrichment analysis suggested that this signal stems primarily from red blood cells and blood platelets. Indeed, a large clinical database with 51 142 observations of blood cell counts over 3 years confirmed a corresponding seasonal pattern of counts of red blood cells, reticulocytes and platelets. We found no direct evidence that these changes are linked to genes known to be key players in regulating immune function or circadian rhythm. It is likely, however, that these seasonal changes in cell counts and gene expression profiles in whole blood represent biological and clinical relevant phenomena. Moreover, our findings highlight possible confounding factors relevant to the study of gene expression profiles in subjects collected at geographical locations with disparaging seasonality patterns.
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Affiliation(s)
- Simone De Jong
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
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The involvement of the CD40-CD40L pathway in activated platelet-induced changes in HUVEC COX-2 and PPARα expression. Inflammation 2012; 35:1184-90. [PMID: 22219050 DOI: 10.1007/s10753-011-9427-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We aim to determine the extent of the CD40-CD40L pathway involvement in activated platelet-induced changes in human umbilical endothelial cells (HUVECs). Activated platelets were co-incubated with HUVECs in the presence or absence of CD40LmAb. HUVECs were also directly stimulated with rhCD40L. HUVEC endothelial cyclooxygenase 2 (COX-2) and peroxisome proliferator-activated receptor alpha (PPARα) expression was then assessed. To estimate COX-2 activity, PGE2 concentration was determined. PPARα activity was assessed using a nuclear factor activity kit. Co-incubation with activated platelets increased HUVEC COX-2 and PPARα mRNA expression (P < 0.01). The addition of CD40L mAb significantly attenuated these increases in mRNA and protein (both P < 0.01). Direct stimulation by rhCD40L increased HUVEC COX-2 mRNA and protein (P < 0.05) but did not significantly change the expression of PPARα mRNA and protein. CD40LmAb significantly decreased (P < 0.05) and rhCD40L significantly (P < 0.01) increased COX-2 enzymatic activity, but had almost no effects on PPARα binding activity. Activated platelets may increase HUVEC COX-2 expression and activity partly through the CD40-CD40L pathway.
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Noerholm M, Balaj L, Limperg T, Salehi A, Zhu LD, Hochberg FH, Breakefield XO, Carter BS, Skog J. RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls. BMC Cancer 2012; 12:22. [PMID: 22251860 PMCID: PMC3329625 DOI: 10.1186/1471-2407-12-22] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Accepted: 01/17/2012] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients. METHODS Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9) and normal controls (N = 7) were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups). RESULTS Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down) in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size < 500 nt. Gene ontology of the down-regulated genes indicated these are coding for ribosomal proteins and genes related to ribosome production. CONCLUSIONS Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down-regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size < 500 nt.
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Affiliation(s)
- Mikkel Noerholm
- Department of Neurology, Neurosurgery and Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02114, USA.
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Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PLoS One 2011; 6:e26905. [PMID: 22046403 PMCID: PMC3203156 DOI: 10.1371/journal.pone.0026905] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Accepted: 10/06/2011] [Indexed: 01/08/2023] Open
Abstract
Background Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. Methodology/Principal Findings Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R2 methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. Conclusions By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study.
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Li XJ, Yang H, Li GX, Zhang GH, Cheng J, Guan H, Yang GS. Transcriptome profile analysis of porcine adipose tissue by high-throughput sequencing. Anim Genet 2011; 43:144-52. [DOI: 10.1111/j.1365-2052.2011.02240.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Williams MS, Weiss EJ, Sabatine MS, Simon DI, Bahou WF, Becker LC, Parise LV, Dauerman HL, French PA, Smyth SS, Becker RC. Genetic regulation of platelet receptor expression and function: application in clinical practice and drug development. Arterioscler Thromb Vasc Biol 2010; 30:2372-84. [PMID: 21084706 DOI: 10.1161/atvbaha.110.218131] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering (1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, (2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and (3) the role of platelet function/genetic testing in guiding antiplatelet therapy.
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Affiliation(s)
- Marlene S Williams
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, Md 21224, USA.
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Abstract
PURPOSE OF REVIEW The proteome is the pool of proteins expressed at a given time and circumstance. The word 'proteomics' summarizes several technologies for visualization, quantitation and identification of these proteins. Recent advances in these techniques are helping to elucidate platelet processes which are relevant to bleeding and clotting disorders, transfusion medicine and regulation of angiogenesis. RECENT FINDINGS Over 1100 platelet proteins have been identified using proteomic techniques. Various subproteomes have been characterized, including platelet releasates (the 'secretome'), alpha and dense granules, membrane and cytoskeletal proteins, platelet-derived microparticles, and the platelet 'phosphoproteome'. Proteomic data about platelets have become increasingly available in integrated databases. SUMMARY Proteomic experiments in resting and activated platelets have identified novel signaling pathways and secreted proteins which may represent therapeutic targets, as well as potential cancer biomarkers.
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